YAHOO.namespace("module");
YAHOO.namespace("ptools");
function validPosNumberCheck(_1,_2){
var _3=parseFloat(_1);
if(_1&&(isNaN(_3)||(_3<=0))){
alert("The value "+_1+" for "+_2+" is not a positive number.");
return false;
}else{
return true;
}
};
function validMinMaxCheck(_4,_5,_6){
if(_4&&_5&&(parseFloat(_4)>parseFloat(_5))){
alert("In the "+_6+" field, the minimum value, "+_4+", is greater than the maximum value, "+_5+".");
return false;
}else{
return true;
}
};
function removeWS(_7){
if(_7){
return _7.replace(/ /g,"");
}
};
function ACNameSelector(_8,_9,_a,_b){
var _c=new YAHOO.util.XHRDataSource("/"+orgID()+"/ajax-frame-search");
_c.responseType=YAHOO.util.XHRDataSource.TYPE_JSON;
_c.responseSchema={resultsList:"Results",fields:[{key:"id"},{key:"label"},{key:"qName"}]};
var _d=new YAHOO.widget.AutoComplete(_8,_9,_c);
_d.generateRequest=function(_e){
return "?type="+_b+"&max=10&object="+_e;
};
_d.formatResult=function(_f,_10,_11){
return (_f[2]);
};
var _12=function(_13,_14){
var _15=_14[2];
_a.value=_15[0];
_8.value=_15[1];
};
_d.itemSelectEvent.subscribe(_12);
_d.textboxKeyEvent.subscribe(function(_16,_17){
_a.value="";
});
return {oDS:_c,oAC:_d};
};
YAHOO.widget.TaskNodeLink=function(_18,_19,_1a,_1b){
YAHOO.widget.TaskNode.superclass.constructor.call(this,_18,_19,_1a,_1b);
this.setUpCheck(_1b||_18.checked);
};
YAHOO.lang.extend(YAHOO.widget.TaskNodeLink,YAHOO.widget.TaskNode,{getContentHtml:function(){
var sb=[];
sb[sb.length]="<td";
sb[sb.length]=" id=\""+this.getCheckElId()+"\"";
sb[sb.length]=" class=\""+this.getCheckStyle()+"\"";
sb[sb.length]=">";
sb[sb.length]="<div class=\"ygtvspacer\"></div></td>";
sb[sb.length]="<td>";
sb[sb.length]=this.href?"<a":"<span";
sb[sb.length]=" id=\""+this.labelElId+"\"";
if(this.title){
sb[sb.length]=" title=\""+this.title+"\"";
}
sb[sb.length]=" class=\""+this.labelStyle+"\"";
if(this.href){
sb[sb.length]=" href=\""+this.href+"\"";
sb[sb.length]=" target=\""+this.target+"\"";
}
sb[sb.length]=" >";
sb[sb.length]=this.label;
sb[sb.length]=this.href?"</a>":"</span>";
sb[sb.length]="</td>";
return sb.join("");
}});
var trees=new Array();
function classBrowser(_1d,_1e,_1f,_20,_21){
var _22=false;
function _23(){
if(!_22){
tree=new YAHOO.widget.TreeView(_1d);
tree.setDynamicLoad(_24,1);
var _25=tree.getRoot();
var top=new YAHOO.widget.TaskNodeLink(_1e,_25,false,false);
if(_20){
top.data={id:_1e,label:_20};
top.label=_20;
}
var _27=top;
trees[_1f]=tree;
tree.draw();
top.expand();
_22=true;
}
};
function _24(_28,_29){
var _2a=encodeURI(_28.label);
if(_28.data.id){
_2a=_28.data.id;
}
var _2b="/"+orgID()+"/ajax-direct-subs?object="+_2a;
if(_21){
_2b=_2b+"&type="+_21;
}
var _2c={success:function(_2d){
YAHOO.log("XHR transaction was successful.","info",_2d.responseText);
var _2e=eval("("+_2d.responseText+")");
if((_2e)&&(_2e.length)){
if(YAHOO.lang.isArray(_2e)){
for(var i=0,j=_2e.length;i<j;i++){
var _31=_2e[i];
if(_31.isClass){
var _32=new YAHOO.widget.TaskNodeLink(_31,_28,false,_28.checked);
_32.data=_31;
_32.label=_31.label+" ("+_31.numInstances+")";
_32.href=orgID()+"/new-image?object="+_32.data.id;
_32.isLeaf=(_31.numInstances==0);
if(_2e.length==1){
_32.expand();
}
}else{
var _32=new YAHOO.widget.TextNode(_31,_28,false);
_32.data=_31;
_32.href=orgID()+"/new-image?object="+_32.data.id;
_32.isLeaf=true;
}
}
}else{
var _32=new YAHOO.widget.TaskNodeLink(_2e,_28,false,false);
if(!_32.isClass){
_32.isLeaf=true;
}
}
}
_2d.argument.fnLoadComplete();
},failure:failLoadSubclasses,argument:{"node":_28,"fnLoadComplete":_29},timeout:14000};
YAHOO.util.Connect.asyncRequest("GET",_2b,_2c);
};
_1f.beforeShowEvent.subscribe(_23);
};
function evcodeChecklist(_33,_34,_35){
classOnlyBrowser(_33,"Evidence",_34,"ajax-evidence-subs",_35);
};
function classOnlyBrowser(_36,_37,_38,_39,_3a,_3b){
var _3c=false;
function _3d(){
if(!_3c){
tree=new YAHOO.widget.TreeView(_36);
tree.setDynamicLoad(_3e,1);
var _3f=tree.getRoot();
var top=new YAHOO.widget.TextNode(_37,_3f,false);
if(_3b){
top.data={id:_37,label:_3b};
top.label=_3b;
}
trees[_3a]=tree;
tree.draw();
top.expand();
_3c=true;
}
};
function _3e(_41,_42){
var _43=encodeURI(_41.label);
if(_41.data.id){
_43=_41.data.id;
}
var _44="/"+orgID()+"/"+_39+"?type="+_38+"&object="+_43;
var _45={success:function(_46){
YAHOO.log("XHR transaction was successful.","info",_46.responseText);
var _47=eval("("+_46.responseText+")");
if((_47)&&(_47.length)){
if(YAHOO.lang.isArray(_47)){
for(var i=0,j=_47.length;i<j;i++){
var _4a=_47[i];
var _4b=new YAHOO.widget.TaskNode(_4a,_41,false,_41.checked);
_4b.data=_4a;
if(_4a.numInstances){
_4b.label=_4a.label+" ("+_4a.numInstances+")";
}
_4b.isLeaf=_4a.hasChild=="false";
if((_47.length==1)&&!_4b.isLeaf){
_4b.expand();
}
}
}else{
var _4b=new YAHOO.widget.TaskNode(_47,_41,false,false);
}
}
_46.argument.fnLoadComplete();
},failure:failLoadSubclasses,argument:{"node":_41,"fnLoadComplete":_42},timeout:14000};
YAHOO.util.Connect.asyncRequest("GET",_44,_45);
};
_3a.beforeShowEvent.subscribe(_3d);
};
function failLoadSubclasses(_4c){
YAHOO.log("Failed to process XHR transaction.","info","loadSubclasses");
_4c.argument.fnLoadComplete();
};
function getCheckedNodes(_4d,_4e){
_4e=_4e||_4d.children;
checkedNodes=[];
for(var i=0;i<_4e.length;i++){
var n=_4e[i];
if(n.checkState===2){
checkedNodes.push(n.data.id);
}else{
if(n.checkState!=0){
checkedNodes=checkedNodes.concat(getCheckedNodes(_4d,n.children));
}
}
}
return checkedNodes;
};
function clearTree(_51){
var _52=trees[_51];
if(_52){
var _53=_52.getRoot().children;
for(j=0;j<_53.length;j++){
_53[j].uncheck();
}
}
};
function clearEvTree(_54){
if(!_54){
_54=YAHOO.module.evidence;
}
var _55=trees[_54];
if(_55){
var _56=_55.getRoot().children;
for(j=0;j<_56.length;j++){
var _57=_56[j].children;
for(var i=0;i<_57.length;i++){
_57[i].uncheck();
}
}
}
};
function toggleShow(_59,_5a){
if(isVisible(_5a)){
YAHOO.util.Dom.removeClass(_59,"open");
YAHOO.util.Dom.addClass(_59,"closed");
_5a.hide();
}else{
YAHOO.util.Dom.addClass(_59,"open");
YAHOO.util.Dom.removeClass(_59,"closed");
_5a.show();
}
};
function isVisible(_5b){
return _5b.cfg.getProperty("visible");
};
function addCheckedNodesToQuery(_5c,_5d){
var _5e="";
if(isVisible(_5c)){
var _5f=getCheckedNodes(trees[_5c].getRoot());
if(_5f.length>0){
_5e="&"+_5d+"="+encodeURIComponent(_5f.join(" "));
}
}
return _5e;
};
function addPubFieldsToQuery(){
var _60="";
if(isVisible(YAHOO.module.pub)){
var _61=removeWS(document.getElementById("pmid").value);
var _62=document.getElementById("auth").value;
var _63=document.getElementById("title").value;
if(_61){
_60=_60+"&pmid="+_61;
}
if(_62){
_60=_60+"&auth="+_62;
}
if(_63){
_60=_60+"&title="+_63;
}
}
return _60;
};
var originalTitleContents="";
function addOrgNameToTitle(){
var _64=orgNameFromOrgID(orgID());
var _65=document.getElementsByTagName("h1")[0];
var _66=_65.innerHTML;
if(originalTitleContents.length==0){
originalTitleContents=_66;
}
if(_66.search(_64)==-1){
_65.innerHTML="<i>"+_64+"</i>  "+originalTitleContents;
}
};
function hideMultiOrgDivs(){
if(isMultiOrgPGDB()){
var _67=YAHOO.util.Dom.getElementsByClassName("multiorg","div",false,function(elt){
elt.style.display="block";
});
}else{
var _67=YAHOO.util.Dom.getElementsByClassName("multiorg","div",false,function(elt){
elt.style.display="none";
});
}
};
organismChangedEvent.subscribe(function(){
addOrgNameToTitle();
hideMultiOrgDivs();
});
function buildGeneQueryURL(){
var _6a=document.getElementById("geneName").value;
var _6b=document.getElementById("prodName").value;
var _6c=removeWS(document.getElementById("minLen").value);
var _6d=removeWS(document.getElementById("maxLen").value);
var _6e=document.getElementById("seqTypeA").checked?"a":"n";
var _6f=removeWS(document.getElementById("minMP").value);
var _70=removeWS(document.getElementById("maxMP").value);
var _71=removeWS(document.getElementById("minMW").value);
var _72=removeWS(document.getElementById("maxMW").value);
var _73=removeWS(document.getElementById("minPI").value);
var _74=removeWS(document.getElementById("maxPI").value);
var _75=document.getElementById("cpdName").value;
var _76=document.getElementById("cpdID").value;
var _77="/"+orgID()+"/search-query?type=GENE";
var _78="";
var _79=false;
if(isVisible(YAHOO.module.geneNameSearch)&&_6a){
_78=_78+"&gname="+encodeURIComponent(_6a);
}
if(isVisible(YAHOO.module.prodNameSearch)&&_6b){
_78=_78+"&pname="+encodeURIComponent(_6b);
}
if(isVisible(YAHOO.module.seqLength)){
if(!(validPosNumberCheck(_6c,"minimum sequence length")&&validPosNumberCheck(_6d,"maximum sequence length")&&validMinMaxCheck(_6c,_6d,"sequence length"))){
_79=true;
}
if(_6c){
_78=_78+"&minlen="+encodeURIComponent(_6c);
}
if(_6d){
_78=_78+"&maxlen="+encodeURIComponent(_6d);
}
if(_6c||_6d){
_78=_78+"&seqtype="+_6e;
}
}
if(isVisible(YAHOO.module.mapPos)){
if(!(validPosNumberCheck(_6f,"minimum map position")&&validPosNumberCheck(_70,"maximum map position")&&validMinMaxCheck(_6f,_70,"map position"))){
_79=true;
}
if(_6f){
_78=_78+"&minmp="+encodeURIComponent(_6f);
}
if(_70){
_78=_78+"&maxmp="+encodeURIComponent(_70);
}
if(replicons.length>0){
var chr="";
var all=true;
for(var i=0;i<replicons.length;i++){
if(replicons[i].checked){
if(i>0){
chr=chr+" ";
}
chr=chr+replicons[i].value;
}else{
all=false;
}
}
if(!all&&(chr.length>0)){
_78=_78+"&chr="+encodeURIComponent(chr);
}
}
}
if(isVisible(YAHOO.module.mw)){
if(!(validPosNumberCheck(_71,"minimum molecular weight")&&validPosNumberCheck(_72,"maximum molecular weight")&&validMinMaxCheck(_71,_72,"molecular weight"))){
_79=true;
}
if(_71){
_78=_78+"&minmw="+encodeURIComponent(_71);
}
if(_72){
_78=_78+"&maxmw="+encodeURIComponent(_72);
}
}
if(!(validPosNumberCheck(_73,"minimum pI")&&validPosNumberCheck(_74,"maximum pI")&&validMinMaxCheck(_73,_74,"pI"))){
_79=true;
}
if(isVisible(YAHOO.module.pi)){
if(_73){
_78=_78+"&minpi="+encodeURIComponent(_73);
}
if(_74){
_78=_78+"&maxpi="+encodeURIComponent(_74);
}
}
if(isVisible(YAHOO.module.cpd)){
var _7d="";
if(_75||_76){
if(document.getElementById("activator").checked){
if(_7d.length>0){
_7d=_7d+" ";
}
_7d=_7d+"act";
}
if(document.getElementById("inhibitor").checked){
if(_7d.length>0){
_7d=_7d+" ";
}
_7d=_7d+"inh";
}
if(document.getElementById("cofactor").checked){
if(_7d.length>0){
_7d=_7d+" ";
}
_7d=_7d+"cof";
}
if(document.getElementById("substrate").checked){
if(_7d.length>0){
_7d=_7d+" ";
}
_7d=_7d+"sub";
}
if(document.getElementById("ligand").checked){
if(_7d.length>0){
_7d=_7d+" ";
}
_7d=_7d+"lig";
}
if(_7d.length>0){
_78=_78+"&regtype="+_7d;
if(_76){
_78=_78+"&cpdid="+encodeURIComponent(_76);
}else{
_78=_78+"&cpdname="+encodeURIComponent(_75);
}
}
}
}
if(isVisible(YAHOO.module.GO)){
var _7e=document.getElementById("GOID").value;
var _7f=document.getElementById("GOName").value;
var _80=getCheckedNodes(trees[YAHOO.module.GO].getRoot());
if(_80.length>0){
_78=_78+"&go="+encodeURIComponent(_80.join(" "));
}else{
if(_7e){
_78=_78+"&go="+encodeURIComponent(_7e);
}else{
if(_7f){
_78=_78+"&go="+encodeURIComponent(_7f);
}
}
}
}
_78=_78+addCheckedNodesToQuery(YAHOO.module.MultiFun,"mf");
_78=_78+addCheckedNodesToQuery(YAHOO.module.evidence,"ev");
_78=_78+addCheckedNodesToQuery(YAHOO.module.cco,"cco");
if(YAHOO.util.Dom.get("speciesModule")){
_78=_78+addCheckedNodesToQuery(YAHOO.module.species,"orgs");
}
_78=_78+addPubFieldsToQuery();
if(_78.length>0){
_78=_77+_78;
}else{
alert("No search criteria specified.");
_79=true;
}
if(_79){
return false;
}else{
return _78;
}
};
function clearGeneForm(){
YAHOO.util.Dom.get("geneID").value="";
YAHOO.util.Dom.get("prodID").value="";
YAHOO.util.Dom.get("cpdID").value="";
YAHOO.util.Dom.get("GOID").value="";
clearTree(YAHOO.module.GO);
clearEvTree();
clearEvTree(YAHOO.module.cco);
if(YAHOO.util.Dom.get("speciesModule")){
clearTree(YAHOO.module.species);
}
};
function initGeneForm(){
addOrgNameToTitle();
ACNameSelector(YAHOO.util.Dom.get("geneName"),YAHOO.util.Dom.get("geneNameContainer"),YAHOO.util.Dom.get("geneID"),"GENE");
YAHOO.module.geneNameSearch=new YAHOO.widget.Module("geneNameSearchModule",{visible:true});
YAHOO.module.geneNameSearch.render();
ACNameSelector(YAHOO.util.Dom.get("prodName"),YAHOO.util.Dom.get("prodNameContainer"),YAHOO.util.Dom.get("prodID"),"GENE-PRODUCT");
YAHOO.module.prodNameSearch=new YAHOO.widget.Module("prodNameSearchModule",{visible:true});
YAHOO.module.prodNameSearch.render();
YAHOO.module.seqLength=new YAHOO.widget.Module("seqLengthModule",{visible:false});
YAHOO.module.seqLength.render();
YAHOO.module.mapPos=new YAHOO.widget.Module("mapPosModule",{visible:false});
YAHOO.module.mapPos.render();
YAHOO.module.mapPos.beforeShowEvent.subscribe(loadReplicons);
YAHOO.module.mw=new YAHOO.widget.Module("mwModule",{visible:false});
YAHOO.module.mw.render();
YAHOO.module.pi=new YAHOO.widget.Module("piModule",{visible:false});
YAHOO.module.pi.render();
ACNameSelector(YAHOO.util.Dom.get("cpdName"),YAHOO.util.Dom.get("cpdContainer"),YAHOO.util.Dom.get("cpdID"),"COMPOUND");
YAHOO.module.cpd=new YAHOO.widget.Module("cpdModule",{visible:false});
YAHOO.module.cpd.render();
var _81=ACNameSelector(YAHOO.util.Dom.get("GOName"),YAHOO.util.Dom.get("GOContainer"),YAHOO.util.Dom.get("GOID"),"GO-TERMS");
YAHOO.module.GO=new YAHOO.widget.Module("GOModule",{visible:false});
classBrowser("goTree","Gene-Ontology-Terms",YAHOO.module.GO);
YAHOO.module.GO.render();
_81.oAC.textboxKeyEvent.subscribe(function(_82,_83){
clearTree(YAHOO.module.GO);
});
YAHOO.module.GO.showEvent.subscribe(function(){
var _84=trees[YAHOO.module.GO];
_84.subscribe("checkClick",function(_85){
YAHOO.util.Dom.get("GOID").value="";
YAHOO.util.Dom.get("GOName").value="";
});
});
YAHOO.module.evidence=new YAHOO.widget.Module("evidenceModule",{visible:false});
evcodeChecklist("evidenceTree","Macromolecules",YAHOO.module.evidence);
YAHOO.module.evidence.render();
YAHOO.module.cco=new YAHOO.widget.Module("ccoModule",{visible:false});
classOnlyBrowser("ccoTree","CCO","Macromolecules","ajax-cco-subs",YAHOO.module.cco,"Cellular Compartments");
YAHOO.module.cco.render();
YAHOO.module.MultiFun=new YAHOO.widget.Module("MultiFunModule",{visible:false});
classBrowser("multifunTree","MultiFun",YAHOO.module.MultiFun);
YAHOO.module.MultiFun.render();
if(YAHOO.util.Dom.get("speciesModule")){
YAHOO.log("speciesModule");
YAHOO.module.species=new YAHOO.widget.Module("speciesModule",{visible:false});
classBrowser("speciesTree","TAX-131567",YAHOO.module.species,"Cellular Organisms","Macromolecules");
YAHOO.module.species.render();
}
YAHOO.module.pub=new YAHOO.widget.Module("pubModule",{visible:false});
YAHOO.module.pub.render();
hideMultiOrgDivs();
};
var repliconsLoaded=false;
var replicons=[];
var originalMapPosBody;
function loadReplicons(){
var _86=orgID();
var url="/"+_86+"/ajax-get-slot-values?object="+_86+"&slot=GENOME";
var _88={success:function(_89){
YAHOO.log("XHR transaction was successful.","info",_89.responseText);
var _8a=eval("("+_89.responseText+")");
if((_8a)&&(_8a.length)&&(_8a.length>1)){
var _8b=YAHOO.module.mapPos;
_8b.appendToBody(document.createElement("br"));
for(var i=0;i<_8a.length;i++){
var el=document.createElement("input");
el.type="checkbox";
el.id="rID"+i;
el.name="rName"+i;
el.value=_8a[i].id;
replicons[i]=el;
_8b.appendToBody(document.createElement("br"));
_8b.appendToBody(el);
_8b.appendToBody(document.createTextNode(" "+_8a[i].label));
}
}
repliconsLoaded=true;
},failure:function(_8e){
YAHOO.log("Failed to process XHR transaction.","info","loadReplicons");
}};
if(!repliconsLoaded){
originalMapPosBody=YAHOO.module.mapPos.body.innerHTML;
YAHOO.util.Connect.asyncRequest("GET",url,_88);
organismChangedEvent.subscribe(unloadReplicons);
}
};
function unloadReplicons(){
repliconsLoaded=false;
replicons=[];
YAHOO.module.mapPos.setBody(originalMapPosBody);
};
function submitGeneQuery(){
var id=document.getElementById("prodID").value||document.getElementById("geneID").value;
if(id){
window.location="/"+orgID()+"/new-image?object="+id;
}else{
var _90=buildGeneQueryURL();
if(_90){
window.location=_90;
}
}
};
function buildPwyQueryURL(){
var _91=document.getElementById("pwyName").value;
var _92=removeWS(document.getElementById("minRxns").value);
var _93=removeWS(document.getElementById("maxRxns").value);
var _94="/"+orgID()+"/search-query?type=PATHWAY";
var _95="";
var _96=false;
_95=_95+addCheckedNodesToQuery(YAHOO.module.classBrowse,"class");
if(isVisible(YAHOO.module.nameSearch)&&_91){
_95=_95+"&name="+encodeURIComponent(_91);
}
if(isVisible(YAHOO.module.numRxns)){
if(!(validPosNumberCheck(_92,"minimum number of reactions")&&validPosNumberCheck(_93,"maximum number of reactions")&&validMinMaxCheck(_92,_93,"number of reactions"))){
_96=true;
}
if(_92){
_95=_95+"&minrxns="+_92;
}
if(_93){
_95=_95+"&maxrxns="+_93;
}
}
if(isVisible(YAHOO.module.substrates)){
var _97="";
var ids="";
for(var i=0;i<substrateNameFields.length;i++){
var _9a=substrateNameFields[i].value;
var id=substrateIDFields[i].value;
if(id){
if(ids.length>0){
ids=ids+" ";
}
ids=ids+id;
}else{
if(_9a&&_9a.match(/\S/)){
if(_97.length>0){
_97=_97+" ";
}
_97=_97+_9a;
}
}
}
if(_97.match(/\S/)){
_95=_95+"&subnames="+encodeURIComponent(_97);
}
if(ids.match(/\S/)){
_95=_95+"&subids="+encodeURIComponent(ids);
}
}
_95=_95+addCheckedNodesToQuery(YAHOO.module.evidence,"ev");
if(YAHOO.util.Dom.get("speciesModule")){
_95=_95+addCheckedNodesToQuery(YAHOO.module.species,"orgs");
_95=_95+addCheckedNodesToQuery(YAHOO.module.tax,"tax");
}
_95=_95+addPubFieldsToQuery();
if(_95.length>0){
_95=_94+_95;
}else{
alert("No search criteria specified.");
_96=true;
}
if(_96){
return false;
}else{
return _95;
}
};
var substrateNameFields=new Array();
var substrateIDFields=new Array();
function clearPwyForm(){
YAHOO.util.Dom.get("pwyName").value="";
YAHOO.util.Dom.get("pwyID").value="";
YAHOO.util.Dom.get("minRxns").value="";
YAHOO.util.Dom.get("maxRxns").value="";
for(var i=0;i<substrateNameFields.length;i++){
substrateNameFields[i].value="";
substrateIDFields[i].value="";
}
clearTree(YAHOO.module.classBrowse);
clearEvTree();
if(YAHOO.util.Dom.get("speciesModule")){
clearTree(YAHOO.module.species);
clearEvTree(YAHOO.module.tax);
}
};
function initPwyForm(){
addOrgNameToTitle();
ACNameSelector(YAHOO.util.Dom.get("pwyName"),YAHOO.util.Dom.get("pwyNameContainer"),YAHOO.util.Dom.get("pwyID"),"PATHWAY");
YAHOO.module.nameSearch=new YAHOO.widget.Module("nameSearchModule",{visible:true});
YAHOO.module.nameSearch.render();
YAHOO.module.classBrowse=new YAHOO.widget.Module("classBrowseModule",{visible:false});
classBrowser("classTree","Pathways",YAHOO.module.classBrowse);
YAHOO.module.classBrowse.render();
YAHOO.module.numRxns=new YAHOO.widget.Module("numRxnsModule",{visible:false});
YAHOO.module.numRxns.render();
for(var i=0;i<4;i++){
var _9e=YAHOO.util.Dom.get("substrate"+i+"Name");
var _9f=YAHOO.util.Dom.get("substrate"+i+"ID");
var _a0=YAHOO.util.Dom.get("substrate"+i+"Container");
substrateNameFields[i]=_9e;
substrateIDFields[i]=_9f;
ACNameSelector(_9e,_a0,_9f,"COMPOUND");
}
YAHOO.module.substrates=new YAHOO.widget.Module("substratesModule",{visible:false});
YAHOO.module.substrates.render();
YAHOO.module.evidence=new YAHOO.widget.Module("evidenceModule",{visible:false});
evcodeChecklist("evidenceTree","Pathways",YAHOO.module.evidence);
YAHOO.module.evidence.render();
if(YAHOO.util.Dom.get("speciesModule")){
YAHOO.log("speciesModule");
YAHOO.module.species=new YAHOO.widget.Module("speciesModule",{visible:false});
classBrowser("speciesTree","TAX-131567",YAHOO.module.species,"Cellular Organisms","Pathways");
YAHOO.module.species.render();
}
if(YAHOO.util.Dom.get("taxModule")){
YAHOO.module.tax=new YAHOO.widget.Module("taxModule",{visible:false});
classOnlyBrowser("taxTree","TAX-131567","Pathways","ajax-tax-range-subs",YAHOO.module.tax,"Cellular Organisms");
YAHOO.module.tax.render();
}
YAHOO.module.pub=new YAHOO.widget.Module("pubModule",{visible:false});
YAHOO.module.pub.render();
hideMultiOrgDivs();
};
function submitPwyQuery(){
var _a1=document.getElementById("pwyID").value;
if(_a1){
window.location="/"+orgID()+"/new-image?object="+_a1;
}else{
var _a2=buildPwyQueryURL();
if(_a2){
window.location=_a2;
}
}
};
function buildCpdQueryURL(){
var _a3=document.getElementById("cpdName").value;
var _a4=removeWS(document.getElementById("minMW").value);
var _a5=removeWS(document.getElementById("maxMW").value);
var _a6=document.getElementById("inchi").value;
var _a7=document.getElementById("formula").value;
var _a8="/"+orgID()+"/search-query?type=COMPOUND";
var _a9="";
var _aa=false;
_a9=_a9+addCheckedNodesToQuery(YAHOO.module.classBrowse,"class");
if(isVisible(YAHOO.module.nameSearch)&&_a3){
_a9=_a9+"&name="+encodeURIComponent(_a3);
}
if(isVisible(YAHOO.module.mw)){
if(!(validPosNumberCheck(_a4,"minimum molecular weight")&&validPosNumberCheck(_a5,"maximum molecular weight")&&validMinMaxCheck(_a4,_a5,"molecular weight"))){
_aa=true;
}
if(_a4){
_a9=_a9+"&minmw="+_a4;
}
if(_a5){
_a9=_a9+"&maxmw="+_a5;
}
}
if(isVisible(YAHOO.module.inchi)&&_a6){
var _ab=_a6.split(/[\s\t\n]/).join("");
_a9=_a9+"&inchi="+encodeURIComponent(_ab);
}
if(isVisible(YAHOO.module.formula)&&_a7){
var _ac=chemicalFormulaToArg(_a7);
if(_ac){
_a9=_a9+"&formula="+encodeURIComponent(_ac);
}
}
if(_a9.length>0){
_a9=_a8+_a9;
}else{
alert("No search criteria specified.");
_aa=true;
}
if(_aa){
return false;
}else{
return _a9;
}
};
function chemicalFormulaToArg(_ad){
YAHOO.log("Formula: "+_ad,"info");
var _ae=/(([A-Z][a-z]?)|[a-z])[0-9]*/g;
var _af=_ad.replace(/\s/g,"").match(_ae);
if(_af.length>0){
return _af.join(" ").toUpperCase();
}
};
function clearCpdForm(){
YAHOO.util.Dom.get("cpdName").value="";
YAHOO.util.Dom.get("frameID").value="";
YAHOO.util.Dom.get("minMW").value="";
YAHOO.util.Dom.get("maxMW").value="";
YAHOO.util.Dom.get("formula").value="";
YAHOO.util.Dom.get("inchi").value="";
clearTree(YAHOO.module.classBrowse);
};
function initCpdForm(){
addOrgNameToTitle();
ACNameSelector(YAHOO.util.Dom.get("cpdName"),YAHOO.util.Dom.get("nameContainer"),YAHOO.util.Dom.get("frameID"),"COMPOUND");
YAHOO.module.nameSearch=new YAHOO.widget.Module("nameSearchModule",{visible:true});
YAHOO.module.nameSearch.render();
YAHOO.module.classBrowse=new YAHOO.widget.Module("classBrowseModule",{visible:false});
classBrowser("classTree","Compounds",YAHOO.module.classBrowse);
YAHOO.module.classBrowse.render();
YAHOO.module.mw=new YAHOO.widget.Module("mwModule",{visible:false});
YAHOO.module.mw.render();
YAHOO.module.formula=new YAHOO.widget.Module("formulaModule",{visible:false});
YAHOO.module.formula.render();
YAHOO.module.inchi=new YAHOO.widget.Module("inchiModule",{visible:false});
YAHOO.module.inchi.render();
};
function submitCpdQuery(){
var cpd=document.getElementById("frameID").value;
if(cpd){
window.location="/"+orgID()+"/new-image?object="+cpd;
}else{
var _b1=buildCpdQueryURL();
if(_b1){
window.location=_b1;
}
}
};
function buildRxnQueryURL(){
var _b2=orgID();
var _b3="/"+_b2+"/search-query?type=REACTION";
var _b4="";
var _b5=document.getElementById("rxnName").value;
_b4=_b4+addCheckedNodesToQuery(YAHOO.module.classBrowse,"class");
if(isVisible(YAHOO.module.nameSearch)&&_b5){
_b4=_b4+"&name="+encodeURIComponent(_b5);
}
if(isVisible(YAHOO.module.substrates)){
var _b6="";
var ids="";
for(var i=0;i<substrateNameFields.length;i++){
var _b9=substrateNameFields[i].value;
var id=substrateIDFields[i].value;
if(id){
if(ids.length>0){
ids=ids+" ";
}
ids=ids+id;
}else{
if(_b9&&_b9.match(/\S/)){
if(_b6.length>0){
_b6=_b6+" ";
}
_b6=_b6+_b9;
}
}
}
if(_b6.match(/\S/)){
_b4=_b4+"&subnames="+encodeURIComponent(_b6);
}
if(ids.match(/\S/)){
_b4=_b4+"&subids="+encodeURIComponent(ids);
}
}
if(_b4.length>0){
_b4=_b3+_b4;
}else{
alert("No search criteria specified.");
return false;
}
return _b4;
};
function clearRxnForm(){
YAHOO.util.Dom.get("rxnName").value="";
YAHOO.util.Dom.get("frameID").value="";
for(var i=0;i<substrateNameFields.length;i++){
substrateNameFields[i].value="";
substrateIDFields[i].value="";
}
clearTree(YAHOO.module.classBrowse);
};
function initRxnForm(){
addOrgNameToTitle();
ACNameSelector(YAHOO.util.Dom.get("rxnName"),YAHOO.util.Dom.get("nameContainer"),YAHOO.util.Dom.get("frameID"),"REACTION");
YAHOO.module.nameSearch=new YAHOO.widget.Module("nameSearchModule",{visible:true});
YAHOO.module.nameSearch.render();
YAHOO.module.classBrowse=new YAHOO.widget.Module("classBrowseModule",{visible:false});
classBrowser("classTree","Reactions",YAHOO.module.classBrowse);
YAHOO.module.classBrowse.render();
for(var i=0;i<4;i++){
var _bd=YAHOO.util.Dom.get("substrate"+i+"Name");
var _be=YAHOO.util.Dom.get("substrate"+i+"ID");
var _bf=YAHOO.util.Dom.get("substrate"+i+"Container");
substrateNameFields[i]=_bd;
substrateIDFields[i]=_be;
ACNameSelector(_bd,_bf,_be,"COMPOUND");
}
YAHOO.module.substrates=new YAHOO.widget.Module("substratesModule",{visible:false});
YAHOO.module.substrates.render();
};
function submitRxnQuery(){
var _c0=document.getElementById("frameID").value;
if(_c0){
window.location="/"+orgID()+"/new-image?object="+_c0;
}else{
var _c1=buildRxnQueryURL();
if(_c1){
window.location=_c1;
}
}
};