// JavaScript Document
/***********************************************************************************
func_libs.js
2001, 2002 (c) Arthur J. Milgram
***********************************************************************************/
/* INVARIANT FUNCTIONS USABLE BY OTHER JAVASCRIPTS. DO NOT CHANGE THIS FILE WITHOUT THE */
/* CONSENT OF A VERY LARGE AND VERY INFORMED COMMITTEE!!!!! */
/****************************************************************************************/
/* Universal Header printer */
/* */
/****************************************************************************************/
function resolveName (name) {
var result = name.match("Pf");
if (result != null) {
return("Plasmodium falciparum ");
}
result = name.match("Py");
if (result != null) {
return("Plasmodium yoelii ");
}
result = name.match("Pv");
if (result != null) {
return("Plasmodium vivax ");
}
// need to fail silently, ecause this is a high profile function.
// i.e. appears at the top of important pages.
return("Plasmodium spp. ");
}
function myWindowResizeTo (w, h) {
if (w > window.screen.availWidth) {
w = window.screen.availWidth;
}
if (h > window.screen.availHeight) {
h = window.screen.availHeight;
}
window.resizeTo(w,h);
}
// added target=\"_parent\" 5-29-02 to deal with framset pages. AJM
// also added mouseover functions
function printHeader(PAGE_TITLE, baseURL)
{
var rootBaseURL = makeRootPath2ThisFile();
var headerString = "" +
"
";
// document.write(headerString);
return headerString;
} //end of printHeader()
// Jessie requested that feature pages and all other JavaScript DHTML pages have a footer
// like those on the front "chatty text" pages. This function is called by DHTML pages.
// It should also be used by front "chatty text" pages. STICYDKIWYD.
function printPagesDesiredFooter() {
document.write("GenePlot v4.1. - 12/2005; P. falciparum data release February 2005. P. vivax data release November 2005. P. yoelii data release October 2002. Please address questions, suggestions and comments on Plasmodium GenePlot to helpcd@plasmodb.org");
return;
}
/****************************************************************************************/
/* Functions from header scripts */
/* */
/****************************************************************************************/
/*******************************************************/
/* support paraphenalia for determining paths and etc. */
/*******************************************************/
function findPath2RootOfDB(currentLocation) {
var retString;
var directoryName = "geneplot/";
var offset = currentLocation.lastIndexOf(directoryName);
if (offset == -1) {
// Need to trim of HTML file name from current location
offset = currentLocation.lastIndexOf("/");
if (offset == -1) {
// can't do anything with this
alert("Bad path data! auto-path generation failed!");
} else {
retString = currentLocation.substr(0, offset) + "/plasmodium_geneplot/";
}
} else {
offset = offset + directoryName.length;
retString = currentLocation.substr(0, offset);
}
return(retString);
}
function findRootPathOfCD(currentLocation) {
var retString;
var directoryName = "publications";
var offset = currentLocation.lastIndexOf(directoryName);
if (offset == -1) {
//alert("Bad path data! auto-path generation failed!");
directoryName = "plasmodium_geneplot";
offset = currentLocation.lastIndexOf(directoryName);
if (offset == -1) {
retString = currentLocation;
} else {
retString = currentLocation.substr(0, offset);
}
} else {
retString = currentLocation.substr(0, offset);
}
return(retString);
}
function makeRootPath2ThisFile() {
var retString = findRootPathOfCD(window.location.href);
return(retString);
}
function makePath2ThisFile() {
var retString = findPath2RootOfDB(window.location.href);
return(retString);
}
// hard code a path to SequenceTranslationTool
function retSequenceTranslationToolPath (currentLocation) {
//alert("in retSequenceTranslationToolPath. Checking " + currentLocation);
var directoryName = "geneplot/";
var offset = currentLocation.lastIndexOf(directoryName);
if (offset == -1) {
alert("Bad path data! auto-path generation failed!");
return;
}
offset = offset + directoryName.length;
//alert("Offset calculated");
var retString = currentLocation.substr(0, offset);
retString = retString + "sequencetranslationtool/";
//alert("Will send you to path\n" + retString);
return(retString);
}
/****************************************************************************************/
/* End Universal Header printer */
/* */
/****************************************************************************************/
/*
A small family of functions to check for cookie values for configuration
parameters.
*/
/*
Local Cookie Handlers
*/
function setUpCookieSpecs4SiteConfig (additionalData) {
// function is called by configuresite applet
var baseData = document.cookie;
if (baseData.length < 2) {
document.cookie = escape(additionalData);
} else {
document.cookie = baseData + escape(additionalData);
}
// appends information to site wide cookie
// alert("setting cookie");
return;
}
function checkProjectname () {
// retrieves data from document.cookie
var myString = unescape(document.cookie);
// alert("got: " + myString);
// specifically just the ProjectName tag's value
var pointOfContact = myString.indexOf("ProjectName=");
if (pointOfContact == -1){
//alert("found nothing");
return;
}
var startOfVal = myString.indexOf("=\"", pointOfContact);
startOfVal += 2;
var endOfVal = myString.indexOf("\";", startOfVal);
if (endOfVal == -1) {
// send back the whole rest of the line
return(myString.substr(startOfVal));
} else {
// this name value pair is in the middle of the line
// somewhere, so tease it out.
return(myString.substr(startOfVal, (endOfVal - startOfVal)));
}
}
/*
check4Flag
resolveFlag2Text
functions to find FLAG value, and resolve it to a text translation
*/
// First seen in headerscript.js This evidently tries to identify the
// type of feature by investigating the FLAG value from the calling URL.
//
function check4Flag() {
//alert("sideline one pursued");
var myTitle;
var flagRegex = /FLAG=([0-9]+)/;
var flagArray = flagRegex.exec(callingURLString);
var flag;
if(flagArray == null) {
myTitle = "Sequence Retrieval";
return(0);
} else {
flag = flagArray[1];
//myTitle = resolveFlag2Text(flag);
return(flag);
}
}
// called directly by headerscript2 if args object initialized.
// otherwise if args fails for some reason the URL is investigated
// through check4Flag, and then this is called.
// --resolveFlag2Text's purpose is to attach an english meaning to a
// feature's XML FLAG parameter value
function resolveFlag2Text(flag) {
// convert flag to a text value;
// you can find the key to the magic numbers elswhere in the source.
// I'd put it here, but the peopl ein the lab aren't very nice to me, so
// why should I? Nyah!
var textOfFlag;
if ((flag & 8) == 8) {
textOfFlag = "CDS";
}
if ((flag & 16) == 16) {
textOfFlag = "tRNA";
}
if ((flag & 32) == 32) {
textOfFlag = "rRNA";
}
if ((flag & 256) == 256) {
textOfFlag = "ORF";
}
if ((flag & 512) == 512) {
textOfFlag = "Blast Hit";
}
if ((flag & 1024) == 1024) {
textOfFlag = "GlimmerM";
}
if ((flag & 2048) == 2048) {
textOfFlag = "Genefinder";
}
if ((flag & 4096) == 4096) {
textOfFlag = "PHAT";
}
if ((flag & 8192) == 8192) {
textOfFlag = "Hexamer";
}
if ((flag & 16384) == 16384) {
textOfFlag = "Tandem Repeat Finder";
}
if ((flag & 4194304) == 4194304) {
textOfFlag = "SNP";
}
if ((flag & 16777216) == 16777216) {
textOfFlag = "BAC";
}
return(textOfFlag);
}
function findContiginURL (callingURLString) {
var mycontigFromURL = /Contig=([a-zA-Z0-9_\.]+)/;
var theContigs;
var temp = callingURLString.match(mycontigFromURL);
if(temp == null) {
theContigs = "None";
} else {
theContigs = temp[1];
}
return(theContigs);
}
function findFeatureinURL (callingURLString) {
var featureRegex = /feature=([|a-zA-Z0-9_]+)/;
var featureArray = featureRegex.exec(callingURLString);
var feature;
if(featureArray == null) {
feature = "None";
} else {
feature = featureArray[1];
}
return(feature);
}
function makebannerTitle (theContigs, feature, textOfFlag) {
var bannerTitle = theContigs + ": " + feature + " " + textOfFlag + " Summary";
return(bannerTitle);
}
/****************************************************************************************/
/* window opening and */
/* positioning */
/****************************************************************************************/
// global counter per page
var pgCounter = 0;
var myX = window.screenX;
var myY = window.screenY;
function incrementWinName(winName) {
var retName = winName + "_" + pgCounter;
pgCounter = parseInt(parseInt(pgCounter) + 1);
return(retName);
}
function nowUCanOpenIt(aURL, winName) {
//var myX = window.screenX;
//var myY = window.screenY;
myX = parseInt(parseInt(myX) + 7);
myY = parseInt(parseInt(myY) + 22);
if (navigator.appName == "Netscape") {
var controlString = "screenX=" + myX + ",screenY=" + myY +
",status=yes,toolbar=yes,width=600,height=500,scrollbars=yes,resizable=yes" +
",menubar=yes,location=yes";
} else {
var controlString = "left=" + myX + ",top=" + myY +
",status=yes,toolbar=yes,width=600,height=500,scrollbars=yes,resizable=yes" +
",menubar=yes,location=yes";
}
//alert("win control: " + controlString);
window.open(aURL, winName, controlString);
return;
}
function setUpANewWindowAndOpen(aURL, winName) {
var locName = incrementWinName(winName);
nowUCanOpenIt(aURL, locName)
return;
}
/* ****************************** end new window open accounting scripts ********************************* */
/*
General functions
*/
function checkOrderAndValidate(smallest, largest) {
var nonDigit = /\D/;
var smallLet = nonDigit.exec(smallest);
var largeLet = nonDigit.exec(largest);
//alert("received " + smallest +" and "+ largest);
if (nonDigit.exec(smallest) || nonDigit.exec(largest)) {
//alert("No characters please");
return(1);
} else {
if (parseInt(smallest) > parseInt(largest)) {
//alert ("large: " + parseInt(largest) + " small: " + parseInt(smallest));
return(1);
} else {
return(0);
}
}
}
// convert a number into a human representation of it. i.e. add commas for each thousand.
function commaLizeNumber(aNumber) {
var charHere, retString = "";
var aNumberAsAString = aNumber.toString();
var length = aNumberAsAString.length;
var i, j;
j = 0;
for (i=(length - 1); i >= 0; i--) {
charHere = aNumberAsAString.charAt(i);
retString = charHere + retString;
j++;
if ((j%3) == 0 && j < length) {
//if ((j%3) == 0) {
retString = "," + retString;
}
}
return(retString);
}
// another number conversion thing. Using this, let's people put commas in their
// numbers making it easier for them to read.
function removeCommas(someNumber) {
var retNum = someNumber.replace(/,/g, "");
return(retNum);
}
// because a span should always have coordinates relative to the top strand, make
// sure the span's numbers are in the correct order.
function checknumericPairVals(lessernum, greaternum) {
// check is a valid number
var aDigits = /^\d+$/;
if (aDigits.exec(lessernum) == null || aDigits.exec(greaternum) == null) {
alert("invalid numeric format");
return(-3);
}
if (parseInt(lessernum) == parseInt(greaternum)) {
alert("Start and end give dimensionless length.");
return(-1);
}
if (parseInt(lessernum) > parseInt(greaternum)) {
alert("Start less than end. Can't transform to negative coordinates.");
return(-2);
}
return(0);
}
/*
Function from David Pearson's dr.html
Added 6-20-2002
*/
function checkInternet () {
if (document.cookie.indexOf("PlasmoDB_Accessed=") != -1) return true
if (confirm("Note: this link will only work if you are connected to the Internet; click 'OK' to continue")) {
document.cookie = "PlasmoDB_Accessed=true"
return true
} else {
return false
}
}