By Ted Kandell
Has 5 other scripts.
// Find an NCBI GenBank full human mtDNA sequence on the complete human mitochondrial tree
// 2007-05-21
// Copyright (c) 2007, Ted Kandell ted underscore kandell at yahoo dot com
// Released under the GPL license
// http://www.gnu.org/copyleft/gpl.html
// http://www.flickr.com/photos/Archaeogenetics
// ----------------------------------------------------------------------------
//
// This is a Greasemonkey user script. To install it,
// you need Greasemonkey: http://greasemonkey.mozdev.org/
// Then restart Firefox and revisit this script.
//
// To uninstall, go to Tools/Manage User Scripts,
// select "Find a Genbank mtDNA sequence on the full human mitochondrial tree", and click Uninstall.
//
// ----------------------------------------------------------------------------
// ==UserScript==
// @name Find an NCBI GenBank mtDNA full sequence on the complete human mitochondrial tree
// @namespace http://www.flickr.com/photos/Archaeogenetics
// @description Create a human mitochondrial DNA phylogenetic tree from an NCBI GenBank mtDNA full sequence, with a green line from the root of the tree pointing to its position.
// @include http://www.ncbi.nlm.nih.gov/entrez/*db=*ucleotide*
// @include http://www.ncbi.nlm.nih.gov/entrez/*db=*uccore*
// @include http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=*
// @include http://www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi?request=page&rid=*&dbname=nr&*
// ==/UserScript==
// The current version to compare with the latest version of this script
var version = 0.94;
var source = "http://userscripts.org/scripts/source/7101.user.js";
// Remember, everything here runs in the Greasemonkey "sandbox"
// so these are not actually global variables, but they are private
// and so are the functions (methods). Once Greasemonkey exits,
// nothing here is available to the window. Conversely, no external
// scripts are available to Greasemonkey, even if a SCRIPT tag is
// dynamically added, except if eval() is run the string containing
// the Javascript code, retrieved by GM_xmlhttpRequest().
// You can think of this entire script as being an instance of
// the "Greasemonkey" class, which indeed it is.
var baseUrl = "http://members.cox.net/tkandell/mtDNA/roots/";
var accession;
var entrezQuery;
var limit;
var RID;
var seconds;
var intervalID;
var treeWindow;
var callback;
var treeUrl;
var retry;
var close;
var error;
function getPre()
{
return document.evaluate("//pre[@class='genbank']", document, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
}
function getAccession(pre)
{
var sequence;
if (pre != null)
{
sequence = pre.firstChild.nodeValue;
}
else
{
return null;
}
// This will include both humans and neanderthals
if (sequence.search(/SOURCE[ ]+mitochondrion Homo sapiens/) > 0)
{
var matches = sequence.match(/165[5-8]\d bp/);
if (!matches)
{
return null;
}
var bp = parseInt(matches[0].substr(0,5));
if (bp < 16556 || bp > 16587)
{
return null;
}
var accession = sequence.match(/ACCESSION\s+\w+/);
if (!accession)
{
return null;
}
accession = accession[0].split(/\s+/)[1];
return accession;
}
return null;
}
// A hack to for HTML 4.0 that is non-valid XHTML:
// the XMLHttpRequest.responseXML is null so we have to create an
// "html" HTMLElement, set the innerHTML property to the responseText,
// and then add the element to a new XML document. This allows us to parse
// the response with an XPath query. Even if the document mime type is forced
// to be returned as "text/xml" using XMLHttpRequest.overrideMimeType(),
// if the HTML is not valid XML(XHTML) then the XML Document returned in
// XMLHttpRequest.responseXML will have one node,
// with a node name of "parsererror".
function getDocument(responseText)
{
var html = document.createElement("html");
html.innerHTML = responseText;
var response = document.implementation.createDocument("", "", null);
response.appendChild(html);
return response;
}
function checkWindowOpen()
{
if (!treeWindow)
{
window.clearInterval(intervalID);
setActionMessage(
"Firefox prevented this site<BR/>from opening a new window:");
onError("Please allow popups for<BR/><U>www.ncbi.nlm.nih.gov</U>");
document.getElementById("close").addEventListener("click",
function(event)
{
getTreeWithPathToAccession();
},
true);
}
else if (treeWindow.document != null &&
treeWindow.document.getElementById("imgTree") != null)
{
window.clearInterval(intervalID);
enableBlast(true);
showProgressBox(false);
treeUrl = null;
}
}
function getTreeUrl(target)
{
if (treeUrl != null && treeUrl.length > 0)
{
return treeUrl;
}
// treeUrl is uninitialized
var response = getDocument(target.responseText);
var node;
node = response.evaluate("//input[@name='queryID']/@value",
response, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
var queryID = node ? node.nodeValue : "";
node = response.evaluate('//area[starts-with(@title,"gb|' +
accession + '")]/@href',
response, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
var mouseHit = node ? node.nodeValue.match(/\d+/) : "";
node = response.evaluate("//input[@name='tree_nc_id']/@value",
response, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
var treeNetCacheID = node ? node.nodeValue : "";
node = response.evaluate("//input[@name='seqaln_nc_id']/@value",
response, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
var alignmentNetCacheID = node ? node.nodeValue : "";
if (!queryID || !treeNetCacheID || !alignmentNetCacheID)
{
return null;
}
if (!mouseHit)
{
mouseHit = "-2";
}
treeUrl =
"http://www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi?" +
"request=page" +
"&rid=" + RID +
"&dbname=nr" +
"&hit_id=" + mouseHit +
"&inpParamName=rid" +
"&inpParamVal=" + RID +
"&subTreeNodeID=-2" +
"&renderer=rectangle" +
"&distmode=on" +
"&labelType=Sequence+ID" +
"&treeMethod=Fast+Minimum+Evolution" +
"&tree_nc_id=" + treeNetCacheID +
"&seqaln_nc_id=" + alignmentNetCacheID +
"&maxPercentDif=0.75" +
"&screenHeight=" + screen.height +
"&screenWidth=" + screen.width +
"&loadBioSeq=" +
"&seqType=Nucleotide" +
"&queryID=" + queryID +
"&queryAccession=" + accession +
"&dispAlignsID=-2" +
"&recalcLabels=" +
"&m_recalcTree=";
return treeUrl;
}
var attempt = 0;
function getTreeWithPathToAccession(target)
{
treeUrl = getTreeUrl(target);
if (treeUrl)
{
treeWindow = window.open(treeUrl);
intervalID = window.setInterval(checkWindowOpen, 2500);
}
else
{
onError("Server error: incomplete page.");
}
}
function setActionMessage(msg)
{
document.getElementById("action").innerHTML = msg;
}
function setStatusMessage(msg)
{
document.getElementById("status").innerHTML = msg;
}
function createErrorIcon()
{
// prefetch error icon and save it globally
error = document.createElement("img");
error.id = "error";
error.src = baseUrl + "error.gif";
error.style.opacity = "1";
error.style.position = "relative";
error.style.left = "-302px";
error.style.bottom = "45%";
error.style.padding = "10px";
error.style.visibility = "hidden";
}
function createCloseBox()
{
// prefetch close box and save it globally
close = document.createElement("img");
close.id = "close";
close.src = baseUrl + "close.gif";
close.style.position = "relative";
close.style.right = "-209px";
close.style.top = "-20px";
close.style.opacity = "1";
}
function showProgressBox(b)
{
var progress = document.getElementById("progressBox");
if (!b)
{
progress.style.visibility = "hidden";
var error = document.getElementById("error");
var close = document.getElementById("close");
if (error)
{
error.style.visibility = "hidden";
}
if (close)
{
close.style.visibility = "hidden";
}
}
else
{
progress.style.visibility = "visible";
}
}
function showCloseBox(b)
{
if (b)
{
document.getElementById("close").style.visibility = "visible";
}
else
{
document.getElementById("close").style.visibility = "hidden";
}
}
function showErrorIcon(b)
{
if (b)
{
document.getElementById("error").style.visibility = "visible";
}
else
{
document.getElementById("error").style.visibility = "hidden";
}
}
function onError(target)
{
if (!error || !close)
{
removeProgressBox();
createErrorIcon();
createCloseBox();
createProgressBox();
}
document.getElementById("progressBar").style.visibility = "hidden";
document.getElementById("progressBar").alt = "";
showProgressBox(true);
if (typeof target == "string" ||
target instanceof String)
{
setStatusMessage(target);
// more than one line
if (target.match(/<BR\\>/i))
{
document.getElementById("error").style.bottom = "50%";
document.getElementById("progressBox").style.height = "180px";
}
}
else if (typeof target.status != "undefined" ||
typeof target.target != "undefined")
{
// we get an event from the XMLHttpRequest.onerror callback
// with the XMLHttpRequest as the target attribute
if (typeof target.target != "undefined")
{
target = target.target;
}
document.getElementById("progressBox").style.height = "140px";
setStatusMessage("Error: " + target.status + " - " + target.statusText);
document.getElementById("error").style.bottom = "45%";
}
document.getElementById("error").style.visibility = "visible";
document.getElementById("close").style.visibility = "visible";
showProgressBox(true);
}
function createProgressBox()
{
if (document.getElementById("progressBox") instanceof Element)
{
return;
}
var body = document.getElementsByTagName('body')[0];
var div = document.createElement('div');
div.id = "progressBox";
div.classname = "progressBox";
div.style.position = "absolute";
div.style.top='50%';
div.style.left='50%';
// prefetched and stored globally or not
if (error)
{
div.style.width='400px';
div.style.height='140px';
}
else
{
div.style.width = '300px';
div.style.height = '90px';
}
div.style.margin = "-50px 0 0 -170px";
div.style.border = "3px double black";
div.style.padding = "20px";
div.style.opacity = "0.85";
div.style.zIndex='30';
div.style.textAlign = "center";
div.style.backgroundColor ='yellow';
div.border = 10;
div.style.visibility = "hidden";
// Directly setting the onclick property to a function doesnt work in
// the Greasemonkey sandbox because the context no longer exists when the
// callback executes. The proper way to do this is to call:
// element.addEventListener("click", function_name, true);
// prefetched and stored globally or not
if (close)
{
close.addEventListener("click", function()
{
showProgressBox(false);
enableBlast(true);
}, false);
close.style.visibility = "visible";
div.appendChild(close);
}
var msg = document.createElement("div");
msg.style.top = "-10px";
msg.style.right = "-20px";
var gap = document.createElement("div");
gap.id = "gap";
gap.style.height = "10px";
msg.appendChild(gap);
var action = document.createElement("span");
action.id = "action";
action.innerHTML = " ";
msg.appendChild(action);
msg.appendChild(document.createElement("br"));
var status = document.createElement("span");
status.id = "status";
status.innerHTML = " ";
msg.appendChild(status);
div.appendChild(msg);
var progressBar = document.createElement("img");
progressBar.id = "progressBar";
progressBar.style.opacity = "1";
progressBar.style.position = "relative";
if (error)
{
progressBar.style.right = "-33px";
progressBar.style.top = "-37px";
}
else
{
div.appendChild(gap);
}
div.appendChild(progressBar);
progressBar.alt = "Error: No network connection.";
progressBar.src = baseUrl + "progress.gif";
if (error)
{
error.style.visibility = "hidden";
div.appendChild(error);
}
body.appendChild(div);
}
function getTree()
{
// we may have re-entered, so only set the callback in case of status 500
callback = null;
setActionMessage("Calculating distance tree:");
showCloseBox(false);
var request = new XMLHttpRequest();
request.open('GET', "http://www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi?request=page&dbname=nr&distmode=on&labelType=Sequence+ID&rid=" + RID);
request.setRequestHeader('User-agent',
'Mozilla/5.0 (compatible) Greasemonkey');
request.onreadystatechange =
function()
{
if (!request)
{
window.clearInterval(intervalID);
onError("Error: Lost network connection.");
}
if (request.readyState == 4)
{
switch (request.status)
{
case 200:
window.clearInterval(intervalID);
retry = 0;
// Somehow, an plain text page listing an Error 500
// has a status of 200 and has content-type "text/html"
var errorMessage = request.responseText.match(/ERROR:.*/i);
if (errorMessage && errorMessage.length > 0)
{
onError(errorMessage[0]);
}
else
{
callback = null;
window.setTimeout(
function()
{
getTreeWithPathToAccession(request);
}, 0);
}
break;
case 500:
window.clearInterval(intervalID);
setStatusMessage("(Resending request)");
if (!retry)
{
retry = 5;
seconds = retry;
}
else if (retry < 60)
{
retry += 1;
seconds = retry;
}
callback = getTree;
intervalID = window.setInterval(countdown, 1000);
break;
default:
window.clearInterval(intervalID);
onError(request);
}
}
};
if (!callback)
{
seconds = 180;
}
intervalID = window.setInterval(countdown, 1000);
request.send(null);
}
function countdown()
{
seconds--;
if (seconds > 0)
{
var secs = "0" + (seconds % 60);
setStatusMessage("(This will take about " +
(Math.floor(seconds / 60)) + ":" +
secs.substring(secs.length -2) +
" to complete)");
}
else
{
window.clearInterval(intervalID);
setStatusMessage("(Please wait a few more seconds)");
if (callback != null)
{
callback();
}
}
}
function getRID(target)
{
var response = getDocument(target.responseText);
RID = response.evaluate("//input[@name='RID']/@value",
response, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue.nodeValue;
var estimatedReady = target.responseText.match(/ready in [0-9]+/);
seconds = parseInt(estimatedReady.toString().substring(9));
seconds += 12;
retry = 0;
callback = getTree;
intervalID = window.setInterval(countdown, 1000);
}
function removeProgressBox()
{
var progressBox = document.getElementById('progressBox');
var error = document.getElementById("error");
var close = document.getElementById("close");
if (error && error.parentNode)
{
error.parentNode.removeChild(error);
}
if (close && close.ParentNode)
{
close.parentNode.removeChild(close);
}
if (progressBox && progressBox.parentNode)
{
progressBox.parentNode.removeChild(progressBox);
}
}
function submitBlastQuery(ancestralSequence)
{
// This query contains the hypothetical common ancestral human mitochondrial
// full sequence. This was derived by retrieving sequences from GenBank from
// the most basal mtDNA haplogroups, L0d, L0k, L0f, L0a, L1b, L5, and L3e,
// selecting sequences which were least distant from the root, then aligning
// them with the existing partial Neanderthal control-region sequences, and
// the two common chimpanzee (Pan troglodytes) and two bonobo (Pan paniscus)
// full sequences in GenBank. A consensus was derived by seeing which sites
// among these basal human haplotypes were the same as *any* among the
// chimpanzees and bonobos.
// This sequence of course is an approximation, but it is good enough to serve
// as the query to generate a *balanced* human mtDNA tree.
var query=
"ALIGNMENTS=0&ALIGNMENT_VIEW=FlatQueryAnchored&AUTO_FORMAT=Off&CLIENT=web&CMD=Put&DATABASE=nr&EXPECT=0.01&FORMAT_BLOCK_ON_RESPAGE=None&FORMAT_ENTREZ_QUERY=All+organisms&FORMAT_OBJECT=Alignment&FORMAT_TYPE=Text&LAYOUT=OneWindow&MASK_CHAR=2&MASK_COLOR=1&MEGABLAST=on&NUM_OVERVIEW=0&PAGE=MegaBlast&PERC_IDENT=None%2C+1%2C-2&PROGRAM=blastn&FILTER=&REPEATS=repeat_9606&SERVICE=plain&SET_DEFAULTS=no&SHOW_LINKOUT=&USER_TYPE=2&WORD_SIZE=64&DBTYPE=hc&DESCRIPTIONS=0"
+ "&ENTREZ_QUERY=" + entrezQuery
+ "&HITLIST_SIZE=" + limit
+ "&QUERY=%3EHomo+sapiens+ancestral+mitochondrion%2C+complete+genome%0A";
// Native Javascript XMMHttpRequest version to send the request.
// Unlike GM_xmlhttpRequest() XMLHttpRequest is limited to the same domain
// as the current page.
// The single callback function takes no parameters, but must get the status and response
// out of the request object stored in a global variable.
var request = new XMLHttpRequest();
request.onreadystatechange =
function()
{
if (request.readyState == 4)
{
if (request && request.status == 200)
{
// Check if this is an error page
var errorMessage = request.responseText.match(/ERROR:.*/i);
if (errorMessage && errorMessage.length > 0)
{
onError(errorMessage[0]);
}
else
{
getRID(request);
}
}
else
{
onError(request);
}
}
};
request.open('POST', 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi');
request.setRequestHeader('Content-type',
'application/x-www-form-urlencoded');
request.setRequestHeader('User-agent',
'Mozilla/5.0 (compatible) Greasemonkey');
request.setRequestHeader("Content-length", query.length +
ancestralSequence.length);
request.setRequestHeader("Connection", "close");
setActionMessage("Submitting BLAST query:");
setStatusMessage("(Waiting for response)");
request.send(query + ancestralSequence);
}
function getAncestralSequence()
{
setActionMessage("Getting ancestral human mtDNA haplotype:");
setStatusMessage("(Sending request)");
GM_xmlhttpRequest({
method: 'GET',
url: baseUrl + "mtMRCA.fas",
headers: {
'User-agent': 'Mozilla/4.0 (compatible) Greasemonkey'
},
onerror: onError,
onload: function(response)
{
if (response.readyState == 4)
{
if (response && response.status == 200)
{
var ancestralSequence =
response.responseText.replace(/^.*$/m, "");
ancestralSequence =
ancestralSequence.replace(/$/mg, "");
ancestralSequence =
ancestralSequence.replace(/[\s\-]+/g, "");
submitBlastQuery(ancestralSequence);
}
else
{
onError(response);
}
}
}
});
}
function getLimit()
{
setActionMessage("Getting maximum number of sequences:");
setStatusMessage("(Sending request)");
showCloseBox(true);
GM_xmlhttpRequest({
method: 'GET',
url: baseUrl + "limit.txt",
headers: {
'User-agent': 'Mozilla/4.0 (compatible) Greasemonkey'
},
onerror: onError,
onload: function(response)
{
if (response.readyState == 4)
{
if (response && response.status == 200)
{
limit = escape(response.responseText);
getAncestralSequence();
}
else
{
onError(response);
}
}
}
});
}
function getEntrezQuery()
{
setActionMessage("Getting query for all sequences:");
setStatusMessage("(Sending request)");
showCloseBox(true);
GM_xmlhttpRequest({
method: 'GET',
url: baseUrl + "query.txt",
headers: {
'User-agent': 'Mozilla/4.0 (compatible) Greasemonkey'
},
onerror: onError,
onload: function(response)
{
if (response.readyState == 4)
{
if (response && response.status == 200)
{
entrezQuery = escape(response.responseText);
getLimit();
}
else
{
onError(response);
}
}
}
});
}
function reinstallScript()
{
try
{
window.location = source;
}
catch (e) {};
enableBlast(false);
document.getElementById("close").addEventListener("click",
function(event)
{
window.location.reload();
}, false);
}
function updateScript()
{
setActionMessage("A new version of this script was found:");
onError("Please update this script<BR/> by selecting install in the popup.");
window.setTimeout(reinstallScript, 3000);
}
function getVersion(sourceText)
{
return sourceText.
match(/version[ ]*=[ ]*\d*\.?\d*/i)[0].match(/\d*\.\d*/);
}
function checkVersion()
{
removeProgressBox();
createProgressBox();
document.getElementById("close").addEventListener("click",
function()
{
showProgressBox(false);
}, false);
setActionMessage("Checking for script update:");
setStatusMessage("(version " + version.toFixed(2) + ")");
enableBlast(false);
showProgressBox(true);
GM_xmlhttpRequest({
method: 'GET',
url: source,
headers: {
'User-agent': 'Mozilla/4.0 (compatible) Greasemonkey'
},
onerror: onError,
onload: function(response)
{
if (response.readyState == 4)
{
if (response && response.status == 200)
{
var latestVersion = getVersion(response.responseText);
if (parseFloat(latestVersion) > version)
{
updateScript(source);
}
else
{
getEntrezQuery();
}
}
else
{
// http://userscripts.org being down
// doesnt stop execution
onError(response);
setTimeout(
function()
{
showErrorIcon(false);
setStatusMessage("(check failed - continuing)");
window.setTimeout(getEntrezQuery, 1000);
}, 1000);
}
}
}
});
}
function enableBlast(flag)
{
if (flag)
{
document.getElementById("blast").addEventListener("click",
checkVersion, false);
}
else
{
document.getElementById("blast").removeEventListener("click",
checkVersion, false);
}
}
function insertButton(pre)
{
var label = document.createElement("div");
label.id = "blastQuery";
label.setAttribute("style", "font-size:16pt;background-color:CCFFFF;");
label.innerHTML = "Create a distance tree of all complete human mitochondrial sequences and display the position of this sequence on the tree:<BR/>";
var blast = document.createElement("input");
blast.id = "blast";
blast.type = "image";
blast.src = "http://www.ncbi.nlm.nih.gov/blast/html/blast_but.gif";
blast.alt = "Generate a tree of all complete human mitochondrial sequences and show the position of this haplotype on the tree.";
blast.style.borderColor = "#CCFFFF";
blast.style.borderStyle = "solid";
blast.style.borderWidth = "5";
blast.style.verticalAlign = "bottom";
blast.addEventListener("click", checkVersion, false);
label.appendChild(blast);
node = pre.parentNode.parentNode;
node.parentNode.insertBefore(label, node);
// prefetch these images in case the network connection goes down
createErrorIcon();
createCloseBox();
}
function createQuery()
{
var pre = getPre();
accession = getAccession(pre);
if (!accession)
{
return;
}
insertButton(pre);
}
function alterPage()
{
document.title = "mtDNA Tree View";
// remove everything we dont want to see
var colorMap = document.getElementById("divBlastColorMap");
if (colorMap)
{
colorMap.style.display = "none";
}
var hideColorMap = document.getElementById("hideColorMap");
if (hideColorMap)
{
hideColorMap.style.display = "none";
}
document.getElementsByTagName("h1")[0].style.display = "none";
var disclaimer = document.evaluate("//div[@class='disclaimer']",
document, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
disclaimer.style.display = "none";
var mainsection = document.evaluate("//table[@class='mainsection']",
document, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue;
mainsection.style.display = "none";
document.getElementById("treeHelp").style.display = "none";
var distMode = document.getElementById("distMode");
distMode.childNodes[1].style.visibility = "hidden";
distMode.childNodes[3].firstChild.nodeValue =
"Branch lengths are proportional to the genetic distance.";
document.getElementsByTagName("hr")[0].style.display = "none";
// create the new layout:
// this is a table which allows the haplotype data table on the right
// to resize horizontally but not vertically
var forceScreenWidth = document.createElement("table");
forceScreenWidth.rules = "none";
forceScreenWidth.style.align = "left";
forceScreenWidth.style.borderWidth = "0";
forceScreenWidth.style.marginWidth = "0";
forceScreenWidth.style.cellPadding = "0";
forceScreenWidth.style.cellSpacing = "0";
forceScreenWidth.style.height = "" + ((screen.height * 0.65) - 3) + "px";
forceScreenWidth.style.maxHeight = "" + ((screen.height * 0.65) - 3) + "px";
forceScreenWidth.style.width = "1024px";
forceScreenWidth.style.display = "none";
var imageArea = document.getElementById("imageArea");
imageArea.parentNode.style.width = "auto";
var row;
var cell;
row = forceScreenWidth.insertRow(-1);
var heading = row.insertCell(-1);
heading.colSpan = 2;
var queryID = document.evaluate("//input[@name='queryAccession']/@value",
document, null,
XPathResult.FIRST_ORDERED_NODE_TYPE,
null).singleNodeValue.nodeValue;
heading.innerHTML = "Tree view for <span style='color: yellow'>" +
queryID + "</span>";
heading.className = "header";
heading.style.color = "white";
heading.style.backgroundColor = "#336699";
heading.style.textAlign = "center";
heading.style.borderWidth = "0px";
heading.style.padding = "0.25em";
heading.style.margin = "0";
heading.style.fontFamily = "Verdana,Helvetia,Sans-Serif";
heading.style.fontWeight = "bold";
heading.style.fontSize = "100%";
cell = row.insertCell(-1);
cell.style.width = "auto";
row = forceScreenWidth.insertRow(-1);
var help = row.insertCell(-1);
help.colSpan = 2;
help.style.borderWidth = "3";
help.style.borderColor = "black";
help.style.borderStyle = "groove";
help.style.backgroundColor = "FFFFCC";
help.style.textAlign = "center";
help.style.paddingLeft = "5px";
help.style.paddingRight = "5px";
var explanation =
"Follow the green line to the haplotype, or click on any branching point using the cross-hairs to zoom in on a particular part of the tree. Mouse over the end of a branch to see the haplotype details and compare it with others.";
help.appendChild(document.createTextNode(explanation));
cell = row.insertCell(-1);
row = forceScreenWidth.insertRow(-1);
cell = row.insertCell(-1);
cell.colSpan = 2;
cell.style.verticalAlign = "top";
cell.appendChild(document.createElement("hr"));
row = forceScreenWidth.insertRow(-1);
row.style.width = "auto";
cell = row.insertCell(-1);
cell.style.verticalAlign = "top";
cell.appendChild(document.getElementById("divTabButtons"));
cell = row.insertCell(-1);
var statusMessage = document.createElement("span");
statusMessage.id = "statusMessage";
statusMessage.className = "hlp";
statusMessage.style.paddingLeft = "7px";
statusMessage.style.paddingRight = "7px";
statusMessage.style.textAlign = "left";
statusMessage.appendChild(document.createTextNode(""));
cell.appendChild(statusMessage);
row = forceScreenWidth.insertRow(-1);
row.style.height = "" + ((screen.height * 0.65) - 3) + "px";
row.style.maxHeight = "" + ((screen.height * 0.65) - 3) + "px";
row.style.width = "auto";
cell = row.insertCell(-1);
var dataTable =
document.getElementById("imageArea").parentNode.
parentNode.parentNode.parentNode;
cell.style.verticalAlign = "top";
cell.appendChild(dataTable);
// this is the element in which snps.js places the haplotype table
cell = row.insertCell(-1);
cell.id = "data";
var body = document.getElementsByTagName("body")[0];
body.insertBefore(forceScreenWidth, body.firstChild);
body.style.width = "auto";
forceScreenWidth.style.display = "table";
var haplotypeCount =
document.evaluate("count(//area[@title])",
document, null,
XPathResult.NUMBER_TYPE, null).numberValue;
statusMessage.firstChild.nodeValue = "" + haplotypeCount + " haplotypes";
}
function addScripts()
{
var head = document.getElementsByTagName("head")[0];
var script;
script = document.createElement("script");
script.type = "text/javascript";
script.src = baseUrl + "snps.js";
head.appendChild(script);
script = document.createElement("script");
script.type = "text/javascript";
script.src = baseUrl + "crs.js";
head.appendChild(script);
script = document.createElement("script");
script.type = "text/javascript";
script.src = baseUrl + "haplotypes.js";
head.appendChild(script);
}
function addStylesheet()
{
var stylesheet = document.createElement("link");
stylesheet.rel = "stylesheet";
stylesheet.type = "text/css";
stylesheet.href = baseUrl + "snps.css";
document.getElementsByTagName('head')[0].appendChild(stylesheet);
}
function getWindowType()
{
if (window.location.pathname.match(/\/blast\/treeview/))
{
var imgTree = document.getElementById("imgTree");
// test to see if this is an actual Blast TreeView page
// or a server error page or an incomplete page
// and if the haplotypes are labelled by sequence ID
if (imgTree &&
document.forms[0].elements.namedItem('labelType').value ==
"Sequence ID")
{
window.setTimeout(function()
{
addScripts();
addStylesheet();
alterPage();
}, 0);
}
}
else
{
createQuery();
}
}
window.addEventListener("load", getWindowType, false);
