Mercurial > repos > jankanis > blast2html
annotate Blast output page example_files/format.js @ 27:4e6ac737ba17
improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
author | Jan Kanis <jan.code@jankanis.nl> |
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date | Thu, 15 May 2014 16:46:09 +0200 |
parents | bad241dc701f |
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1 |
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2 function UpdateDisplayTypes(displayTypes) { |
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3 dispMenu = displayTypes.options; |
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4 for(i=0; i < dispMenu.length; i++) { |
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5 //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") || |
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6 if($("stepNumber").value == "" || $("stepNumber").value < 2) { |
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7 if(dispMenu[i].value.indexOf("PSSM") != -1) { |
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8 dispMenu[i--] = null; |
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9 //break; |
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10 } |
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11 } |
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12 } |
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13 } |
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14 |
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15 function GetIndexByValue(selectElem,val) { |
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16 var idx = 0; |
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17 var opts = selectElem.options; |
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18 for(i=0; i < opts.length; i++) { |
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19 if(opts[i].value == val) { |
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20 idx = i; |
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21 break; |
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22 } |
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23 } |
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24 return idx; |
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25 } |
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26 |
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27 function resetAdvView(show) |
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28 { |
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29 var advView = $("advView"); |
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30 if(show) { |
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31 if(utils.hasClass(advView, "hidden")) { |
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32 utils.removeClass(advView, "hidden"); |
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33 } |
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34 } |
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35 else { |
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36 utils.addClass(advView, "hidden"); |
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37 } |
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38 } |
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39 |
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40 |
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41 function ShowOrHide(hide,elem) |
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42 { |
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43 if(hide) { |
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44 if(!utils.hasClass(elem, "hidden")) { |
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45 utils.addClass(elem, "hidden"); |
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46 } |
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47 } |
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48 else { |
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49 if(utils.hasClass(elem, "hidden")) { |
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50 utils.removeClass(elem, "hidden"); |
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51 } |
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52 } |
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53 } |
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54 |
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55 function UpdateFormatTypes(form) { |
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56 var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value; |
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57 var hideAdvView = false; |
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58 bioseqFormatHide = true; |
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59 pssmFormatHide = true; |
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60 pssmScFormatHide = true; |
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61 formatTypeHide = true; |
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62 if (selectedObjType == "Alignment") { |
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63 formatObjectSelectedIndex = 0; //HTML |
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64 formatTypeHide = false; |
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65 hideAdvView = true; |
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66 } |
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67 if (selectedObjType == "PSSM") { |
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68 formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text"); |
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69 pssmFormatHide = false; |
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70 } |
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71 if (selectedObjType == "PSSM_Scoremat") { |
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72 formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1"); |
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73 pssmScFormatHide = false; |
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74 } |
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75 else if (selectedObjType == "Bioseq") { |
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76 formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1"); |
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77 bioseqFormatHide = false; |
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78 } |
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79 form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex; |
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80 ShowOrHide(formatTypeHide,form.FORMAT_TYPE); |
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81 if ($("bioseqFormat")) { |
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82 ShowOrHide(bioseqFormatHide,$("bioseqFormat")); |
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83 $("bioseqFormat").readOnly=true; |
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84 } |
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85 if ($("pssmFormat")) { |
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86 ShowOrHide(pssmFormatHide,$("pssmFormat")); |
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87 $("pssmFormat").readOnly=true; |
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88 } |
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89 if ($("pssmScFormat")) { |
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90 ShowOrHide(pssmScFormatHide,$("pssmScFormat")); |
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91 $("pssmScFormat").readOnly=true; |
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92 } |
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93 resetAdvView(hideAdvView); |
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94 } |
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95 |
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96 function ResetForm() |
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97 { |
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98 //var defValNodes = cssQuery(".reset"); |
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99 defValNodes = $("FormatForm").elements; |
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100 for(i=0; i < defValNodes.length; i++) { |
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101 if(utils.hasClass(defValNodes[i],"reset")) |
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102 setDefalValue(defValNodes[i]); |
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103 } |
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104 if ($("FormatForm").FORMAT_OBJECT.type == "select-one") { |
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105 UpdateFormatTypes($("FormatForm")); |
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106 UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT); |
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107 } |
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108 if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH) |
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109 else $("FormatForm").I_THRESH.value=""; |
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110 //resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM); |
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111 resetOrganismControls($("FormatForm").FORMAT_ORGANISM); |
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112 //TO DO: add threshold |
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113 } |
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114 |
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115 function LimitByHitlistSize(list) |
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116 { |
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117 var listBreak = false; |
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118 var optSel = false; |
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119 for(i=0; i < list.options.length; i++) { |
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120 var optVal = parseInt(list.options[i].value ,10); |
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121 var hitListSize = parseInt($("maxNumSeq").value ,10); |
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122 if(list.options[i].selected) optSel = true; |
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123 if(optVal >= hitListSize) { |
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124 if(!optSel) {list.options[i].selected = true;} |
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125 list.options.length = i + 1; |
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126 break; |
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127 } |
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128 } |
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129 } |
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130 |
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131 function AddFormatOrgField(e) { |
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132 AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE"); |
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133 } |
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134 |
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135 function initSubmit() { |
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136 |
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137 |
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138 } |
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139 |
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140 function adjustFormatOptions() |
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141 { |
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142 var alignView = $("FormatForm").ALIGNMENT_VIEW; |
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143 var formatType = $("FormatForm").FORMAT_TYPE; |
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144 var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities"); |
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145 var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch; |
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146 dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities"); |
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147 |
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148 UpdateDescriptions(dynFormatPW); |
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149 if (dynFormatPW) { |
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150 jQuery("#frmAln").addClass("hidden"); |
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151 if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT |
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152 jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE |
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153 jQuery("#scf").removeClass("hidden");//show CDS_FEAT |
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154 $("FormatForm").SHOW_LINKOUT.checked = true; |
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155 } |
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156 else { |
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157 if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex; |
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158 |
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159 jQuery("#frmAln").removeClass("hidden"); |
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160 if (dynFormatQA) { |
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161 if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT |
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162 } |
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163 else { |
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164 jQuery("#shl").removeClass("hidden"); |
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165 } |
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166 if (queryAnch) { |
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167 jQuery("#scf").addClass("hidden"); //hide CDS_FEAT |
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168 } |
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169 else {//pairwise old_view=false |
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170 jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT |
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171 } |
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172 jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE |
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173 } |
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174 if ($("blastSpec").value == "VecScreen") { |
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175 adjustVecscreen(dynFormatPW); |
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176 } |
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177 } |
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178 |
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179 function adjustVecscreen(dynFormatPW) |
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180 { |
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181 var dfltDescrInd = 0; //0 |
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182 var dfltDynDescrInd = 5; //1000 |
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183 var dfltAlnInd = 6; //1000 |
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184 if (dynFormatPW) { |
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185 utils.addClass($("lr"), "hidden"); |
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186 $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd; |
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187 } |
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188 else { |
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189 utils.removeClass($("lr"), "hidden"); |
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190 $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd; |
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191 } |
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192 $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd; |
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193 } |
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194 |
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195 |
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196 function UpdateDescriptions(removeZero) |
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197 { |
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198 if (removeZero) { |
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199 dispMenu = $("FormatForm").DESCRIPTIONS; |
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200 dispMenu.remove(0); |
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201 } |
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202 else { |
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203 dispMenu = $("FormatForm").DESCRIPTIONS; |
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204 if (dispMenu.options[0].value != "0") { |
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205 if (navigator.userAgent.match(/ie/i)) { |
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206 dispMenu.add(new Option("0", "0"), 0); |
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207 } |
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208 else { |
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209 dispMenu.add(new Option("0", "0"), dispMenu[0]); |
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210 } |
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211 } |
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212 } |
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213 } |
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214 |
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215 function InitDynFormatOptions() |
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216 { |
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217 if ($("OLD_VIEW")) { |
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218 utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false); |
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219 utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false); |
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220 utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false); |
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221 adjustFormatOptions(); |
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222 } |
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223 } |
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224 |
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225 function InitFormatPage() |
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226 { |
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227 if ($("FormatForm").FORMAT_OBJECT.type == "select-one") { |
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228 UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT); |
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229 UpdateFormatTypes($("FormatForm")); |
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230 list = $("FormatForm").FORMAT_OBJECT; |
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231 utils.addEvent(list, "change", function() { |
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232 UpdateFormatTypes($("FormatForm")); |
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233 }, |
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234 false); |
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235 } |
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236 utils.addEvent($("resetAll"), "click", ResetForm, false); |
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237 if($("maxNumSeq") != null) { |
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238 if($("maxNumSeq").value != "") { |
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239 LimitByHitlistSize($("FormatForm").DESCRIPTIONS); |
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240 LimitByHitlistSize($("FormatForm").ALIGNMENTS); |
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241 LimitByHitlistSize($("FormatForm").NUM_OVERVIEW); |
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242 } |
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243 } |
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244 setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM); |
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245 utils.addEvent($("FormatForm"), "submit", function() { |
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246 adjustOrgVal($("FormatForm").FORMAT_ORGANISM);}, |
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247 false); |
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248 |
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249 if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false); |
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250 InitDynFormatOptions(); |
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251 /* add this code if decide image for View Report |
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252 var imgButtons = jQuery("[class='viewReport']"); |
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253 for (var i = 0; i < imgButtons.length; i++) { |
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254 var l = imgButtons[i]; |
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255 utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false); |
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256 utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false); |
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257 utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false); |
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258 utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false); |
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259 utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false); |
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260 } |
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261 */ |
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262 } |
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Jan Kanis <jan.code@jankanis.nl>
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263 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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264 utils.addEvent(window, 'load', InitFormatPage, false); |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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265 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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266 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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267 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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268 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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269 |
bad241dc701f
add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
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270 |