9a49290fedc8b4f9c7a631dedcfe8ac3aa2b4cee
chinhli
  Thu Oct 20 14:10:43 2011 -0700
merge conflict resolved
diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js
index 2afc3f0..479caec 100644
--- src/hg/js/encodeChipMatrix.js
+++ src/hg/js/encodeChipMatrix.js
@@ -1,27 +1,27 @@
 // encodeChipMatrix.js - pull experiment table and metadata from server 
 //      and display ChIP antibodies vs. cell types in a 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 = [
+    var dataType, server, requests = [
     // Requests to server API
-    encodeProject.serverRequests.experiment, encodeProject.serverRequests.cellType, encodeProject.serverRequests.antibody],
-        dataType;
+            encodeProject.serverRequests.experiment,
+        encodeProject.serverRequests.cellType,
+        encodeProject.serverRequests.antibody];
 
     function tableOut(matrix, cellTiers, cellTypeHash, antibodyGroups, antibodyHash, targetHash) {
         // 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=6>Antibody Targets</td></tr>' + '<tr id="columnHeaders"><td class="axisType">Cell Types</td></tr>');
         tableHeader = $('#columnHeaders', table);
         $.each(antibodyGroups, function (i, group) {
             tableHeader.append('<th class="groupType"><div class="verticalText">' + group.label + '</div></th>');
             $.each(group.targets, function (i, target) {
                 if (targetHash[target] === undefined) {
                     return true;
                 }
                 // prune out targets with no experiments
@@ -56,31 +56,31 @@
                         //$(".cellType").click(matrixClickHandler);
                         //"searchWindow");
                         // prune out targets with no experiments
                         if (targetHash[target] === undefined) {
                             return true;
                         }
                         if (targetHash[target].count === undefined) {
                             return true;
                         }
                         td = '<td class="cellType';
                         if (matrix[cellType][target]) {
                             td += ' experiment';
                         }
                         td += '">';
                         if (matrix[cellType][target]) {
-                            td += '<a target=_blank href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=target&hgt_mdbVal1=';
+                            td += '<a target="searchWindow" href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=target&hgt_mdbVar3=view&hgt_mdbVal2=Any&hgt_mdbVal1=';
                             td += cellType;
                             td += '&hgt_mdbVal2=';
                             // TODO: needs to be join of all antibodies for this target
                             td += target;
                             //td += '"><font color=#00994D>';
                             td += '"><font>';
                             td += matrix[cellType][target];
                             //td += ".....";
                             td += '</font></a>';
                             td += '</td>';
                         }
                         row.append(td);
                     });
                     table.append(row);
                 });
@@ -90,33 +90,33 @@
         $("body").append(table);
     }
 
     function handleServerData(responses) {
         // Main actions, called when loading data from server is complete
         var experiments = responses[0],
             cellTypes = responses[1],
             antibodies = responses[2],
             antibodyGroups, antibodyHash = {},
             targetHash = {},
             cellTypeHash = {},
             antibody, target, cellTiers, cellType, matrix = {},
             organism, assembly, header;
 
         // variables passed in hidden fields
-        organism = $("#var_organism").val();
-        assembly = $("#var_assembly").val();
-        header = $("#var_pageHeader").val();
+        organism = encodeChipMatrix_organism;
+        assembly = encodeChipMatrix_assembly;
+        header = encodeChipMatrix_pageHeader;
 
         $("#pageHeader").text(header);
         $("title").text('ENCODE ' + header);
 
         // set up structures for antibodies and their groups
         $.each(antibodies, function (i, item) {
             antibodyHash[item.term] = item;
         });
         antibodyGroups = encodeProject.getAntibodyGroups(antibodies);
 
         // set up structures for cell types and their tiers
         $.each(cellTypes, function (i, item) {
             cellTypeHash[item.term] = item;
         });
         cellTiers = encodeProject.getCellTiers(cellTypes);
@@ -153,23 +153,28 @@
 
             cellType = exp.cellType;
             if (!matrix[cellType]) {
                 matrix[cellType] = {};
             }
             if (!matrix[cellType][target]) {
                 matrix[cellType][target] = 0;
             }
             matrix[cellType][target]++;
         });
 
         // fill in table
         tableOut(matrix, cellTiers, cellTypeHash, antibodyGroups, antibodyHash, targetHash);
     }
 
+    // get server from calling web page (intended for genome-preview)
+    if ('encodeDataMatrix_server' in window) {
+        server = encodeDataMatrix_server;
+    } else {
+        server = document.location.hostname;
+    }
+
     // initialize
     encodeProject.setup({
-        // todo: add hidden page variable for server
-        server: "hgwdev.cse.ucsc.edu"
-        //server: "genome-preview.ucsc.edu"
+        server: server
     });
     encodeProject.loadAllFromServer(requests, handleServerData);
 });