9fcaa31c8804e83206a790dd129f239cbdcd180b
kate
  Wed Oct 12 15:12:54 2011 -0700
Prettify a bit.  Using -k option of jsbeautify allows this layout of array literals
diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js
index 2afc3f0..ebf22d9 100644
--- src/hg/js/encodeChipMatrix.js
+++ src/hg/js/encodeChipMatrix.js
@@ -1,175 +1,178 @@
 // encodeChipMatrix.js - pull experiment table and metadata from server 
 //      and display ChIP antibodies vs. cell types in a matrix
-
-// Formatted: jsbeautify.py -j
+// Formatted: jsbeautify.py -j -k
 // Syntax checked: jslint indent:4, plusplus: true, continue: true, unparam: true, sloppy: true, browser: true */
 /*global $, encodeProject */
 
 $(function () {
-    var requests = [
+    var dataType;
+    var 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
                 if (targetHash[target].count !== undefined) {
                     tableHeader.append('<th class="elementType"><div class="verticalText">' + target + '</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">' + cellType + '</th>');
 
                 $.each(antibodyGroups, function (i, group) {
                     // skip group header
                     row.append('<td></td>');
                     $.each(group.targets, function (i, target) {
                         // TODO: change this class to matrixElementType
                         //$(".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 += 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);
                 });
                 table.append(row);
             });
         });
         $("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();
 
         $("#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);
 
         // 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;
             }
             // todo: filter out with arg to hgApi ?
             if (exp.dataType !== 'ChipSeq') {
                 return true;
             }
             // count experiments per target so we can prune those having none
             // (the matrix[cellType] indicates this for cell types 
             // so don't need hash for those
             antibody = encodeProject.antibodyFromExp(exp);
             target = encodeProject.targetFromAntibody(antibody, antibodyHash);
             if (!targetHash[target]) {
                 targetHash[target] = {
                     count: 0,
                     antibodies: {}
                 };
             }
             if (!targetHash[target].antibodies[antibody]) {
                 targetHash[target].antibodies[antibody] = antibody;
             }
             targetHash[target].count++;
 
             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);
     }
 
     // initialize
     encodeProject.setup({
         // todo: add hidden page variable for server
         server: "hgwdev.cse.ucsc.edu"
         //server: "genome-preview.ucsc.edu"
     });
     encodeProject.loadAllFromServer(requests, handleServerData);
 });