Galaxy |

Changeset 1:17a3f755d472 (2013-08-21)

Previous changeset 0:f653fd06f055 (2013-08-15) Next changeset 2:b65518a007fa (2013-09-08)

Commit message:
Uploaded

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/Scilligence.JSDraw.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jmoleditor/Jmoleditor/Scilligence.JSDraw.js Wed Aug 21 03:07:12 2013 -0400

[

b'@@ -0,0 +1,15 @@\n+//////////////////////////////////////////////////////////////////////////////////\r\n+//\r\n+// JSDraw\x99 and JsSDF\r\n+// Version 1.3.2.2012-1-27\r\n+//\r\n+// JSDraw\x99 1.3.2 is built on Dojo 1.7.0 (http://www.dojotoolkit.org/)\r\n+//\r\n+// Copyright (c) 2009-2012 Scilligence\r\n+// - Free for academia\r\n+// - Please contact [support@scilligence.com] for commercial licenses\r\n+// http://wwww.jsdraw.com/\r\n+//\r\n+//////////////////////////////////////////////////////////////////////////////////\r\n+\r\n+eval(function (p, a, c, k, e, r) { e = function (c) { return (c < a ? \'\' : e(parseInt(c / a))) + ((c = c % a) > 35 ? String.fromCharCode(c + 29) : c.toString(36)) }; if (!\'\'.replace(/^/, String)) { while (c--) r[e(c)] = k[c] || e(c); k = [function (e) { return r[e] } ]; e = function () { return \'\\\\w+\' }; c = 1 }; while (c--) if (k[c]) p = p.replace(new RegExp(\'\\\\b\' + e(c) + \'\\\\b\', \'g\'), k[c]); return p } (\'1b hu="1r L0.3.2";4i={8v:1t,4e:1d(){if(4i.8v)2C.hx("4i").1K=\\\'\\\'},7i:1d(s){if(4i.8v){1b a=2C.hx("4i");a.1K+=s+"\\\\n"}}};1O={5n:1d(){}};w1=1O;1O.6a=1d(a,b,c){if(c)1O.6a(a,c);if(a&&b&&3l b==\\\'6c\\\'){1h(1b k in b)a[k]=b[k]}1e a};1O.6a(1O,{4S:1d(){1b g=1d(a){1h(1b k in a)1a[k]=a[k]};1b h=KZ.bu.4I;1e 1d(b,c,d){if(3l c==\\\'6c\\\'){d=c;c=b;b=d.4I!=h?d.4I:1d(){c.6a(1a,KY)}}1b F=1d(){};1b e=c.bu;F.bu=e;1b f=b.bu=1q F();f.4I=b;b.vJ=e;if(e.4I==h)e.4I=c;b.en=1d(a){1O.en(b,a)};f.vJ=f.KX=(1d(){1e e});f.en=g;1O.en(b,d);b.4S=1d(a){1e 1O.4S(b,a)};1e b}}(),en:1d(a,b){if(b){1b p=a.bu;1O.6a(p,b);if(2C.au!=1c&&b.KW(\\\'7C\\\'))p.7C=b.7C}},1A:1d(a){if(a==1c)1e 1c;1b b={};1O.6a(b,a);1e b}});1d vp(){if(5K.7F.KV!="ve KL KJ")1e 1t;1e 2C.uX==1c?(2C.i9=="KH"?7:6):2C.uX};1b 7A=vp();if(7A&&7A<9)1w.KF.KD="ub,KB,Ku";1w.8l("1w.io.gC");1w.8l("1w.io.iH");1w.8l("2Z.3P");1w.8l("2Z.3P.tE");1w.8l("1w.5K");1w.8l("2Z.ce.tA");1w.8l("2Z.ce.Kq.iQ");1w.8l("2Z.ce.Km.iQ");1w.8l("2Z.ce.tb.sZ");1w.8l("2Z.gr.gn");1w.cE(1d(){2Z.3P.jr.bu.Kg=1d(a){1b s=1a.8n;a.7G();a.8H=s.8H;a.sz=s.8H;a.sy=s.cC;a.3M=s.8A;a.Kd(s.2P,s.x,s.y);a.so();a.K9()}});g5={G:\\\'\\\\4u\\\\n\\\\n 5 4 0 0 0 0 0 0 0 4B 3p\\\\n 2.K5 -2.5R 0.1p 3W 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 3.K3 -1.3A 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 4.s9 -2.5R 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 6.K1 -1.3A 0.1p 4a 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 4.s9 -3.3C 0.1p O 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 1 2 1 0 0 0 0\\\\n 2 3 1 0 0 0 0\\\\n 3 4 1 0 0 0 0\\\\n 3 5 2 0 0 0 0\\\\nM 3h\\\\n\\\',A:\\\'\\\\4u\\\\n\\\\n 6 5 0 0 0 0 0 0 0 4B 3p\\\\n 3.s1 -3.3C 0.1p 3W 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 4.fZ -3.8L 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 5.fY -3.3C 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 7.rB -3.8L 0.1p 4a 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 5.fY -5.8m 0.1p O 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 4.fZ -1.3A 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 1 2 1 0 0 0 0\\\\n 2 3 1 0 0 0 0\\\\n 3 4 1 0 0 0 0\\\\n 3 5 2 0 0 0 0\\\\n 2 6 1 1 0 0 0\\\\nM 3h\\\\n\\\',S:\\\'\\\\4u\\\\n\\\\n 7 6 0 0 0 0 0 0 0 4B 3p\\\\n 3.ci -4.5L 0.1p 3W 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 5.aj -3.3C 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 6.6K -4.5L 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 7.fK -3.3C 0.1p 4a 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 6.6K -6.4m 0.1p O 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 5.aj -2.5R 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 6.6K -1.3A 0.1p O 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 1 2 1 0 0 0 0\\\\n 2 3 1 0 0 0 0\\\\n 3 4 1 0 0 0 0\\\\n 3 5 2 0 0 0 0\\\\n 2 6 1 1 0 0 0\\\\n 6 7 1 0 0 0 0\\\\nM 3h\\\\n\\\',T:\\\'\\\\4u\\\\n\\\\n 8 7 0 0 0 0 0 0 0 4B 3p\\\\n 3.ci -4.5L 0.1p 3W 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 5.aj -3.3C 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n 6.6K -4.5L 0.1p C 0 0 0 0 0 0 0 0 0 0 0 0\\\\n '..b"|8A4FE3|785CE3|545CF2|006BFF|0080FF||235|index|molweight|234|0291|029|008FFF|00A1FF|00BAFF|70ABFA|Append|007D00|420066|428296|754F45|AB5C00|9E4FB5|206|575961|delete|Pb|205|203|3829|383|A6544D|Tl|202|201|199|5991|B8B8D0|197|FFD123|194|D0D0E0|193|2163|175487|188|showformula|showmolweight|2246|266696||185|2069||||267DAB|182|8416|2194D6|rowid|||9479||4DA6FF|179|||177||4852|4DC2FF|175|00AB24|172|171|0376|04|00BF38|169|00D452|166|256|163|161|4971|1FFFC7|159|30FFC7|2521|45FFC7|153|9643|964|61FFC7|3664|8FFFC7|A3FFC7|143|spreadsheet|Define|2362|insertafterv|C7FFC7|Pivot|searchable|141|D9FFC7|1153|FFFFC7|Lines|StackedAreas||139|Markers|Series|9051|70D4FF|3268|327|00C900|57178F|129|fontColor|labelOffset|radius|shadows|tension|gap||2924|293|429EB0|940094|vertical||setTheme||addSeries|125||6028|D47A00|Checkbox|7598|Density|9E63B5|Float|7101|Integer|668080|Mass|8182|Weight|818|Moles|Radio||A67573|Temperature|4114|Percentage|411|Volume|FFD98F|8682|868|C0C0C0|4152|006985|0A7D8C|0648|add|07|Manager|248F8F|moveRow|3B9E9E|9313|54B5B5|73C2C9|2236|insertColumn|94E0E0|9058|setColumnKey|9059|change|from|into|||will||94FFFF|lost|6166|00FF00|4677|4678|702EB0|7993|moveup|5CB8D1|movedown|9035|A62929|9594|FFA100|BD80E3|6128|Title|668F8F|7231|previousSibling|723|C28F8F|3955|7D80B0|removeAttribute|innerText|5456|546|C88033|6933|6934|50D050|F090A0|8451|845|number|E06633|9C7AC7|8A99C7|A6A6AB|8667|867|BFC2C7|E6E6E6||1000000|3DFF00|kmol|8F40D4|hits|9477|80D1E3||4526|453|1FF01F|0661||f2f2f2|065|__|C0C000|FF8000|0854|0855|F0C8A0|BFA6A6|unselectable|8AFF00|AB5CF2|1797|B3E3F5|90E050|FF0D0D|0068|0067|3050F8|FFB5B5|asc|C2FF00|941|sortdsc|sortasc|8804|8805|CC80FF|D9FFFF|909090|3126|C12H21O3N3|0529|C3H7NO2Se|1188|C4H9O3N|1881|TABLE|C9H11NO3|2247|C11H12O2N2|0923|C3H7O3N|setTimeout||clearTimeout|1301|||C5H9O2N|1887|C9H11NO2|10000000000|2109|ddd|C5H11SNO2|2135|C7H16N2O2|1724|10004|rsaquo|C6H13O2N|1542|C6H9N3O2|TBODY|0664|__jsdialog|C2H5NO2|1441|WRAPPER|C5H10O3N2|1289|C5H9O4N|1579|C3H7NO2S|C4H7O4N|1176|C4H8O3N2|2004|C6H14N4O2|0929|C3H7NO2|C4H6N2O2|2250|fff|4f6d81|Close|dlgclose|284|C10H12N4O6|999|onscroll|1113|C5H4N4O|ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789|0866|C4H4N2O2|1018|C4H5N3O|1131|C5H6N2O2|1180|Za|C5H4N5O|2048|Guanine||1265|downloaddlg|C5H5N5||||0540|inchi|HTML|cml|Chemical|Markup|Language||5280|CDX|cdxml||CDXML|png|PNG|Picture|0880|5700|6590|Xml|Json|chemistry|skc|9600|openjsd|5200|8600|6400|2000|9800|8800|6580|6060|Web|3381|3413|9022|6826|2435|0239|9261|CAS|Convert|Appending|Mode|appendingmode|csv|openjss|3923|3391|json2Str|9550|CD_CONTROL150CLSID|8850|F974516A|2072|4af1|B063|489FAA6D4177|CD_CONTROL140CLSID|4F48D182|B7C5|4e2c|B95D|5C318E62CE04|CD_CONTROL130CLSID|8B0D4252|4E82||463a|84ED|E8A796C4808A||5360||0620|8420|0700|7980|4360|3730|45C31980|E065|49A1||A3D7|E69CD40DAF66|2160|7EF697A4|D9F3|4303|9161|BBBEA1C30097|1160|60257C74|D60B|41D6|9296|A08BD51F15B5|7230|51A649C4|3E3D|4557|9BD8|B14C0AD44B0C|6720|AF2D2DC1|75E4|4123|BC0B|A57BD5C5C5D2|0245|FA549D21|6F54|11D2|B61B|00C04F736BDF|2360|3795|9045|box|then|EMBED|showtoolswhenvisible|4210|6405|9999999|getData|7870|classid|5660|ActiveDocument|mdl|4660|5665|ChemDrawControl12|5145|e12|9820|ChemDrawControl11|e11|2280|ChemDrawControl10|e10|4607|ChemDrawControl9|1710|ChemDrawControl8|Something|wrong|installers|which|causes|7847|cannot|used|4950|3950|ChemDrawLib|ChemDrawCtl6|installed|retval|1477|99999|0967|textTransform|uppercase|fontFamily|courier|e1e1e1|1210|eef|4200|ebf1fa|0690|ABCFE2|ECCDDC|fCdDeC|stroke|bgred|FfeEf8|E7A6DF|fillText|C7EEDF|d7fEeF|_renderShape|bggreen|dCFff8|95D09C|CDD0EC|dDe0fC|plot2d|bgblue|eCeFFf|8BB6CC|axis2d||ECECCD|fCfCdD|svg|bgyellow|F4F4B8|C8BA8F|STEREO_LABEL|Generic|Component|vml|Copolymer|gfxRenderer|Mixture|config|Monomer|CSS1Compat|Formulation|Explorer|Mer|Internet|Multiple|Ordered|Unordered|Alternating|alt|Block|blk|Random|ran|appName|hasOwnProperty|supr|arguments|Object|V1|COM|COP|MIX|MON|FOR|SUP|MER|ANY|MUL||objects'.split('|'), 0, {}))\n\\ No newline at end of file\n"

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/editor.htm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jmoleditor/Jmoleditor/editor.htm Wed Aug 21 03:07:12 2013 -0400

[

@@ -0,0 +1,71 @@
+
+
+<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" >
+<head>
+<title>JSDraw - A Javascript Chemical Structure Editor/Viewer</title>
+<meta http-equiv="X-UA-Compatible" content="IE=edge" >
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+<script src="http://ajax.googleapis.com/ajax/libs/dojo/1.6/dojo/dojo.xd.js" type="text/javascript"></script>
+<script type="text/javascript" src='Scilligence.JSDraw.js'></script>
+
+
+</head>
+<body>
+
+<h2>Paint your structure and add it to Galaxy!</h2>
+
+<table border=1><tr><td>
+Editor:<br />
+<div class='JSDraw' id="test" style="width: 760px; height: 300px;border:1px solid gray" ondatachange='molchange'
+    dataformat='molfile' data=''></div>
+</td></tr></table>
+<button onclick='document.getElementById("data_type").value ="mol";document.getElementById("galaxyData").value = JSDraw.get("test").getMolfile();document.getElementById("galaxyform").submit();'>Export Molfile to Galaxy</button>
+<button onclick='document.getElementById("data_type").value ="smi";document.getElementById("galaxyData").value = JSDraw.get("test").getSmiles();document.getElementById("galaxyform").submit();'>Export Smiles to Galaxy</button>
+
+<form name="galaxyform" id="galaxyform" enctype="multipart/form-data" action="" method="post">
+    <input name='galaxyData' id='galaxyData' type='hidden' value='' />
+    <input name='data_type' id='data_type' type='hidden' value='mol' />
+    <input name='tool_id' id='tool_id' type='hidden' value='' />
+</form>
+
+<br />
+Mol. Weight: <label id='mw' style='width:120px;font-weight:bold'></label>
+Formula: <label id='formula' style='width:300px;font-weight:bold'></label>
+
+<script type="text/javascript">
+    JSDraw.init();
+
+    function molchange(jsdraw) {
+    document.getElementById('formula').innerHTML = jsdraw.getFormula(true);
+    document.getElementById('mw').innerHTML = jsdraw.getMolWeight();
+    }
+
+    function getParameterByName(name)
+    {
+      name = name.replace(/[\[]/, "\\\[").replace(/[\]]/, "\\\]");
+      var regexS = "[\\?&]" + name + "=([^&#]*)";
+      var regex = new RegExp(regexS);
+      var results = regex.exec(window.location.search);
+      if(results == null)
+        return "";
+      else
+        return decodeURIComponent(results[1].replace(/\+/g, " "));
+    }
+
+    document.getElementById('tool_id').value = getParameterByName('tool_id') ;
+
+    document.getElementById('galaxyform').action = getParameterByName('GALAXY_URL')+"?tool_id="+getParameterByName('tool_id')+"&URL="+getParameterByName('URL')+" " ;
+
+</script>
+
+</body>
+</html>

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/Question.gif

Binary file jmoleditor/Jmoleditor/img/Question.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/add.gif

Binary file jmoleditor/Jmoleditor/img/add.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/animator.gif

Binary file jmoleditor/Jmoleditor/img/animator.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/antibody.gif

Binary file jmoleditor/Jmoleditor/img/antibody.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/arrow.gif

Binary file jmoleditor/Jmoleditor/img/arrow.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/benzene.gif

Binary file jmoleditor/Jmoleditor/img/benzene.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/bracket.gif

Binary file jmoleditor/Jmoleditor/img/bracket.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/cancel.gif

Binary file jmoleditor/Jmoleditor/img/cancel.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/center.gif

Binary file jmoleditor/Jmoleditor/img/center.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/chargen.gif

Binary file jmoleditor/Jmoleditor/img/chargen.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/chargep.gif

Binary file jmoleditor/Jmoleditor/img/chargep.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/chart.gif

Binary file jmoleditor/Jmoleditor/img/chart.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/chembl.gif

Binary file jmoleditor/Jmoleditor/img/chembl.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/chemene.gif

Binary file jmoleditor/Jmoleditor/img/chemene.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/chemspider.gif

Binary file jmoleditor/Jmoleditor/img/chemspider.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/cleanup.gif

Binary file jmoleditor/Jmoleditor/img/cleanup.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/copy.gif

Binary file jmoleditor/Jmoleditor/img/copy.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/copyprod.gif

Binary file jmoleditor/Jmoleditor/img/copyprod.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/cut.gif

Binary file jmoleditor/Jmoleditor/img/cut.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/del.gif

Binary file jmoleditor/Jmoleditor/img/del.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/delocalized.gif

Binary file jmoleditor/Jmoleditor/img/delocalized.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/dlgclose.gif

Binary file jmoleditor/Jmoleditor/img/dlgclose.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/dlgheader-blue.gif

Binary file jmoleditor/Jmoleditor/img/dlgheader-blue.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/dlgheader-green.gif

Binary file jmoleditor/Jmoleditor/img/dlgheader-green.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/dlgheader-red.gif

Binary file jmoleditor/Jmoleditor/img/dlgheader-red.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/dlgheader-yellow.gif

Binary file jmoleditor/Jmoleditor/img/dlgheader-yellow.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/dlgheader.gif

Binary file jmoleditor/Jmoleditor/img/dlgheader.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/double.gif

Binary file jmoleditor/Jmoleditor/img/double.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/doublearomatic.gif

Binary file jmoleditor/Jmoleditor/img/doublearomatic.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/down.gif

Binary file jmoleditor/Jmoleditor/img/down.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/either.gif

Binary file jmoleditor/Jmoleditor/img/either.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/eraser.gif

Binary file jmoleditor/Jmoleditor/img/eraser.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/find.gif

Binary file jmoleditor/Jmoleditor/img/find.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/fliph.gif

Binary file jmoleditor/Jmoleditor/img/fliph.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/flipv.gif

Binary file jmoleditor/Jmoleditor/img/flipv.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbg-blue.gif

Binary file jmoleditor/Jmoleditor/img/hbg-blue.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbg-green.gif

Binary file jmoleditor/Jmoleditor/img/hbg-green.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbg-red.gif

Binary file jmoleditor/Jmoleditor/img/hbg-red.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbg-yellow.gif

Binary file jmoleditor/Jmoleditor/img/hbg-yellow.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbg.gif

Binary file jmoleditor/Jmoleditor/img/hbg.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbg.jpg

Binary file jmoleditor/Jmoleditor/img/hbg.jpg has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/hbk.gif

Binary file jmoleditor/Jmoleditor/img/hbk.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/header-bg.gif

Binary file jmoleditor/Jmoleditor/img/header-bg.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/header-bgblue.gif

Binary file jmoleditor/Jmoleditor/img/header-bgblue.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/header-bggreen.gif

Binary file jmoleditor/Jmoleditor/img/header-bggreen.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/header-bgred.gif

Binary file jmoleditor/Jmoleditor/img/header-bgred.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/header-bgyellow.gif

Binary file jmoleditor/Jmoleditor/img/header-bgyellow.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/helix.gif

Binary file jmoleditor/Jmoleditor/img/helix.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/information.gif

Binary file jmoleditor/Jmoleditor/img/information.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/insertafter.gif

Binary file jmoleditor/Jmoleditor/img/insertafter.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/insertafterv.gif

Binary file jmoleditor/Jmoleditor/img/insertafterv.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/insertbefore.gif

Binary file jmoleditor/Jmoleditor/img/insertbefore.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/jsdraw.gif

Binary file jmoleditor/Jmoleditor/img/jsdraw.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/lasso.gif

Binary file jmoleditor/Jmoleditor/img/lasso.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/movedown.gif

Binary file jmoleditor/Jmoleditor/img/movedown.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/moveup.gif

Binary file jmoleditor/Jmoleditor/img/moveup.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/n2s.gif

Binary file jmoleditor/Jmoleditor/img/n2s.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/new.gif

Binary file jmoleditor/Jmoleditor/img/new.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/open.gif

Binary file jmoleditor/Jmoleditor/img/open.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/paste.gif

Binary file jmoleditor/Jmoleditor/img/paste.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/pastechemdraw.gif

Binary file jmoleditor/Jmoleditor/img/pastechemdraw.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/pivot.gif

Binary file jmoleditor/Jmoleditor/img/pivot.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/plasmid.gif

Binary file jmoleditor/Jmoleditor/img/plasmid.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/plus.gif

Binary file jmoleditor/Jmoleditor/img/plus.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/protein.gif

Binary file jmoleditor/Jmoleditor/img/protein.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/pubchem.gif

Binary file jmoleditor/Jmoleditor/img/pubchem.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/redo.gif

Binary file jmoleditor/Jmoleditor/img/redo.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/ring3.gif

Binary file jmoleditor/Jmoleditor/img/ring3.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/ring4.gif

Binary file jmoleditor/Jmoleditor/img/ring4.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/ring5.gif

Binary file jmoleditor/Jmoleditor/img/ring5.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/ring6.gif

Binary file jmoleditor/Jmoleditor/img/ring6.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/ring7.gif

Binary file jmoleditor/Jmoleditor/img/ring7.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/ring8.gif

Binary file jmoleditor/Jmoleditor/img/ring8.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/rotate.gif

Binary file jmoleditor/Jmoleditor/img/rotate.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/rxn.gif

Binary file jmoleditor/Jmoleditor/img/rxn.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/rxnmap.gif

Binary file jmoleditor/Jmoleditor/img/rxnmap.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/rxnmap2.gif

Binary file jmoleditor/Jmoleditor/img/rxnmap2.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/save.gif

Binary file jmoleditor/Jmoleditor/img/save.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/select.gif

Binary file jmoleditor/Jmoleditor/img/select.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/selectall.gif

Binary file jmoleditor/Jmoleditor/img/selectall.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/selfrag.gif

Binary file jmoleditor/Jmoleditor/img/selfrag.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/sep.gif

Binary file jmoleditor/Jmoleditor/img/sep.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/seq.gif

Binary file jmoleditor/Jmoleditor/img/seq.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/sgroup.gif

Binary file jmoleditor/Jmoleditor/img/sgroup.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/single.gif

Binary file jmoleditor/Jmoleditor/img/single.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/singlearomatic.gif

Binary file jmoleditor/Jmoleditor/img/singlearomatic.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/singledouble.gif

Binary file jmoleditor/Jmoleditor/img/singledouble.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/sortasc.gif

Binary file jmoleditor/Jmoleditor/img/sortasc.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/sortdsc.gif

Binary file jmoleditor/Jmoleditor/img/sortdsc.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/splash.gif

Binary file jmoleditor/Jmoleditor/img/splash.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/stop.gif

Binary file jmoleditor/Jmoleditor/img/stop.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/text.gif

Binary file jmoleditor/Jmoleditor/img/text.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/tick.gif

Binary file jmoleditor/Jmoleditor/img/tick.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/toolbar-bg.gif

Binary file jmoleditor/Jmoleditor/img/toolbar-bg.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/triple.gif

Binary file jmoleditor/Jmoleditor/img/triple.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/undo.gif

Binary file jmoleditor/Jmoleditor/img/undo.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/unknown.gif

Binary file jmoleditor/Jmoleditor/img/unknown.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/unlock.gif

Binary file jmoleditor/Jmoleditor/img/unlock.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/up.gif

Binary file jmoleditor/Jmoleditor/img/up.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/vbk.gif

Binary file jmoleditor/Jmoleditor/img/vbk.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/vssver2.scc

Binary file jmoleditor/Jmoleditor/img/vssver2.scc has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/warning.gif

Binary file jmoleditor/Jmoleditor/img/warning.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/wiggly.gif

Binary file jmoleditor/Jmoleditor/img/wiggly.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/zoomin.gif

Binary file jmoleditor/Jmoleditor/img/zoomin.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/img/zoomout.gif

Binary file jmoleditor/Jmoleditor/img/zoomout.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/plugins/jmol.gif

Binary file jmoleditor/Jmoleditor/plugins/jmol.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/plugins/pubchem.gif

Binary file jmoleditor/Jmoleditor/plugins/pubchem.gif has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/Jmoleditor/plugins/vssver2.scc

Binary file jmoleditor/Jmoleditor/plugins/vssver2.scc has changed

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/jmoleditor.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jmoleditor/jmoleditor.py Wed Aug 21 03:07:12 2013 -0400

[

@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+# Retrieves data from external data source applications and stores in a dataset file.
+# Data source application parameters are temporarily stored in the dataset file.
+import socket, urllib, sys, os
+from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg...
+from galaxy.util.json import from_json_string, to_json_string
+import galaxy.model # need to import model before sniff to resolve a circular import dependency
+from galaxy.datatypes import sniff
+from galaxy.datatypes.registry import Registry
+from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+GALAXY_PARAM_PREFIX = 'GALAXY'
+GALAXY_ROOT_DIR = os.path.realpath( os.path.join( os.path.split( os.path.realpath( __file__ ) )[0], '..', '..' ) )
+GALAXY_DATATYPES_CONF_FILE = os.path.join( GALAXY_ROOT_DIR, 'datatypes_conf.xml' )
+
+def load_input_parameters( filename, erase_file = True ):
+    datasource_params = {}
+    try:
+        json_params = from_json_string( open( filename, 'r' ).read() )
+        datasource_params = json_params.get( 'param_dict' )
+    except:
+        json_params = None
+        for line in open( filename, 'r' ):
+            try:
+                line = line.strip()
+                fields = line.split( '\t' )
+                datasource_params[ fields[0] ] = fields[1]
+            except:
+                continue
+    if erase_file:
+        open( filename, 'w' ).close() #open file for writing, then close, removes params from file
+    return json_params, datasource_params
+
+def __main__():
+    filename = sys.argv[1]
+    try:
+        max_file_size = int( sys.argv[2] )
+    except:
+        max_file_size = 0
+
+    job_params, params = load_input_parameters( filename )
+    if job_params is None: #using an older tabular file
+        enhanced_handling = False
+        job_params = dict( param_dict = params )
+        job_params[ 'output_data' ] =  [ dict( out_data_name = 'output',
+                                               ext = 'data',
+                                               file_name = filename,
+                                               extra_files_path = None ) ]
+        job_params[ 'job_config' ] = dict( GALAXY_ROOT_DIR=GALAXY_ROOT_DIR, GALAXY_DATATYPES_CONF_FILE=GALAXY_DATATYPES_CONF_FILE, TOOL_PROVIDED_JOB_METADATA_FILE = TOOL_PROVIDED_JOB_METADATA_FILE )
+    else:
+        enhanced_handling = True
+        json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata
+
+    datatypes_registry = Registry()
+    datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
+
+    URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded
+    URL_method = params.get( 'URL_method', None )
+    simpleD = params.get('galaxyData')
+    # The Python support for fetching resources from the web is layered. urllib uses the httplib
+    # library, which in turn uses the socket library.  As of Python 2.3 you can specify how long
+    # a socket should wait for a response before timing out. By default the socket module has no
+    # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2
+    # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by
+    # doing the following.
+    socket.setdefaulttimeout( 600 )
+    cur_filename = params.get('output')
+    outputfile = open( cur_filename, 'w' ).write( simpleD )
+
+if __name__ == "__main__": __main__()
+
+
+

diff -r f653fd06f055 -r 17a3f755d472 jmoleditor/jmoleditor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jmoleditor/jmoleditor.xml Wed Aug 21 03:07:12 2013 -0400

@@ -0,0 +1,51 @@
+<tool id="jmoleditor" name="JMol Editor" tool_type="data_source">
+    <description>A Chemical Structure Editor</description>
+    <command interpreter="python">jmoleditor.py $output</command>
+    <inputs action="http://localhost:8000/Jmoleditor/editor.htm" check_values="false" method="GET">
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
+        <param name="URL" type="hidden" value="http://localhost:8000/Jmoleditor/editor.htm" />
+        <param name="tool_id" type="hidden" value="jmoleditor" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="galaxyData" remote_name="galaxyData" missing="?" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
+        <request_param galaxy_name="output_label" remote_name="data_type" missing="txt" >
+            <value_translation>
+                <value galaxy_value="Molecule" remote_value="mol" />
+                <value galaxy_value="SMILES" remote_value="smi" />
+            </value_translation>
+        </request_param>
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="smi" label='imported ${output_label} file'>
+            <change_format>
+                <when input="output_label" value="SMILES" format="smi"/>
+            </change_format>
+        </data>
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Paint a structure and load it into your Galaxy history.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+Jmol_: an open-source Java viewer for chemical structures in 3D
+
+.. _Jmol: http://jmol.sourceforge.net/
+
+    </help>
+</tool>
+
+