var MixedBaseNames=''
var MixedBaseArray=[1];
var _MixedBaseArray=[];
function storeCaret(ftext){
if(ftext.createTextRange){
selectedRange=document.selection.createRange().duplicate();
selectedInputArea=ftext;
}
}
function sethasFocus(ftext)
{
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
for(i=0;i<theForm.length;i=i+1)
{
if(theForm.elements[i].type=='textarea')
{
if(theForm.elements[i].name==ftext.name)
{
theForm.elements[i].hasFocus=true;
}
else
{
theForm.elements[i].hasFocus=false;
}
}
}
}
function storeCaretImproved(textE1){
if(textE1.createTextRange){
selectedRange=document.selection.createRange().duplicate();
selectedInputArea=textE1;
}
}
function InsertAtCursor(txtToInsert){
var retval;
retval='OligoAnalyzer_SequenceSettingsControl_tbSequence';
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
for(i=0;i<theForm.length;i=i+1)
{
if(theForm.elements[i].type=='textarea')
{
if(theForm.elements[i].hasFocus)
{
retval=theForm.elements[i].id;
}
}
}
var vtext;
vtext=eval('theForm.'+retval);
if(txtToInsert.substring(0,2)=='/5')
{
if(vtext.value.substring(0,2)=='/5')
{
alert("Unable to add 5' Mod. Please verify that a 5' Mod is not already added to the Sequence.");
}
else
{
vtext.value=txtToInsert+vtext.value;
vtext.focus();
}
}
else if(txtToInsert.substring(0,2)=='/3')
{
if(vtext.value.indexOf('/3')>0)
{
alert("Unable to add 3' Mod. Please verify that a 3' Mod is not already added to the Sequence.");
}
else
{
vtext.value=vtext.value+txtToInsert;
vtext.focus();
}
}
else
{
if(vtext.createTextRange&&vtext.caretPos)
{
var caretPos=vtext.caretPos;
caretPos.text=caretPos.text.charAt(caretPos.text.length-1)==' '?txtToInsert+' ':txtToInsert;
vtext.focus();
}
else
{
vtext.value+=txtToInsert;
vtext.focus();
}
}
}
function InsertMixedBase(txtToInsert,MixedBase){
var retval;
retval='OligoAnalyzer_SequenceSettingsControl_tbSequence';
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
for(i=0;i<theForm.length;i=i+1)
{
if(theForm.elements[i].type=='textarea')
{
if(theForm.elements[i].hasFocus)
{
retval=theForm.elements[i].id;
}
}
}
var vtext;
vtext=eval('theForm.'+retval);
var caretPos=vtext.caretPos;
if(vtext.createTextRange&&vtext.caretPos)
{
var caretPos=vtext.caretPos;
caretPos.text=caretPos.text.charAt(caretPos.text.length-1)==' '?txtToInsert+' ':txtToInsert;
vtext.focus();
}
else
{
vtext.value+=txtToInsert;
vtext.focus();
}
if(MixedBaseNames!='')
{
VerifyMixedBasePosition();
}
}
function verifymixedbases()
{
var mx_total;
var a;
var c;
var t;
var g;
var name;
var Mixture;
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
mx_total=0;
mx_total=parseInt(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentA.value)+parseInt(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentC.value)+parseInt(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentG.value)+parseInt(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentT.value);
if(mx_total>=99&&mx_total<=100)
{
a=Make_CMB_Pct(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentA.value);
c=Make_CMB_Pct(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentC.value);
g=Make_CMB_Pct(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentG.value);
t=Make_CMB_Pct(theForm.OligoAnalyzer_TabsMenu_EntryTabs_percentT.value);
name=(theForm.OligoAnalyzer_TabsMenu_EntryTabs_tbMixBaseName.value);
name=replace(name,' ','');
Mixture=a+c+g+t;
if(name=='')
{
InsertAtCursor('('+Mixture+')');
}
else
{
if(MixedBaseNames.indexOf(name+":")>0)
{
var isValid=false;
if(_MixedBaseArray.length>0)
{
var i=0;
for(i=0;i<_MixedBaseArray.length;i=i+1)
{
if(_MixedBaseArray[i].Name==name&&_MixedBaseArray[i].Mix==Mixture)
{
InsertAtCursor('('+name+')');
isValid=true;
break;
}
}
}
if(isValid==false)
{
alert("Unable to create the specified custom mix base. Please verify that the name is unique.");
}
}
else
{
InsertAtCursor('('+name+':'+Mixture+')');
MixedBaseNames=MixedBaseNames+'('+name+':'+a+c+g+t+')';
var MixedBaseItem=aMixedBaseItm(name,Mixture);
_MixedBaseArray.push(MixedBaseItem);
AddMixedBaseNames();
}
}
return true;
}
else
{
alert("Unable to create the specified custom mix base. Please verify that the total is 99% or 100%.");
return false;
}
if(MixedBaseNames!='')
{
VerifyMixedBasePosition();
}
}
function CreateLabel(CustName,CustMix)
{
var tdCustMixedBase=$get('OligoAnalyzer_TabsMenu_EntryTabs_tdCustMixedBase');
var aLabel=document.createElement("Div");
aLabel.innerText=CustName+' ('+CustMix+')';
aLabel.id=CustName+i;
aLabel.style.cursor="hand";
aLabel.className="linkItem";
aLabel.onclick=function(){InsertMixedBase('('+CustName+')',CustMix);}
tdCustMixedBase.appendChild(aLabel);
}
function aMixedBaseItm(aName,aMix)
{
return{Name:aName,Mix:aMix};
}
function AddMixedBaseNames()
{
var SelectionArray=MixedBaseNames.split(")");
var i=0;
var tdCustMixedBase=$get('OligoAnalyzer_TabsMenu_EntryTabs_tdCustMixedBase');
tdCustMixedBase.innerText='';
for(i=0;i<_MixedBaseArray.length;i=i+1)
{
if(_MixedBaseArray[i].Name!='')
{
CreateLabel(_MixedBaseArray[i].Name,_MixedBaseArray[i].Mix);
}
}
}
function Make_CMB_Pct(theNum)
{
var RetVal;
if(parseInt(theNum)>=10)
{
RetVal=theNum;
}
else
{
RetVal="0"+theNum;
}
return RetVal;
}
function checkFor_r(theString)
{
if(theString.indexOf("r")>-1)
{
return 1;
}
else
{
return 0;
}
}
function BaseCounter(theSequence,MaxLength)
{
var divSeqWarning=$get('divSeqWarning');
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
var textareaName=theSequence.name;
textareaName=replace(textareaName,'OligoAnalyzer:SequenceSettingsControl','')
textareaName=replace(textareaName,'OligoAnalyzer$SequenceSettingsControl','')
textareaName=replace(textareaName,':tbSequence','')
textareaName=replace(textareaName,'$tbSequence','')
textareaName='OligoAnalyzer_SequenceSettingsControl'+textareaName+'_NumberOfBases';
var textareaValue=theSequence.value;
var thelength=textareaValue.length;
var countMods=Math.round((CountChar(textareaValue,"/"))/2);
countMods=countMods+Math.round((CountChar(textareaValue,"(")));
var ModChars=CountModChars(textareaValue);
textareaValue=RemoveMods(textareaValue);
textareaValue=RemoveNonBase(textareaValue);
thelength=(CountChar(textareaValue,"A")+CountChar(textareaValue,"a")+CountChar(textareaValue,"C")
+CountChar(textareaValue,"c")+CountChar(textareaValue,"G")+CountChar(textareaValue,"g")
+CountChar(textareaValue,"T")+CountChar(textareaValue,"t")+(CountChar(textareaValue,"R"))
+(CountChar(textareaValue,"Y"))+(CountChar(textareaValue,"M"))+(CountChar(textareaValue,"K"))
+(CountChar(textareaValue,"S"))+(CountChar(textareaValue,"W"))+(CountChar(textareaValue,"H"))
+(CountChar(textareaValue,"B"))+(CountChar(textareaValue,"V"))+(CountChar(textareaValue,"D"))
+(CountChar(textareaValue,"U"))+(CountChar(textareaValue,"I"))+(CountChar(textareaValue,"|"))
+(CountChar(textareaValue,"N"))+countMods);
var SpacerCount=0;
SpacerCount=SpaceCount(theSequence.value)+MaxLength;
if(theSequence.value.length>SpacerCount-(countMods)+ModChars)
{
if(theSequence.value.charAt(SpacerCount-(countMods)+ModChars)==')'||theSequence.value.charAt(SpacerCount-(countMods)+ModChars)=='/'||theSequence.value.charAt(SpacerCount-(countMods)+ModChars)==']')
{
theSequence.value=RemoveFinalMod(theSequence.value.substring(0,SpacerCount-(countMods)+ModChars));
}
else
{
theSequence.value=theSequence.value.substring(0,SpacerCount-(countMods)+ModChars);
}
thelength=thelength-1;
BaseCounter(theSequence,MaxLength);
}
theForm[textareaName].value=thelength;
if(MaxLength<=thelength)
{
divSeqWarning.style.display='block';
}
else
{
divSeqWarning.style.display='none';
}
if(theSequence.createTextRange)theSequence.caretPos=document.selection.createRange().duplicate();
if(MixedBaseNames!='')
{
VerifyMixedBasePosition();
}
}
function SpaceCount(originalString)
{
var strLength=originalString.length;
var SpaceCounter=0;
if(strLength==0)
{
return SpaceCounter;
}
for(i=0;i<strLength;i=i+1)
{
if(originalString.charAt(i)==" ")
{
SpaceCounter=SpaceCounter+1;
}
}
return SpaceCounter;
}
function OnLoadBaseCounter()
{
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
for(i=0;i<theForm.length;i=i+1)
{
if(theForm.elements[i].type=='textarea')
{
if(theForm.elements[i].name.substring(15,23)=='Sequence')
{
var textareaName=theForm.elements[i];
BaseCounter(textareaName);
}
}
}
}
function RemoveNonBase(theString)
{
var returnString=""
for(var i=0;i<theString.length;i++){
if(((theString.charAt(i)=="A")||(theString.charAt(i)=="a")||(theString.charAt(i)=="G")
||(theString.charAt(i)=="g")||(theString.charAt(i)=="C")||(theString.charAt(i)=="c")
||(theString.charAt(i)=="T")||(theString.charAt(i)=="t")||(theString.charAt(i)=="R")
||(theString.charAt(i)=="Y")||(theString.charAt(i)=="M")||(theString.charAt(i)=="K")
||(theString.charAt(i)=="S")||(theString.charAt(i)=="W")||(theString.charAt(i)=="H")
||(theString.charAt(i)=="B")||(theString.charAt(i)=="V")||(theString.charAt(i)=="D")
||(theString.charAt(i)=="U")||(theString.charAt(i)=="I")||(theString.charAt(i)=="|")
||(theString.charAt(i)=="N"))){
returnString+=theString.charAt(i)
}
}
return returnString
}
function CountModChars(theString)
{
var returnCount=0
var IsMod="False"
for(var i=0;i<theString.length;i++)
{
if(IsMod=="False")
{
if(theString.charAt(i)=="/"||theString.charAt(i)=="["||theString.charAt(i)=="(")
{
IsMod="True"
returnCount=returnCount+1;
}
}
else
{
returnCount=returnCount+1;
if(theString.charAt(i)=="/"||theString.charAt(i)=="]"||theString.charAt(i)==")")
{
IsMod="False"
}
}
}
return returnCount
}
function RemoveFinalMod(theString)
{
var returnString=theString;
var IsMod="False";
var NewLength=theString.length;
for(var i=theString.length;i>1;i--)
{
if(IsMod=="False")
{
if(theString.charAt(i)=="/"||theString.charAt(i)=="["||theString.charAt(i)=="(")
{
IsMod="True"
break;
}
else
{
NewLength=NewLength-1;
}
}
}
returnString=returnString.substring(0,NewLength)
return returnString;
}
function RemoveMods(theString)
{
var returnString="";
var IsMod="False";
for(var i=0;i<theString.length;i++)
{
if(IsMod=="False")
{
if(theString.charAt(i)=="/"||theString.charAt(i)=="["||theString.charAt(i)=="(")
{
IsMod="True";
}
else
{
returnString+=theString.charAt(i);
}
}
else
{
if(theString.charAt(i)=="/"||theString.charAt(i)=="]"||theString.charAt(i)==")")
{
IsMod="False";
if(theString.charAt(i)==")")
{
returnString+=theString.charAt("|");
}
}
}
}
return returnString;
}
function CountChar(theString,theChar){
var returnValue=0
theString=theString.toUpperCase()
for(var i=0;i<theString.length;i++){
if(theString.charAt(i)==theChar){
returnValue++
}
}
return returnValue
}
function replace(originalString,searchText,replaceText)
{
var strLength=originalString.length;
var txtLength=searchText.length;
if((strLength==0)||(txtLength==0))
{
return originalString;
}
var i=originalString.indexOf(searchText);
if((!i)&&(searchText!=originalString.substring(0,txtLength)))
{
return originalString;
}
if(i==-1)
{
return originalString;
}
var newstr=originalString.substring(0,i)+replaceText;
if(i+txtLength<strLength)
{
newstr+=replace(originalString.substring(i+txtLength,strLength),searchText,replaceText);
}
return newstr;
}
function convertDNAToRNA(theSequence)
{
var theField=theSequence;
var selectedText=document.selection;
var x;
if(selectedText.type=='Text'){
var newRange=selectedText.createRange();
theField.focus();
x=newRange.text
if(checkFor_r(x)<1)
{
x=replace(x,"t","T");
x=replace(x,"a","A");
x=replace(x,"c","C");
x=replace(x,"g","G");
x=replace(x,"u","U");
x=replace(x,"U","rU");
x=replace(x,"T","rU");
x=replace(x,"A","rA");
x=replace(x,"C","rC");
x=replace(x,"G","rG");
}
else
{
alert('Your selection already contains RNA bases');
}
document.selection.createRange().text=x
}else{
alert('select text in the page and then press this button');
}
}
function textCounter(field,maxlimit)
{
var newField=replace(field.value," ","M")
if(newField.value.length>maxlimit)
{
field.value=newField.value.substring(0,maxlimit);
}
}
function VerifyMixedBasePosition(){
var retval;
retval='OligoAnalyzer_SequenceSettingsControl_tbSequence';
var theForm=document.forms['frmMain'];
if(!theForm){
theForm=theForm;
}
for(i=0;i<theForm.length;i=i+1)
{
if(theForm.elements[i].type=='textarea')
{
if(theForm.elements[i].hasFocus)
{
retval=theForm.elements[i].id;
}
}
}
var vtext;
vtext=eval('theForm.'+retval);
var theSequence=vtext.value;
for(i=0;i<_MixedBaseArray.length;i=i+1)
{
var aMixedBase=_MixedBaseArray[i];
if(_MixedBaseArray[i].Name!='')
{
if(theSequence.indexOf(_MixedBaseArray[i].Name+")")>0)
{
if(theSequence.indexOf(_MixedBaseArray[i].Name+":")>theSequence.indexOf(_MixedBaseArray[i].Name+")"))
{
var MixedBaseIndex=theSequence.indexOf(_MixedBaseArray[i].Name+")");
var OrigSeqLen=theSequence.length;
theSequence=replace(theSequence,'('+_MixedBaseArray[i].Name+":"+_MixedBaseArray[i].Mix+")",'('+_MixedBaseArray[i].Name+')');
var newSeq='';
newSeq=theSequence.substring(0,MixedBaseIndex+_MixedBaseArray[i].Name.length)+':'+_MixedBaseArray[i].Mix+theSequence.substring(MixedBaseIndex+_MixedBaseArray[i].Name.length,theSequence.length+_MixedBaseArray[i].Name.length);
if(OrigSeqLen==newSeq.length)
{
vtext.value=newSeq;
storeCaret($get('OligoAnalyzer_SequenceSettingsControl_tbSequence'));
BaseCounter($get('OligoAnalyzer_SequenceSettingsControl_tbSequence'),255);
sethasFocus('OligoAnalyzer:SequenceSettingsControl:Sequence');
vtext.focus();
}
}
else if(theSequence.indexOf(_MixedBaseArray[i].Name+":")<0&&theSequence.indexOf(_MixedBaseArray[i].Name+")")>=0)
{
var MixedBaseIndex=theSequence.indexOf(_MixedBaseArray[i].Name+")");
var OrigSeqLen=theSequence.length;
var newSeq='';
newSeq=theSequence.substring(0,MixedBaseIndex+_MixedBaseArray[i].Name.length)+':'+_MixedBaseArray[i].Mix+theSequence.substring(MixedBaseIndex+_MixedBaseArray[i].Name.length,theSequence.length+_MixedBaseArray[i].Name.length);
if(OrigSeqLen<=newSeq.length)
{
vtext.value=newSeq;
storeCaret($get('OligoAnalyzer_SequenceSettingsControl_tbSequence'));
BaseCounter($get('OligoAnalyzer_SequenceSettingsControl_tbSequence'),255);
sethasFocus('OligoAnalyzer:SequenceSettingsControl:Sequence');
vtext.focus();
}
}
}
}
}
vtext.focus();
}