dc41bf03c3da78ab593718661fa4e233135ffd26
kate
  Thu Oct 13 19:34:37 2011 -0700
From code review: direct all searches to named window instead of creating endless new ones with _blank.  Also, bring up search with View=Any menu visible, to hint to user they are getting multiple views
diff --git src/hg/js/encodeDataMatrix.js src/hg/js/encodeDataMatrix.js
index 855dee7..5ed729f 100644
--- src/hg/js/encodeDataMatrix.js
+++ src/hg/js/encodeDataMatrix.js
@@ -1,175 +1,175 @@
 /* encodeDataMatrix.js - pull experiment table and metadata from server 
       and display in data matrix
 
  Formatted: jsbeautify.py -j
  Syntax checked: jslint indent:4, plusplus: true, continue: true, unparam: true, sloppy: true, browser: true
 */
 /*global $, encodeProject */
 
 $(function () {
     var requests = [
         // Requests to server API
             encodeProject.serverRequests.experiment,
         encodeProject.serverRequests.dataType,
         encodeProject.serverRequests.cellType
         ],
         dataType, organism, assembly, server;
 
     function tableOut(matrix, cellTiers, cellTypeHash, dataGroups, dataTypeTermHash, dataTypeLabelHash) {
         // Create table where rows = cell types and columns are datatypes
         // create table and first row 2 rows (column title and column headers)
         var table, tableHeader, row, td;
 
         table = $('<table>' + '<tr><td><td class="axisType" colspan=4>Element Types</td></tr>' + '<tr id="columnHeaders"><td class="axisType" title="Click to view information about all cell types"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&type=Cell+Line&organism=' + organism + '">Cell Types</td></tr>');
         tableHeader = $('#columnHeaders', table);
         $.each(dataGroups, function (i, group) {
             tableHeader.append('<th class="groupType"><div class="verticalText">' + group.label + '</div></th>');
             $.each(group.dataTypes, function (i, dataTypeLabel) {
                 dataType = dataTypeLabelHash[dataTypeLabel].term;
 
                 // prune out datatypes with no experiments
                 if (dataTypeLabelHash[dataTypeLabel].count !== undefined) {
                     tableHeader.append('<th class="elementType" title="' + dataTypeLabelHash[dataTypeLabel].description + '"><div class="verticalText">' + dataTypeLabel + '</div></th>');
                 }
             });
         });
         // add rows with cell type labels and matrix elements for indicating if
         //  there's an experiment 
         $.each(cellTiers, function (i, tier) {
             //skip bogus 4th tier (not my property ?)
             if (tier === undefined) {
                 return true;
             }
             // td or th here ?
             table.append($('<tr class="matrix"><th class="groupType">' + "Tier " + tier.term + '</th></td></tr>'));
             $.each(tier.cellTypes, function (i, cellType) {
                 if (!cellType) {
                     return true;
                 }
                 if (!matrix[cellType]) {
                     return true;
                 }
                 row = $('<tr><th class="elementType" title="' + cellTypeHash[cellType].description + '"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=' + cellType + '">' + cellType + '</a><span title="karyotype: ' + cellTypeHash[cellType].karyotype + '" class="' + cellTypeHash[cellType].karyotype + '">&bull;</span></th>');
 
                 $.each(dataGroups, function (i, group) {
                     // skip group header
                     row.append('<td></td>');
                     $.each(group.dataTypes, function (i, dataTypeLabel) {
                         // TODO: change this class to matrixElementType
                         //$(".cellType").click(matrixClickHandler);
                         //"searchWindow");
                         dataType = dataTypeLabelHash[dataTypeLabel].term;
                         // prune out datatypes with no experiments
                         if (dataTypeLabelHash[dataTypeLabel].count === undefined) {
                             return true;
                         }
                         td = '<td class="cellType';
                         if (matrix[cellType][dataType]) {
                             td += ' experiment';
                         }
                         td += '">';
                         if (matrix[cellType][dataType]) {
-                            td += '<a target=_blank title="';
+                            td += '<a target="searchWindow" title="';
                             td += dataTypeLabel + ' in ' + cellType + ' cells "';
-                            td += 'href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=dataType&hgt_mdbVal1=';
+                            td += 'href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=dataType&hgt_mdbVar3=view&hgt_mdbVal3=Any&hgt_mdbVal1=';
                             td += cellType;
                             td += '&hgt_mdbVal2=';
                             td += dataType;
                             //td += '"><font color=#00994D>';
                             td += '"><font>';
                             td += matrix[cellType][dataType];
                             //td += ".....";
                             td += '</font></a>';
                             td += '</td>';
                         }
                         row.append(td);
                     });
                     table.append(row);
                 });
                 table.append(row);
             });
         });
         $("body").append(table);
     }
 
     function handleServerData(responses) {
         // Main actions, called when loading data from server is complete
         var experiments = responses[0],
             dataTypes = responses[1],
             cellTypes = responses[2],
             dataTypeLabelHash = {},
             dataTypeTermHash = {},
             cellTypeHash = {},
             dataType, cellType, matrix = {},
             dataGroups = {},
             cellTiers, header;
 
         // page-specific variables from calling page
         organism = encodeDataMatrix_organism;
         assembly = encodeDataMatrix_assembly;
         header = encodeDataMatrix_pageHeader;
 
         $("#pageHeader").text(header);
         $("title").text('ENCODE ' + header);
 
         // set up structures for data types and their groups
         $.each(dataTypes, function (i, item) {
             dataTypeTermHash[item.term] = item;
             dataTypeLabelHash[item.label] = item;
         });
         // data type labels tucked into their tiers
         dataGroups = encodeProject.getDataGroups(dataTypes);
 
         // set up structures for cell types and their tiers
         $.each(cellTypes, function (i, item) {
             cellTypeHash[item.term] = item;
         });
         cellTiers = encodeProject.getCellTiers(cellTypes);
 
         // gather experiments into matrix
         $.each(experiments, function (i, exp) {
             // todo: filter out with arg to hgApi
             if (exp.organism !== organism) {
                 return true;
             }
             // exclude ref genome annotations
             if (exp.cellType === 'None') {
                 return true;
             }
             // count experiments per dataType so we can prune those having none
             // (the matrix[cellType] indicates this for cell types 
             // so don't need hash for those
             dataType = exp.dataType;
             if (!dataTypeTermHash[dataType].count) {
                 dataTypeTermHash[dataType].count = 0;
             }
             dataTypeTermHash[dataType].count++;
 
             cellType = exp.cellType;
             if (!matrix[cellType]) {
                 matrix[cellType] = {};
             }
             if (!matrix[cellType][dataType]) {
                 matrix[cellType][dataType] = 0;
             }
             matrix[cellType][dataType]++;
         });
 
         // fill in table
         tableOut(matrix, cellTiers, cellTypeHash, dataGroups, dataTypeTermHash, dataTypeLabelHash);
     }
 
     // initialize encodeProject
     // get server from calling web page (intended for genome-preview)
     if ('encodeDataMatrix_server' in window) {
         server = encodeDataMatrix_server;
     } else {
         server = document.location.hostname;
         // or document.domain ?
     }
 
     encodeProject.setup({
         server: server
     });
     encodeProject.loadAllFromServer(requests, handleServerData);
 });