Mercurial > repos > jankanis > blast2html
annotate NCBI Blast reference example_files/formatRes.js @ 58:39df29f647e8
set other environment variables as well
author | Jan Kanis <jan.code@jankanis.nl> |
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date | Tue, 27 May 2014 12:45:50 +0200 |
parents | 344cd76f6fd2 |
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1 // JScript source code |
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2 /*************************new code begin *******************************************************/ |
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3 |
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4 function getHiddenFieldVal(elemName) { |
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5 var val; |
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6 var elem = document.getElementsByName(elemName); |
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7 if (elem) { |
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8 val = (elem.length > 1) ? elem[0].value : elem.value; |
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9 } |
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10 return val; |
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11 } |
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12 |
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13 function getHiddenFieldParamString(elemName) { |
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14 var ret = ""; |
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15 var val = getHiddenFieldVal(elemName); |
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16 if (val) { |
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17 ret = "&" + elemName + "=" + val; |
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18 } |
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19 return ret; |
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20 } |
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21 |
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22 function elementInViewport(el) { |
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23 if (!el) return; |
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24 var rect = el.getBoundingClientRect(); |
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25 |
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26 var myWidth = 0, myHeight = 0; |
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27 if (typeof (window.innerWidth) == 'number') { |
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28 //Non-IE |
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29 myWidth = window.innerWidth; |
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30 myHeight = window.innerHeight; |
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31 } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) { |
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32 //IE 6+ in 'standards compliant mode' |
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33 myWidth = document.documentElement.clientWidth; |
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34 myHeight = document.documentElement.clientHeight; |
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35 } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) { |
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36 //IE 4 compatible |
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37 myWidth = document.body.clientWidth; |
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38 myHeight = document.body.clientHeight; |
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39 } |
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40 //window.alert('Width = ' + myWidth); |
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41 //window.alert('Height = ' + myHeight); |
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42 |
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43 |
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44 //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth) |
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45 //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth) |
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46 return (rect.top >= 0 && rect.bottom <= myHeight); |
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47 } |
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48 |
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49 function DisplayAlignFromDescription(elem) { |
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50 var alignView = $("FormatForm").ALIGNMENT_VIEW; |
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51 if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") { |
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52 DisplayDynamicAlign(elem); |
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53 } |
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54 else { |
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55 location.href = "#" + elem.getAttribute("seqID"); |
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56 } |
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57 } |
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58 |
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59 //<a class="deflnDesc" hsp=<hsp_num> ind="<index>" gi="<gi>" id="deflnDesc_gi" href="#AlnHdrgi">desc</a> |
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60 //<div class="alnHdr" gi="<gi>" id="alnHdr_<index>"> |
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61 function DisplayDynamicAlign(elem) { |
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62 var currGi = elem.getAttribute("gi"); |
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63 var currInd = elem.getAttribute("ind"); |
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64 var stat = elem.getAttribute("stat"); |
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65 if (!currInd || !currGi) return; |
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66 |
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67 if (!stat || stat == "") { |
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68 //Get 4(5) aligns before currInd and 4(5) aligns after |
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69 ReadCurrentSeqAligns(currInd, 5); |
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70 } |
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71 else if (stat == "read") { |
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72 var indexes = getCurrIndexRange(currInd); |
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73 if (indexes) { |
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74 var msgID = "alnShow_" + indexes[0]; |
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75 location.href = "#" + msgID; |
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76 } |
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77 } |
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78 else { |
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79 //error status handling |
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80 } |
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81 } |
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82 |
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83 |
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84 function goToNextAlign(dtrID, next) { |
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85 var currInd = parseInt($(dtrID).getAttribute("ind")); |
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86 var rid = $("Rid").value; |
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87 nextInd = (next) ? currInd + 1 : currInd - 1; |
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88 |
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89 if ($("deflnDesc_" + nextInd)) { |
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90 currGi = $("deflnDesc_" + nextInd).getAttribute("seqID"); |
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91 scrollToGI = currGi; |
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92 if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") { |
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93 |
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94 if (!next) { |
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95 ReadPrevSeqAligns(currInd, 5, scrollToGI); |
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96 } |
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97 else { |
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98 //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!! |
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99 ReadNextSeqAligns(currInd, 5, scrollToGI); |
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100 } |
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101 |
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102 } |
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103 else { |
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104 location.href = "#" + scrollToGI; |
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105 } |
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106 } |
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107 } |
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108 |
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109 function goToDefLine(dtrID) { |
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110 if ($("psiInp")) { |
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111 var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table |
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112 togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1"; |
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113 jQuery($(togglerID)).ncbitoggler("open"); |
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114 } |
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115 } |
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116 |
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117 /* |
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118 readAln.rid = rid; |
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119 readAln.startIndex = parseInt(currInd); |
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120 readAln.numSeq = parseInt(maxNumAligns); |
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121 |
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122 readAln.insertAfterID = insertAfterID; |
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123 readAln.seqList = giList; |
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124 readAln.scrollToSeqID = scrollToGI; |
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125 */ |
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126 function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) { |
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127 var lastDispIdx = 0; |
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128 var rid = $("Rid").value; |
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129 |
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130 var readAln = new Object(); |
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131 readAln.seqList = ""; //giList |
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132 readAln.rid = rid; |
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133 |
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134 currInd = parseInt(currInd); |
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135 |
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136 if (currInd != 0 && $("deflnDesc_" + currInd)) { |
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137 var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_<ind> |
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138 //alert(par.id); |
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139 if (par) par = utils.getParent(par); //"alnShow_<ind> |
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140 //alert(par.id); |
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141 if (par) readAln.insertAfterID = par.id; |
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142 } |
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143 else { |
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144 readAln.insertAfterID = "alnStart"; |
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145 } |
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146 |
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147 |
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148 |
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149 readAln.startIndex = currInd + 1; |
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150 readAln.numSeq = maxNumAligns; |
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151 |
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152 checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next"); |
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153 |
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154 readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : ""; |
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155 readAln.hspSort = 0; |
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156 ReadSeqAlignByIndex(readAln); |
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157 } |
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158 |
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159 function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) { |
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160 var lastDispIdx = 0; |
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161 var rid = $("Rid").value; |
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162 |
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163 var readAln = new Object(); |
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164 readAln.seqList = ""; //giList |
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165 readAln.rid = rid; |
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166 |
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167 currInd = parseInt(currInd); |
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168 |
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169 |
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170 //sets readAln.insertAfterID and returns lastDispIdx; |
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171 //Find the index of the previously displayed alignment |
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172 lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln); |
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173 |
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174 readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1; |
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175 readAln.numSeq = currInd - readAln.startIndex; //stopIndex = currInd |
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176 |
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177 checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev"); |
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178 |
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179 readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID"); |
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180 readAln.hspSort = 0; |
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181 ReadSeqAlignByIndex(readAln); |
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182 } |
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183 |
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184 //When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd |
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185 function ReadCurrentSeqAligns(currInd, maxNumAligns) { |
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186 var rid = $("Rid").value; |
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187 var readAln = new Object(); |
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188 readAln.seqList = ""; //giList |
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189 readAln.rid = rid; |
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190 |
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191 currInd = parseInt(currInd); |
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192 |
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193 |
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194 //sets readAln.insertAfterID and returns lastDispIdx; |
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195 //Find the index of the previously displayed alignment |
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196 var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln); |
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197 |
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198 //lastDispIdx = parseInt(lastDispIdx); |
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199 readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1; |
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200 readAln.numSeq = parseInt(maxNumAligns * 2); |
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201 |
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202 checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr"); |
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203 |
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204 readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID"); |
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205 readAln.hspSort = 0; |
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206 ReadSeqAlignByIndex(readAln); |
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207 g_DisableAutoCheck = true; |
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208 location.href = "#alnShow_" + readAln.startIndex; |
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209 } |
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210 |
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211 |
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212 |
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213 |
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214 function setupDynHSPParams(readAln) |
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215 { |
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216 var currSeqInd = readAln.startIndex; |
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217 hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp")); |
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218 alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len")); |
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219 var maxDispLen = parseInt($("maxDispAlnLen").value);//20000 |
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220 var minDispLen = parseInt($("minDispAlnLen").value);//2000 |
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221 if (alnLen > maxDispLen) { |
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222 var lenPerMatch = alnLen / hspNum; |
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223 readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch); |
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224 readAln.AlignDbPageNum = 0; |
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225 $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize); |
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226 } |
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227 } |
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228 |
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229 |
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230 |
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231 function getCurrSeqsAlnLen(currSeqInd) |
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232 { |
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233 var alnLen = 0; |
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234 if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) { |
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235 alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len"); |
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236 } |
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237 alnLen = (alnLen) ? parseInt(alnLen) : 0; |
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238 return alnLen; |
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239 } |
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240 |
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241 function checkTotalAlignLen(startIndex,stopIndex) |
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242 { |
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243 var dispAlnLen = 0; |
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244 var maxDispLen = parseInt($("maxDispAlnLen").value); |
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245 for (var i = startIndex; i <= stopIndex; i++) { |
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246 alnLen = getCurrSeqsAlnLen(i); |
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247 if (alnLen == 0) break; |
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248 dispAlnLen += alnLen; |
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249 } |
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250 return dispAlnLen; |
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251 } |
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252 //Get total align length for seq currSeqInd and |
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253 //"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs |
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254 function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType) |
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255 { |
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256 var startIndex = readAln.startIndex; |
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257 var stopIndex = readAln.startIndex + readAln.numSeq - 1; |
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258 if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current |
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259 startIndex = Math.max(startIndex, currSeqInd - countSeqs); |
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260 stopIndex = Math.min(stopIndex, currSeqInd + countSeqs); |
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261 } |
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262 else if(dispType == "prev") { |
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263 startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs); |
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264 stopIndex = currSeqInd - 1; |
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265 } |
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266 else {//next |
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267 stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1); |
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268 } |
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269 var totAlnLen = checkTotalAlignLen(startIndex,stopIndex); |
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270 return totAlnLen; |
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271 } |
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272 |
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273 function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType) |
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274 { |
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275 var maxDispLen = parseInt($("maxDispAlnLen").value); |
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276 var totAlnLen = 0; |
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277 var exc = false; |
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278 for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) { |
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279 totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType); |
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280 if(totAlnLen > maxDispLen) { |
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281 break; |
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282 } |
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283 } |
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284 if (totAlnLen > maxDispLen) { |
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285 if (numSeq != 0) numSeq--; |
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286 if (dispType == "curr") { |
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287 readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq); |
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288 //prev + 1(curr) + next |
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289 readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq; |
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290 } |
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291 else if (dispType == "prev") { |
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292 readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq); |
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293 readAln.numSeq = numSeq + 1; |
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294 } |
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295 else { //"next" - readAln.startIndex stays |
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296 readAln.numSeq = numSeq + 1; |
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297 } |
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298 |
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299 if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") { |
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300 setupDynHSPParams(readAln); |
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301 } |
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302 |
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303 exc = true; |
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304 } |
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305 return exc; |
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306 } |
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307 |
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308 |
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309 //readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set |
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310 function ReadSeqAlignByIndex(readAln) { |
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311 var numAligns = 0; |
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312 for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) { |
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313 |
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314 if (!$("deflnDesc_" + i)) { |
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315 break; |
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316 } |
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317 if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") { |
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318 currGi = $("deflnDesc_" + i).getAttribute("seqFSTA"); |
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319 if (readAln.seqList != "") readAln.seqList += ","; |
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320 readAln.seqList += currGi; |
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321 numAligns++; |
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322 } |
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323 else { |
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324 break; |
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325 } |
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326 } |
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327 if (readAln.seqList != "") { |
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328 readAln.numSeq = parseInt(numAligns); |
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329 ReadSeqAlignForSeqList(readAln); |
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330 } |
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331 } |
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332 |
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333 |
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334 var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2... |
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335 //Find the range of indexes of displayed alignments for currAlnInd |
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336 //Returns array of 2 startIndex, stopIndex |
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337 function getCurrIndexRange(currAlinInd) { |
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338 var currRange; |
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339 var ranges = g_DisplayeAlignsRanges.split(","); |
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340 for (var i = 0; i < ranges.length; i++) { |
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341 var indexes = ranges[i].split("-"); |
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342 if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) { |
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343 currRange = indexes; |
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344 break; |
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345 } |
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346 } |
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347 return currRange; |
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348 } |
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349 |
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350 |
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351 //Find the index of the previous displayed alignment |
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352 function getPrevDisplyedAlignInfo(currInd, readAln) { |
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353 readAln.insertAfterID = "alnStart"; |
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354 lastDispIdx = 0; |
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355 for (var i = currInd - 1; i >= 1; i--) { |
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356 indexes = getCurrIndexRange(i); |
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357 if (indexes) { |
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358 lastDispIdx = indexes[1]; |
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359 readAln.insertAfterID = "alnShow_" + indexes[0]; |
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360 break; |
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361 } |
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362 } |
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363 return parseInt(lastDispIdx); |
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364 } |
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365 |
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366 |
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367 //setReadStatus |
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368 function setSeqAlnReadStatus(readAln, status) { |
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369 for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) { |
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370 if ($("deflnDesc_" + i)) { |
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371 jQuery($($("deflnDesc_" + i))).attr("stat", status); |
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372 if (status == "disp") { |
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373 g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex; |
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374 } |
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375 } |
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376 } |
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377 } |
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378 |
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379 /* |
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380 readAln.rid = rid; |
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381 readAln.seqList = giList; |
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382 readAln.startIndex = parseInt(idx); |
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383 readAln.insertAfterID = insertAfterID; |
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384 readAln.numSeq = parseInt(numSeq); |
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385 readAln.scrollToSeqID = scrollToGI; |
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386 */ |
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387 function SendReadSeqAlinRequest(readAln) { |
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388 blastUrl = "t2g.cgi"; |
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389 |
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390 var rp = new RemoteDataProvider(blastUrl); |
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391 |
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392 |
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393 rp.onSuccess = function(obj) { |
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394 if ($("alignView")) utils.removeClass($("alignView"), "hidden"); |
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395 |
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396 if ($("alnShow_" + readAln.startIndex)) { |
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397 var moreHspsLink = getNextHspsLink(readAln); |
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398 jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, { |
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399 'widgets': ['ncbipopper', 'ncbitoggler'], |
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400 'configs': { |
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401 'ncbipopper': { hasArrow: true, arrowDirection: 'top' } |
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402 } |
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403 }); |
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404 setSeqAlnReadStatus(readAln, "disp"); |
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405 jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden"); |
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406 //Saves start and stop indexes of loaded alignments in global variables |
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407 saveIdxesForAutomaticLoad(readAln); |
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408 jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) { |
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409 var seqID = this.getAttribute("seqID"); |
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410 if(seqID) initAlignBatch(seqID); |
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411 }); |
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412 |
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413 } |
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414 |
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415 if (readAln.scrollToSeqID) { |
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416 location.href = "#" + readAln.scrollToSeqID; |
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417 } |
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418 |
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419 }; |
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420 rp.onError = function(obj) { |
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421 if ($("alignView")) utils.removeClass($("alignView"), "hidden"); |
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422 jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden"); |
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423 $("alnShowReal_" + readAln.startIndex).innerHTML = "<div class=\"erm\" id=\"erm_" + readAln.startIndex + "\">Error loading alignment ...<span class=\"db\">requests:" + this.iActiveRequests + " status:" + obj.status + |
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424 "</span><a class=\"gbd\" href=\"#\" onclick=\"ReSubmitReadSeqAligns(event," + readAln.startIndex + ")\">Try again<\a></div>"; |
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425 } |
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426 var params = constructURLParams(readAln); |
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427 if (readAln.numSeq == 1) { |
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428 params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); |
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429 } |
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430 params += "&SEQ_LIST_START=" + readAln.startIndex; |
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431 |
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432 var formatParams = constructFormatParams(); |
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433 params += formatParams; |
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434 |
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435 //alert(params); |
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436 rp.Request(params); |
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437 } |
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438 |
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439 |
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440 function constructURLParams(readAln) { |
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441 var params; |
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442 |
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443 if ($("useAlignDB") && $("useAlignDB").value == "true") { |
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444 |
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445 var alignDbParams = "&USE_ALIGNDB=true"; |
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446 var batchID = document.getElementsByName("ALIGNDB_BATCH_ID"); |
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447 if (batchID) { |
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448 alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID"); |
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449 alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS"); |
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450 alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST"); |
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451 alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH"); |
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452 } |
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453 alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList; |
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454 alignDbParams += "&HSP_SORT=" + readAln.hspSort; |
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455 |
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456 if (readAln.hasOwnProperty("AlignDbPageNum")) { |
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457 alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum; |
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458 alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize; |
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459 alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum; |
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460 } |
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461 |
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462 params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams; |
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463 } |
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464 else { |
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465 params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort; |
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466 } |
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467 if ($("phiPtInd")) { |
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468 params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value; |
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469 } |
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470 return params; |
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471 } |
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472 |
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473 /* |
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474 readAln.rid = rid; |
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475 readAln.seqList = giList; |
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476 readAln.startIndex = parseInt(idx); |
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477 readAln.insertAfterID = insertAfterID; |
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478 readAln.numSeq = parseInt(numSeq); |
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479 readAln.scrollToSeqID = scrollToGI; |
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480 */ |
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481 /*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes |
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482 2. Insert another div with id="alnShowReal_index and class="alnMsgR" |
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483 3. For "alnShow_index" set atrr indexes="startInd-stopInd" |
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484 4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this |
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485 5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes |
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486 6. Send read request |
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487 */ |
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488 |
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489 function ReadSeqAlignForSeqList(readAln) { |
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490 var text = "<div id=\"alnShow_" + readAln.startIndex + "\" class=\"alnMsg\"><div class=\"alnMsgS\" id=\"alnMsg_" + readAln.startIndex + "\">Loading alignment...<span class=\"db\"> for sequences " + readAln.seqList; |
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491 var stopIndex = readAln.startIndex + readAln.numSeq - 1; |
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492 var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : ""; |
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493 text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "</span></div>"; |
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494 text += "<div id=\"alnShowReal_" + readAln.startIndex + "\" class=\"alnMsgR\"></div></div>"; |
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495 var debugControl = "<div id=\"debug\"></div>"; |
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496 if (!$("debug")) { |
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497 jQuery($($("descriptions"))).before(debugControl); |
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498 } |
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499 if (!$("alnShow_" + readAln.startIndex)) { |
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500 jQuery($($(readAln.insertAfterID))).after(text); |
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501 jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex); |
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502 jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList); |
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503 g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex; |
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504 setSeqAlnReadStatus(readAln, "read"); |
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505 $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex; |
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506 |
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507 if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ","; |
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508 g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex; |
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509 |
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510 SendReadSeqAlinRequest(readAln); |
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511 } |
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512 else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) { |
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513 jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden"); |
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514 jQuery($("erm_" + readAln.startIndex)).remove(); |
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515 SendReadSeqAlinRequest(readAln); |
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516 } |
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517 } |
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518 |
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519 |
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520 function ReSubmitReadSeqAligns(e,currInd) { |
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521 var rid = $("Rid").value; |
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522 if ($("alnShow_" + currInd)) { |
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523 var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes"); |
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524 var range = indexRange.split("-"); |
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525 |
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526 |
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527 var readAln = new Object(); |
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528 readAln.seqList = ""; //giList |
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529 readAln.rid = rid; |
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530 readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist"); |
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531 readAln.startIndex = parseInt(range[0]); |
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532 readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1; |
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533 readAln.hspSort = 0; |
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534 ReadSeqAlignForSeqList(readAln); |
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535 utils.preventDefault(e); |
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536 } |
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537 } |
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538 |
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539 |
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540 var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read" |
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541 var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N |
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542 var g_DisableAutoCheck = false; |
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543 |
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544 var g_autoStartIdx = new Array(); |
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545 var g_autoStopIdx = new Array(); |
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546 |
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547 function saveIdxesForAutomaticLoad(readAln) { |
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548 var stopIndex = readAln.startIndex + readAln.numSeq - 1; |
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549 g_autoStartIdx.push(readAln.startIndex); //1,20,25 |
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550 g_autoStopIdx.push(stopIndex); //4,24,29 |
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551 $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex; |
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552 } |
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553 |
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554 function getNextHspsLink(readAln) |
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555 { |
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556 var moreHspsLink = "" |
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557 if (readAln.hasOwnProperty("AlignDbPageNum")) { |
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558 var nextPageNum = readAln.AlignDbPageNum + 1; |
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559 var currHspInd = readAln.AlignDbPageSize * nextPageNum; |
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560 var argstring = readAln.startIndex + "," + currHspInd; |
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561 var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId"); |
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562 var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs"); |
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563 var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); |
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564 var prevHspInd = readAln.AlignDbPageSize * nextPageNum; |
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565 var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize); |
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566 var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1); |
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567 |
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568 moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID); |
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569 moreHspsLink = moreHspsLink.replace(/@accs@/g, accs); |
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570 moreHspsLink = moreHspsLink.replace("@argstring@", argstring); |
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571 moreHspsLink = moreHspsLink.replace(/@segs@/g, segs); |
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572 moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps); |
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573 moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize); |
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574 moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd); |
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575 moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi); |
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576 } |
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577 return moreHspsLink; |
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578 } |
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579 |
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580 |
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581 function ReadNextHSPSet(currSeqInd, currHSPNum) { |
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582 var readAln = new Object(); |
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583 |
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584 readAln.rid = $("Rid").value; |
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585 readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA"); |
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586 readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId"); |
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587 dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps"); |
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588 readAln.startIndex = currSeqInd; |
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589 readAln.numSeq = 1; |
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590 if (dynHsps) { |
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591 readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps); |
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592 readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve |
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593 } |
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594 if (currHSPNum != 0) { |
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595 readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1); |
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596 readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum; |
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597 } |
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598 var sortLink = $("sa_" + readAln.gi); |
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599 readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0; |
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600 SendReadSeqAlinSortHSPRequest(readAln); |
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601 } |
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602 |
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603 function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) { |
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604 ReadNextHSPSet(currSeqInd, currHSPNum); |
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605 utils.preventDefault(e); |
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606 } |
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607 |
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608 |
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609 |
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610 function checkAutoAlignArray() { |
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611 var stop = false; |
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612 var start = false; |
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613 var currAlignViewPos = $("alignView").getBoundingClientRect().top; |
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614 if (currAlignViewPos < g_alignViewPos) {//scrolling down |
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615 g_alignViewPos = currAlignViewPos; |
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616 if (g_DisableAutoCheck) { |
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617 g_DisableAutoCheck = false; |
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618 return; |
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619 } |
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620 for (i = 0; i < g_autoStopIdx.length; i++) { |
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621 if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) { |
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622 //alert("Reading more aligns scrolling down!"); |
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623 var nextInd = parseInt(g_autoStopIdx[i] + 1); |
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624 var currInd = g_autoStopIdx[i]; |
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625 if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) { |
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626 ReadNextSeqAligns(currInd, 5); |
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627 stop = true; |
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628 break; |
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629 } |
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630 } |
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631 } |
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632 if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array |
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633 } |
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634 else if (currAlignViewPos > g_alignViewPos) {//scrolling up |
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635 g_alignViewPos = currAlignViewPos; |
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636 //here maybe return if autoStop found!!! |
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637 /* commenting automic read when scroll up */ |
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638 for (i = 0; i < g_autoStartIdx.length; i++) { |
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639 if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) { |
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640 //alert("Reading more aligns scrolling up!"); |
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641 var currInd = g_autoStartIdx[i]; |
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642 //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!! |
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643 if (currInd > 1) { |
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644 ReadPrevSeqAligns(currInd, 5); |
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645 start = true; |
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646 break; |
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647 } |
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648 } |
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649 } |
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650 if (start) g_autoStartIdx.splice(i, 1); |
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651 } |
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652 /*end of comment*/ |
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653 } |
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654 |
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655 var g_alignViewPos = 0; |
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656 |
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657 function checkAutoAlignLoad() { |
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658 |
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659 |
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660 checkAutoAlignArray(); |
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661 |
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662 if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) { |
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663 //alert("bottom!"); |
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664 |
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665 if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") { |
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666 //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex |
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667 ReadNextSeqAligns(g_MaxDisplayedIndex, 5); |
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668 } |
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669 } |
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670 } |
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671 |
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672 |
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673 function GetPatternLocResults() |
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674 { |
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675 form = $("results"); |
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676 if (!form.PHI_PTTRN_INDEX) { |
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677 var el = document.createElement("input"); |
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678 el.name = "PHI_PTTRN_INDEX"; |
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679 el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value; |
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parents:
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680 form.appendChild(el); |
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681 } |
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682 else { |
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683 form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value; |
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684 } |
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685 form.submit(); |
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686 } |
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|
687 |
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688 function goToNextHSP(elem, next) { |
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parents:
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689 var par = jQuery(elem).parent(); //parent span with class="alnParLinks" |
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parents:
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690 var parts = par[0].id.split("_"); //"hsp<seqid>_hspnum "hsp207524544_2" |
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691 if (parts[0].indexOf("nxHsp") != -1) { |
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692 parts[0] = parts[0].replace("nxHsp", "hsp"); |
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|
693 } |
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694 nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1) |
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parents:
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|
695 |
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696 gotoElem = jQuery($(nextID)); |
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parents:
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|
697 if (gotoElem[0]) { |
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|
698 a = jQuery(gotoElem).offset(); |
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parents:
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|
699 window.scroll(0, a.top); |
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parents:
diff
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|
700 } |
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changeset
|
701 |
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|
702 else { |
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|
703 retrieveNextHSP(parts[0],parts[1]); |
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parents:
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|
704 } |
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parents:
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|
705 |
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parents:
diff
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|
706 } |
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parents:
diff
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|
707 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
708 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
709 //parts[0]//hsp<seqid>, parts[1] hspnum |
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parents:
diff
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|
710 function retrieveNextHSP(currLinkID, currHSPNum) |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
711 { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
712 var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
713 var currSeqInd, totalHsps; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
714 jQuery($($(desLineID))).find(".deflnDesc").each(function(index) { |
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parents:
diff
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|
715 currSeqInd = parseInt(this.getAttribute("ind")); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
716 totalHsps = parseInt(this.getAttribute("hsp")); |
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parents:
diff
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|
717 dynHsps = this.getAttribute("dynHsps"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
718 }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
719 currHSPNum = parseInt(currHSPNum); |
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Jan Kanis <jan.code@jankanis.nl>
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720 if (currHSPNum < totalHsps && dynHsps) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
721 ReadNextHSPSet(currSeqInd, currHSPNum); |
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parents:
diff
changeset
|
722 } |
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Jan Kanis <jan.code@jankanis.nl>
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diff
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|
723 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
724 /********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/ |
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parents:
diff
changeset
|
725 function getUrlCompForEntryField(elem) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
726 var url = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
727 if (elem && elem.value != "") { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
728 url = "&" + elem.name + "=" + escape(elem.value); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
729 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
730 return url; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
731 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
732 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
733 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
734 function getUrlCompForCheckedField(elem) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
735 var url = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
736 if (elem && elem.checked) { |
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parents:
diff
changeset
|
737 url = "&" + elem.name + "=" + elem.value; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
738 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
739 return url; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
740 |
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parents:
diff
changeset
|
741 } |
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parents:
diff
changeset
|
742 |
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parents:
diff
changeset
|
743 function getUrlCompForOptionsField(elem) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
744 var url = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
745 if (elem) { |
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parents:
diff
changeset
|
746 url = "&" + elem.name + "=" + elem[elem.selectedIndex].value; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
747 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
748 return url; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
749 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
750 /****************************************/ |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
751 |
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parents:
diff
changeset
|
752 function constructFormatParams() { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
753 var formatParams = ""; |
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parents:
diff
changeset
|
754 |
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parents:
diff
changeset
|
755 if ($("queryList")) { |
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parents:
diff
changeset
|
756 formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value; |
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parents:
diff
changeset
|
757 } |
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parents:
diff
changeset
|
758 |
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parents:
diff
changeset
|
759 |
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parents:
diff
changeset
|
760 formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT); |
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parents:
diff
changeset
|
761 formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE); |
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parents:
diff
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|
762 formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
763 formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW); |
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parents:
diff
changeset
|
764 formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR); |
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parents:
diff
changeset
|
765 formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
766 formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW); |
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parents:
diff
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|
767 formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH); |
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768 formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW); |
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769 formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH); |
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770 formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH); |
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parents:
diff
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771 |
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diff
changeset
|
772 |
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|
773 formatParams += getHiddenFieldParamString("BUILD_NAME"); |
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parents:
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|
774 |
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|
775 var serviceType = ""; |
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776 if ($("serviceType").value == "sra") { |
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777 serviceType = "sra"; |
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|
778 } |
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779 else if ($("clientType").value == "TMSmart_restricted") { |
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diff
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780 serviceType = "restricted"; |
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|
781 } |
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782 if (serviceType != "") { |
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783 formatParams += "&BOBJSRVC=" + serviceType; |
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|
784 } |
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|
785 if ($("currQuery").value != "") { |
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diff
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786 formatParams += "&CURR_QUERY_ID=" + $("currQuery").value; |
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787 } |
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|
788 |
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|
789 return formatParams; |
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|
790 } |
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parents:
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|
791 |
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792 //readAln.seqList contains one gi only for this |
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793 function SendReadSeqAlinSortHSPRequest(readAln) { |
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parents:
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794 blastUrl = "t2g.cgi"; |
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diff
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|
795 var rp = new RemoteDataProvider(blastUrl); |
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parents:
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|
796 |
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|
797 |
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parents:
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|
798 rp.onSuccess = function(obj) { |
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|
799 var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : ""; |
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800 var alnHtml = obj.responseText + moreHspsLink; |
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801 initHSPRequest(readAln, obj.responseText + moreHspsLink,false); |
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parents:
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802 if (readAln.scrollToSeqID) { |
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parents:
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803 location.href = "#" + readAln.scrollToSeqID; |
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parents:
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|
804 } |
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diff
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|
805 }; |
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parents:
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|
806 rp.onError = function(obj) { |
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parents:
diff
changeset
|
807 var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0; |
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parents:
diff
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|
808 var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1); |
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parents:
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|
809 if (!$(msgID)) { |
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parents:
diff
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810 var msg = "<div class=\"erm\" att=\"1\" id=\"" + msgID + "\">Error loading alignment ...<span class=\"db\">status:" + obj.status + |
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811 "</span><a class=\"gbd\" href=\"#\" onclick=\"ReadNextHSPSetEvt(event," + readAln.startIndex + "," + currHspInd + |
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parents:
diff
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812 ")\">Try again <span class=\"attmt\"></span> <\a></div>"; |
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parents:
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|
813 initHSPRequest(readAln, msg, true); |
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|
814 } |
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parents:
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815 else { |
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parents:
diff
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816 var attNum = parseInt($(msgID).getAttribute("att")) + 1; |
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817 $(msgID).setAttribute("att", attNum); |
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Jan Kanis <jan.code@jankanis.nl>
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818 jQuery($(msgID)).find(".attmt").each(function(index) { |
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parents:
diff
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|
819 jQuery(this).html(", attempt " + attNum); |
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|
820 }); |
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|
821 } |
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|
822 } |
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|
823 |
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824 var params = constructURLParams(readAln); |
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|
825 if (readAln.AlignDbPageSize) { |
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|
826 params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); |
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827 } |
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828 params += "&SORT_ONE_ALN=on"; |
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parents:
diff
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829 var formatParams = constructFormatParams(); |
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parents:
diff
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|
830 |
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diff
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|
831 params += formatParams; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
832 |
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parents:
diff
changeset
|
833 //alert(params); |
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parents:
diff
changeset
|
834 rp.Request(params); |
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parents:
diff
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|
835 } |
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parents:
diff
changeset
|
836 function initHSPRequest(readAln, alnHtml, err) { |
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parents:
diff
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837 var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0; |
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parents:
diff
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|
838 if (currHspInd != 0) { |
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parents:
diff
changeset
|
839 readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd; |
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parents:
diff
changeset
|
840 jQuery($(readAln.insertAfterID)).after(alnHtml); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
841 moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1); |
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parents:
diff
changeset
|
842 jQuery($(moreHspsID)).remove(); |
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parents:
diff
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|
843 if (!err) { |
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parents:
diff
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|
844 errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1); |
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parents:
diff
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|
845 jQuery($(errMsgID)).remove(); |
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parents:
diff
changeset
|
846 } |
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parents:
diff
changeset
|
847 } |
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parents:
diff
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|
848 else { |
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parents:
diff
changeset
|
849 jQuery($("alnAll_" + readAln.gi)).html(alnHtml); |
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parents:
diff
changeset
|
850 } |
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parents:
diff
changeset
|
851 } |
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parents:
diff
changeset
|
852 |
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parents:
diff
changeset
|
853 function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544" |
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parents:
diff
changeset
|
854 var readAln = new Object(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
855 |
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parents:
diff
changeset
|
856 |
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parents:
diff
changeset
|
857 var desLineID = sortLink.id.replace("sa", "dtr"); //tr id |
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parents:
diff
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|
858 var seqInd; |
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parents:
diff
changeset
|
859 |
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parents:
diff
changeset
|
860 jQuery($($(desLineID))).find(".deflnDesc").each(function(index) { |
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parents:
diff
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|
861 seqInd = this.getAttribute("ind"); |
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parents:
diff
changeset
|
862 }); |
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parents:
diff
changeset
|
863 |
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parents:
diff
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|
864 ReadNextHSPSet(parseInt(seqInd), 0); |
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parents:
diff
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|
865 } |
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parents:
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|
866 |
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parents:
diff
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|
867 |
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parents:
diff
changeset
|
868 function configDescriptions(e,btn,dlgId) |
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parents:
diff
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|
869 { |
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parents:
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|
870 var suffix = PsiBelowThresh(dlgId); |
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parents:
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871 var colmnsInfId = "cfcDsInf" + suffix; |
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872 var tblID = "dscTable" + suffix; //"dscTable[_psiw]" |
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parents:
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|
873 var showAllColId = "shcl" + suffix; |
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parents:
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874 var chkBoxes = $C("checkbox", "type", $(dlgId), "input"); |
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parents:
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|
875 if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = ""; |
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|
876 for (i = 0; i < chkBoxes.length; i++) { |
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parents:
diff
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|
877 var check; |
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|
878 if (utils.hasClass(btn, "cnc")) {//cancel |
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|
879 if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) { |
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parents:
diff
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|
880 check = true; |
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diff
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|
881 } |
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|
882 else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) { |
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parents:
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|
883 check = false; |
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parents:
diff
changeset
|
884 } |
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parents:
diff
changeset
|
885 } |
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parents:
diff
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|
886 else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) { |
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parents:
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|
887 check = true; |
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parents:
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|
888 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
889 if (typeof (check) != 'undefined') { |
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parents:
diff
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|
890 chkBoxes[i].checked = check; |
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parents:
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|
891 showHideCol(tblID,parseInt(chkBoxes[i].value), !check); |
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|
892 } |
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|
893 if (!utils.hasClass(btn, "cnc")) { |
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parents:
diff
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|
894 if (chkBoxes[i].checked) { //OK |
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|
895 if ($(colmnsInfId).value != "") $(colmnsInfId).value += ","; |
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|
896 $(colmnsInfId).value += chkBoxes[i].value; |
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parents:
diff
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|
897 } |
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parents:
diff
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|
898 } |
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parents:
diff
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|
899 } |
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parents:
diff
changeset
|
900 if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8" |
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901 jQuery($(showAllColId)).removeClass("hidden"); |
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parents:
diff
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|
902 } |
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parents:
diff
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|
903 else { |
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Jan Kanis <jan.code@jankanis.nl>
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diff
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|
904 jQuery($(showAllColId)).addClass("hidden"); |
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parents:
diff
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|
905 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
906 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
907 var chConfig = $("cfcDsSave").value != $(colmnsInfId).value; |
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parents:
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|
908 |
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parents:
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|
909 var cfds = document.getElementsByName("CONFIG_DESCR"); |
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parents:
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|
910 if (cfds) { |
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diff
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|
911 for (i = 0; i < cfds.length; i++) { |
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parents:
diff
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|
912 cfds[i].value = $(colmnsInfId).value; |
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parents:
diff
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|
913 } |
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parents:
diff
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|
914 } |
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parents:
diff
changeset
|
915 $("cfcDsSave").value = $(colmnsInfId).value; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
916 if (chConfig) SaveConfigTable(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
917 jQuery(document.body).click(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
918 utils.preventDefault(e); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
919 } |
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parents:
diff
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|
920 |
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parents:
diff
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|
921 |
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parents:
diff
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|
922 |
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parents:
diff
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|
923 function initDescConfig() |
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parents:
diff
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|
924 { |
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parents:
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|
925 initConfigColumns("dsConfig"); |
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parents:
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|
926 if ($("psiw") && utils.hasClass($("psiw"), "shown")) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
927 initConfigColumns("dsConfig_psiw"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
928 } |
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parents:
diff
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|
929 } |
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add example input blast xml and output html page
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parents:
diff
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|
930 |
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parents:
diff
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|
931 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
932 function initConfigColumns(cnfDlgID) |
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parents:
diff
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|
933 { |
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|
934 var suffix = PsiBelowThresh(cnfDlgID); |
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parents:
diff
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|
935 //cnfDlgID is "dsConfig[_psiw]" |
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parents:
diff
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|
936 var colmnsInfId = "cfcDsInf" + suffix; |
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parents:
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937 var tblID = "dscTable" + suffix; //"dscTable[_psiw]" |
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parents:
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|
938 var showAllColId = "shcl" + suffix; |
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diff
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|
939 |
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|
940 if (navigator.userAgent.match(/ie/i)) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
941 if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") { |
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parents:
diff
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|
942 jQuery($(tblID)).find("th.c1").each(function(index) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
943 db = getHiddenFieldVal("DATABASE"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
944 var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em"; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
945 jQuery(this).css("width", width); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
946 }); |
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parents:
diff
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|
947 } |
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parents:
diff
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|
948 } |
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parents:
diff
changeset
|
949 |
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parents:
diff
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|
950 jQuery($(tblID)).find("tr.first").each(function(index) { |
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parents:
diff
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|
951 jQuery(this).find("a.dcs").each(function(index) { |
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parents:
diff
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|
952 jQuery(this).bind("click", function(e) { checkConfig(this); }); |
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parents:
diff
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|
953 }); |
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parents:
diff
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|
954 }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
955 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
956 jQuery($(cnfDlgID)).find("button").each(function(index) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
957 jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); }); |
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parents:
diff
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|
958 }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
959 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
960 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
961 jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
962 |
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parents:
diff
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|
963 $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR"); |
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parents:
diff
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|
964 if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") { |
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parents:
diff
changeset
|
965 $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval"); |
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parents:
diff
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|
966 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
967 if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8" |
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parents:
diff
changeset
|
968 jQuery($(showAllColId)).removeClass("hidden"); |
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parents:
diff
changeset
|
969 } |
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parents:
diff
changeset
|
970 else { |
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parents:
diff
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|
971 jQuery($(showAllColId)).addClass("hidden"); |
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parents:
diff
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|
972 } |
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parents:
diff
changeset
|
973 var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input") |
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parents:
diff
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|
974 for (i = 0; i < chkBoxes.length; i++) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
975 jQuery(chkBoxes[i]).bind("click", configColumn); |
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parents:
diff
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|
976 if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) { |
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parents:
diff
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|
977 chkBoxes[i].checked = true; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
978 } |
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parents:
diff
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|
979 else { |
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parents:
diff
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|
980 //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value); |
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parents:
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|
981 showHideCol($(tblID), chkBoxes[i].value, true); |
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parents:
diff
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|
982 } |
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parents:
diff
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|
983 } |
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parents:
diff
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|
984 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
985 function showAllCol(e,elem) |
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parents:
diff
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|
986 { |
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parents:
diff
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|
987 var suffix = PsiBelowThresh(elem.id); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
988 var rdf = "dscRsDf" + suffix; |
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parents:
diff
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|
989 jQuery($(rdf)).click();//click "restore defaults' |
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parents:
diff
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|
990 utils.preventDefault(e); |
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parents:
diff
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|
991 } |
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parents:
diff
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|
992 |
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parents:
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|
993 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
994 function configColumn() { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
995 var suffix = PsiBelowThresh(this.id); |
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|
996 var tblID = "dscTable" + suffix; //"dscTable[_psiw]" |
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diff
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|
997 |
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parents:
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|
998 cCls = "c" + this.value; |
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parents:
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|
999 if (this.checked) {//show |
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diff
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|
1000 showHideCol(tblID,parseInt(this.value), false); |
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parents:
diff
changeset
|
1001 } |
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|
1002 else { |
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diff
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|
1003 showHideCol(tblID,parseInt(this.value), true); |
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parents:
diff
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|
1004 } |
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parents:
diff
changeset
|
1005 } |
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parents:
diff
changeset
|
1006 |
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Jan Kanis <jan.code@jankanis.nl>
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|
1007 function showHideCol(tblID, columnIndex, hide) { |
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diff
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|
1008 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1009 if ($("Transcr")) { |
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diff
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|
1010 colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden"); |
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parents:
diff
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|
1011 hide = hide && !colHidden; |
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parents:
diff
changeset
|
1012 show = !hide && colHidden; |
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parents:
diff
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|
1013 } |
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|
1014 else { |
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diff
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|
1015 show = !hide; |
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parents:
diff
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|
1016 } |
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parents:
diff
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|
1017 if (hide) { |
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diff
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|
1018 jQuery($(tblID)).ncbigrid("hideColumn", columnIndex); |
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parents:
diff
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|
1019 } |
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parents:
diff
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|
1020 else if (show) { |
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parents:
diff
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|
1021 jQuery($(tblID)).ncbigrid("showColumn", columnIndex); |
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diff
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|
1022 } |
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parents:
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|
1023 if ($("Transcr") && (hide || show) ) { |
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parents:
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|
1024 var colsp = parseInt($("Transcr").getAttribute("colspan")); |
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1025 colsp = (hide) ? colsp - 1 : colsp + 1; |
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|
1026 $("Transcr").setAttribute("colSpan", colsp); |
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parents:
diff
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|
1027 if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp); |
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diff
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|
1028 } |
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parents:
diff
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|
1029 } |
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parents:
diff
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|
1030 |
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parents:
diff
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|
1031 function checkConfig(lnk) { |
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parents:
diff
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1032 var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value; |
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1033 lnk.href = lnk.href + cnfCol + "#sort_mark"; |
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|
1034 } |
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|
1035 |
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|
1036 function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists |
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|
1037 { |
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1038 var dflLineLinks = $C(seqID, "gi", document, "a"); |
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diff
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1039 for (i = 0; i < dflLineLinks.length; i++) { |
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parents:
diff
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1040 jQuery(dflLineLinks[i]).click(); |
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parents:
diff
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|
1041 break; |
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|
1042 } |
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parents:
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1043 location.href = dflLineLinks[i].href; |
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|
1044 } |
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diff
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|
1045 |
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diff
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|
1046 |
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diff
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|
1047 |
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|
1048 function initDescSelect() |
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diff
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|
1049 { |
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|
1050 |
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1051 jQuery("#cntDesc").find("a").each(function(index) { |
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1052 jQuery(this).bind("click", configDescrSelect); |
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diff
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|
1053 }); |
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1054 jQuery("#cntSelN").click(); |
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|
1055 jQuery("#descTblCtrl").find("a[view]").each(function(index) { |
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parents:
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1056 jQuery(this).bind("click", DisplaySelectedView); |
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diff
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|
1057 }); |
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1058 if ($("psiw") && utils.hasClass($("psiw"), "shown")) { |
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1059 jQuery("#cntDesc_psiw").find("a").each(function(index) { |
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parents:
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1060 jQuery(this).bind("click", configDescrSelect); |
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|
1061 }); |
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1062 jQuery("#cntSelN_psiw").click(); |
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1063 jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) { |
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parents:
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|
1064 jQuery(this).bind("click", DisplaySelectedView); |
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|
1065 }); |
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|
1066 } |
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parents:
diff
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|
1067 |
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|
1068 |
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|
1069 //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });?? |
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|
1070 |
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|
1071 } |
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|
1072 |
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diff
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1073 function DisplaySelectedView(e) { |
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1074 if (this.getAttribute("view") == "graph") { //seqviewer |
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1075 ViewSelectedSeqViewer(e,this); |
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|
1076 } |
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1077 else { |
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1078 if (this.getAttribute("view") == "tree") { //seqviewer |
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1079 $("scrWidth").value = screen.width; |
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1080 $("scrHeight").value = screen.height; |
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1081 } |
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|
1082 ViewSelectedSeqsEx(e, this); |
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|
1083 } |
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|
1084 } |
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diff
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|
1085 |
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|
1086 function PsiBelowThresh(elemID) |
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diff
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|
1087 { |
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parents:
diff
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|
1088 var suffix = ""; |
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1089 if (elemID.indexOf("_psiw") != -1) { |
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1090 suffix = "_psiw"; |
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|
1091 } |
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parents:
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|
1092 return suffix; |
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diff
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|
1093 } |
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parents:
diff
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|
1094 |
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parents:
diff
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1095 function ViewSelectedSeqsEx(e,elem) { |
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parents:
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|
1096 var sbmForm = elem.getAttribute("frm"); |
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1097 var seqList = elem.getAttribute("seqList"); |
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|
1098 |
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parents:
diff
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|
1099 var cnfElem = utils.getParent(elem); //.cnf div |
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1100 var suffix = PsiBelowThresh(cnfElem.id); |
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1101 var tblID = "dscTable" + suffix; |
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diff
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|
1102 |
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|
1103 $(seqList).value = createSelseqString(tblID,true); |
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parents:
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|
1104 $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces |
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parents:
diff
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|
1105 if ($(seqList).value.indexOf("dbSNP") != -1) { |
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parents:
diff
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|
1106 $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp |
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|
1107 elem.href = $(sbmForm).action + $(seqList).value; |
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parents:
diff
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|
1108 elem.target = "new"; |
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parents:
diff
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|
1109 } |
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diff
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|
1110 else { |
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|
1111 $(sbmForm).submit(); |
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parents:
diff
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|
1112 utils.preventDefault(e); |
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diff
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|
1113 } |
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diff
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|
1114 } |
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parents:
diff
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|
1115 |
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|
1116 function ViewSelectedSeqsTree(e) { |
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parents:
diff
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|
1117 $("scrWidth").value = screen.width; |
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|
1118 $("scrHeight").value = screen.height; |
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|
1119 } |
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diff
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|
1120 |
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diff
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|
1121 function initSeqViewerGet(seqList) { |
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1122 if (seqList.length >= 2000) { |
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|
1123 seqList = seqList.substr(0,2000); |
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|
1124 lastComma = seqList.lastIndexOf(","); |
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|
1125 seqList = seqList.substr(0,lastComma); |
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|
1126 } |
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|
1127 $("seqViewParams").name = "RID"; |
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|
1128 $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]"; |
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|
1129 } |
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parents:
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|
1130 |
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|
1131 function ViewSelectedSeqViewer(e, elem) |
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|
1132 { |
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|
1133 var cnfElem = utils.getParent(elem); //.cnf div |
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diff
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|
1134 var suffix = PsiBelowThresh(cnfElem.id); |
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|
1135 var tblID = "dscTable" + suffix; |
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parents:
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|
1136 |
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|
1137 //change to false when new verison of seqVier is installed in production |
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1138 var seqList = createSelseqString(tblID, false); |
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|
1139 $("sbmtGraphics").action = $("seqViewUrl").value; |
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|
1140 |
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parents:
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|
1141 var rp = new RemoteDataProvider("url2nc.cgi"); |
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|
1142 rp.onSuccess = function(obj) { |
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|
1143 var jsnResp = JSON.parse(obj.responseText); |
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parents:
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|
1144 ncid = jsnResp.ncid; |
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parents:
diff
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|
1145 |
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parents:
diff
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|
1146 if (ncid != "") { |
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parents:
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|
1147 $("seqViewParams").name = "rkey"; |
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parents:
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|
1148 $("seqViewParams").value = ncid; |
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diff
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|
1149 } |
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|
1150 else { |
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parents:
diff
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|
1151 initSeqViewerGet(seqList); |
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parents:
diff
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|
1152 } |
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parents:
diff
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|
1153 $("sbmtGraphics").submit(); |
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|
1154 }; |
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|
1155 rp.onError = function(obj) { |
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diff
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|
1156 initSeqViewerGet(seqList); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1157 $("sbmtGraphics").submit(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1158 utils.preventDefault(e); |
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diff
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|
1159 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1160 var params = $("ridParam").value + "[" + seqList + "]"; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1161 rp.Request(params, "POST"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1162 utils.preventDefault(e); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1163 } |
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parents:
diff
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|
1164 |
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parents:
diff
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|
1165 function configDescrSelect(e) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1166 var sel = this.getAttribute("sel"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1167 if (sel) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1168 var selNum = 0; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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1169 var check = (sel == "all") ? true : false; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
1170 |
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parents:
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1171 var suffix = PsiBelowThresh(this.id); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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1172 var tblID = "dscTable" + suffix; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
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|
1173 var toolbarID = "descTblCtrl" + suffix; |
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parents:
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|
1174 var selElID = "slcNum" + suffix; |
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parents:
diff
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|
1175 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1176 jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1177 jQuery(this)[0].checked = check; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1178 if (check) selNum++; |
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parents:
diff
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|
1179 }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1180 enableDescrLinks(selNum, toolbarID, selElID); |
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parents:
diff
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|
1181 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1182 utils.preventDefault(e); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1183 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1184 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1185 |
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parents:
diff
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|
1186 |
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parents:
diff
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|
1187 function enableDescrLinks(selNum, toolbarID, selElID) { |
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parents:
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|
1188 jQuery($(toolbarID)).find("a[minSlct]").each(function(index) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1189 var minSelected = this.getAttribute("minSlct"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1190 minSelected = parseInt(minSelected); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1191 if (selNum >= minSelected) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1192 this.removeAttribute("disabled"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1193 } |
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parents:
diff
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|
1194 else { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1195 this.setAttribute("disabled", "disabled"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1196 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1197 }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1198 $(selElID).innerHTML = selNum; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1199 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1200 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1201 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1202 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1203 function configDescrLinks(e, elem) |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1204 { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1205 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1206 ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1207 var par = jQuery(elem).parents(".jig-ncbigrid");//parent table |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1208 if (par) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1209 var suffix = PsiBelowThresh(par[0].id); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1210 var tblID = "dscTable" + suffix; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1211 var toolbarID = "descTblCtrl" + suffix; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1212 var selElID = "slcNum" + suffix; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1213 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1214 var currSelNum = parseInt($(selElID).innerHTML); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1215 var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1216 enableDescrLinks(selNum, toolbarID, selElID); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1217 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1218 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1219 /***Download code begin****/ |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1220 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1221 function initDownLoadPopup(dwnDialog) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1222 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1223 jQuery(dwnDialog).find("button").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1224 jQuery(this).bind("click", execDownLoad); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1225 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1226 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1227 jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1228 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1229 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1230 function initDescDownLoad() { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1231 initDownLoadPopup($("dsDownload")); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1232 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1233 if ($("psiw") && utils.hasClass($("psiw"), "shown")) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1234 initDownLoadPopup($("dsDownload_psiw")); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1235 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1236 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1237 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1238 function initAlignDownLoad(navObj) |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1239 { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1240 var seqID = navObj.seqID; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1241 var dwnDialog = $("dlgDwnl_" + seqID); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1242 jQuery(dwnDialog).find("button").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1243 jQuery(this).bind("click", execDownLoad); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1244 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1245 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1246 var dwnFSTW = $("dwFST_" + seqID);//whole seq |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1247 var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1248 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1249 if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1250 if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1251 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1252 jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1253 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1254 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1255 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1256 function execDownLoad(e) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1257 if (!utils.hasClass(this, "cnc")) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1258 par = utils.getParent(this); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1259 dwnDialog = utils.getParent(par); //parent dialog with popDl class |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1260 var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1261 jQuery(dwnDialog).find("input").each(function(index) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1262 if (this.checked) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1263 submitDownLoad(this, descr); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1264 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1265 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1266 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1267 jQuery(document.body).click(); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1268 utils.preventDefault(e); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1269 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1270 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1271 function submitDownLoad(radioElem, descr) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1272 var toolURL = radioElem.getAttribute("url"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1273 if (toolURL) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1274 if (descr) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1275 var getGi = radioElem.getAttribute("getGi"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1276 getGi = (getGi) ? true : false; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1277 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1278 var tblID = "dscTable"; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1279 var suffix = PsiBelowThresh(radioElem.id); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1280 tblID += suffix; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1281 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1282 $("selDnSeqs").value = createSelseqString(tblID,getGi); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1283 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1284 else { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1285 var seqfsta = radioElem.getAttribute("seqfsta"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1286 $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1287 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1288 var addParams = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1289 if (radioElem.getAttribute("addParam")) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1290 addParams = addDwnlParams(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1291 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1292 var submitName = radioElem.getAttribute("sbName") |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1293 $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST"; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1294 $("dwdlSubmit").action = toolURL + addParams; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1295 $("dwdlSubmit").submit(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1296 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1297 else { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1298 var sbFunction = radioElem.getAttribute("sbFunc"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1299 if (sbFunction) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1300 eval(sbFunction + "(radioElem, descr)"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1301 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1302 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1303 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1304 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1305 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1306 function initDownLoadFSTA(radioElem, descr) |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1307 { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1308 if (descr) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1309 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1310 var tblID = "dscTable"; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1311 var suffix = PsiBelowThresh(radioElem.id); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1312 tblID += suffix; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1313 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1314 $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1315 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1316 else { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1317 $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1318 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1319 $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1320 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1321 $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1322 if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1323 var batchID = document.getElementsByName("ALIGNDB_BATCH_ID"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1324 if (batchID) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1325 $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1326 $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1327 $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1328 $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1329 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1330 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1331 $("sbmtFASTA").submit(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1332 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1333 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1334 function createSelseqString(tblID,getGi) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1335 var selSeqs = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1336 jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1337 if (jQuery(this)[0].checked) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1338 if (selSeqs != "") selSeqs += ","; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1339 if (getGi) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1340 selSeqs += jQuery(this)[0].value; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1341 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1342 else { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1343 var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1344 selSeqs += $(linkID).getAttribute("seqFSTA"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1345 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1346 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1347 }); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1348 return selSeqs; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1349 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1350 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1351 /***Download code end****/ |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1352 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1353 /***Init navigation code begin **/ |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1354 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1355 function initNavigation(navObj) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1356 initNextAlnLink(navObj, true); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1357 initNextAlnLink(navObj, false); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1358 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1359 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1360 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1361 function initNavInfo(navObj) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1362 var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind")); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1363 nextInd = currInd + 1; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1364 prevInd = currInd - 1; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1365 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1366 navObj.currSeqID = ""; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1367 navObj.nextSeqID = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1368 navObj.prevSeqID = ""; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1369 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1370 if ($("deflnDesc_" + nextInd)) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1371 navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1372 if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1373 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1374 if ($("deflnDesc_" + prevInd)) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1375 navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1376 if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1377 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1378 if ($("deflnDesc_" + currInd)) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1379 navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1380 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1381 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1382 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1383 |
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parents:
diff
changeset
|
1384 function initNextAlnLink(navObj, next) { |
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parents:
diff
changeset
|
1385 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1386 var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1387 var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID; |
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parents:
diff
changeset
|
1388 |
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parents:
diff
changeset
|
1389 if (nextLinkEl) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1390 if (nextSeqid != "") { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1391 var text = (next) ? "next" : "previous"; |
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parents:
diff
changeset
|
1392 nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1393 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
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|
1394 else { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1395 nextLinkEl.setAttribute("disabled", "disabled"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1396 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1397 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1398 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1399 function scan(link) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1400 var init = link.getAttribute("init"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1401 if (!init) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1402 ncbi.sg.scanLinks(link); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1403 link.setAttribute("init","on"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1404 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1405 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1406 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1407 function initWidth(seqID) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1408 var lineLengthElem = $("FormatForm").LINE_LENGTH; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1409 var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value); |
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parents:
diff
changeset
|
1410 if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1411 |
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parents:
diff
changeset
|
1412 var relWidth = (lineLength > 90) ? "12%" : "15%"; |
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parents:
diff
changeset
|
1413 var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1414 lineLength = (lineLength + parseInt(17)) * charWidth; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1415 var width = lineLength + "px"; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1416 jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1417 jQuery(this).css("width", width); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1418 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1419 jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1420 jQuery(this).css("width", width); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1421 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1422 jQuery($("relInf_" + seqID)).css("width", relWidth); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1423 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1424 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1425 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1426 /***Init navigation code end **/ |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1427 function initAlignBatch(seqID) |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1428 { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1429 var navObj = new Object(); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1430 navObj.seqID = seqID; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1431 initNavInfo(navObj); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1432 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1433 initAlignDownLoad(navObj); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1434 initNavigation(navObj); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1435 ncbi.sg.scanLinks($("alnNxt_" + seqID)); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1436 ncbi.sg.scanLinks($("alnPrv_" + seqID)); |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1437 if ($("serviceType").value == "vecscreen") { |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1438 utils.addClass($("alnDsc_" + seqID), "hidden"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1439 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1440 ncbi.sg.scanLinks($("alnDwnld_" + seqID)); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1441 jQuery($("csLinks_" + seqID)).find("a").each(function(index) { |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1442 ncbi.sg.scanLinks(this); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1443 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1444 jQuery($("relInf_" + seqID)).find("a").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1445 ncbi.sg.scanLinks(this); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1446 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1447 jQuery($("rng_" + seqID)).find("a").each(function(index) { |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1448 ncbi.sg.scanLinks(this); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1449 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1450 jQuery($("dln_" + seqID)).find("a").each(function(index) { |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1451 ncbi.sg.scanLinks(this); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1452 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1453 initWidth(seqID); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1454 /* |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1455 jQuery($("alnHdr_" + seqID)).find("a").each(function(index) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1456 ncbi.sg.scanLinks(this); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1457 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1458 jQuery($("aln_" + seqID)).find("a").each(function(index) { |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1459 ncbi.sg.scanLinks(this); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1460 }); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1461 */ |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1462 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1463 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1464 function SaveConfigTable() { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1465 blastUrl = "fmtsave.cgi"; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1466 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1467 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1468 var rp = new RemoteDataProvider(blastUrl); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1469 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1470 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1471 rp.onSuccess = function(obj) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1472 //alert("success"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1473 }; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1474 rp.onError = function(obj) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1475 //alert("error"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1476 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1477 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1478 var program = getHiddenFieldVal("PROGRAM"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1479 var rid = getHiddenFieldVal("RID"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1480 var blastSpec = getHiddenFieldVal("BLAST_SPEC"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1481 var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1482 if(blastSpec) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1483 params += "&BLAST_SPEC=" + blastSpec; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1484 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1485 rp.Request(params,"POST"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1486 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1487 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1488 function removeRID() { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1489 var rid = document.getElementsByName("RID"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1490 for (var i = 0; i <= rid.length; i++) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1491 jQuery(rid[i]).remove(); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1492 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1493 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1494 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1495 function initAdvancedView() |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1496 { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1497 if ($("dsConfig")) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1498 |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1499 var alnView = getHiddenFieldVal("ALIGNMENT_VIEW"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1500 if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1501 var rid = getHiddenFieldVal("RID"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1502 ReadNextSeqAligns(0, 5); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1503 g_alignViewPos = $("alignView").getBoundingClientRect().top; |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1504 utils.addEvent(window, "scroll", checkAutoAlignLoad, false); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1505 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1506 list = $("phiPtInd"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1507 if (list) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1508 utils.addEvent(list, "change", GetPatternLocResults, false); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1509 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1510 initDescConfig(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1511 initDescSelect(); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1512 initDescDownLoad(); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1513 if ($("psiInp")) { |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1514 var nextIter = document.getElementsByName("NEXT_I"); |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1515 for (var i = 0; i < nextIter.length; i++) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1516 utils.addEvent(nextIter[i], "click", removeRID, false); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1517 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1518 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1519 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1520 } |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1521 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1522 //takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4" |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1523 function initjQry() |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1524 { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1525 var oldCreate = jQuery.ui.ncbipopper.prototype._create; |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1526 jQuery.ui.ncbipopper.prototype._create = function() { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1527 var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1528 this.options.destSelector = destSelector.replace(/\./g, "\\."); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1529 oldCreate.apply(this, arguments); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1530 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1531 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1532 utils.addEvent(window, |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1533 "load", initAdvancedView, |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1534 false); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1535 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1536 initjQry() |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1537 |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1538 /* If user agent has "safari" in it, include safari-specific stylesheet. */ |
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add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1539 if (navigator.userAgent.match(/ie/i)) { |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1540 document.write("<link rel='stylesheet' type='text/css' href='css/ie-descriptions.css' media='screen'/>"); |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1541 } |
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Jan Kanis <jan.code@jankanis.nl>
parents:
diff
changeset
|
1542 /*****************************new code end*********************************************************************/ |