0b18daa6dccb951ca6e7ad097ef56ca01f38bcc3
kate
  Thu Mar 1 23:03:50 2012 -0800
Factoring out a bit more shared code
diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js
index bddb781..775f8e4 100644
--- src/hg/js/encodeChipMatrix.js
+++ src/hg/js/encodeChipMatrix.js
@@ -1,269 +1,207 @@
 /* encodeChipMatrix.js - ENCODE web app to display ChIP-seq data 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 dataType, server, requests = [
         // requests to server API
         encodeProject.serverRequests.experiment,
         encodeProject.serverRequests.cellType,
         encodeProject.serverRequests.antibody,
         encodeProject.serverRequests.expId
         ];
 
     var $matrixTable = $('#matrixTable');
 
     function handleServerData(responses) {
         // Main actions, called when loading data from server is complete
 
         var experiments = responses[0], 
                 cellTypes = responses[1], 
                 antibodies = responses[2], 
                 expIds = responses[3];
 
         var antibodyGroups, cellTiers, expIdHash;
         var antibodyTarget, cellType;
         var matrix, antibodyTargetExps = {};
 
         // hide spinner and show table
         encodeMatrix.show($matrixTable);
 
         // set up structures for antibody targets and groups
         antibodyGroups = encodeProject.getAntibodyGroups(antibodies);
 
         // set up structures for cell types and their tiers
         cellTiers = encodeProject.getCellTiers(cellTypes);
 
         // use to filter out experiments not in this assembly
         expIdHash = encodeProject.getExpIdHash(expIds);
 
         // gather experiments into matrix
         matrix = makeExperimentMatrix(experiments, expIdHash, antibodyTargetExps);
 
        // fill in table using matrix
-        tableOut($matrixTable, matrix, cellTiers, antibodyGroups, antibodyTargetExps);
+        encodeMatrix.tableOut($matrixTable, matrix, cellTiers, 
+                        antibodyGroups, antibodyTargetExps, tableHeaderOut, rowAddCells);
     }
 
     function makeExperimentMatrix(experiments, expIdHash, antibodyTargetExps) {
         // Populate antibodyTarget vs. cellType array with counts of experiments
 
         var antibody, target, cellType;
         var matrix = {};
 
         $.each(experiments, function (i, exp) {
             // exclude ref genome annotations
             if (exp.cellType === 'None') {
                 return true;
             }
             if (expIdHash[exp.ix] === undefined) {
                 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);
             if (antibody === undefined) {
                 return true;
             }
             target = encodeProject.targetFromAntibody(antibody);
             if (target === undefined) {
                 return true;
             }
             if (antibodyTargetExps[target] === undefined) {
                 antibodyTargetExps[target] = 0;
             }
             antibodyTargetExps[target]++;
 
             cellType = exp.cellType;
             if (!matrix[cellType]) {
                 matrix[cellType] = {};
             }
             if (!matrix[cellType][target]) {
                 matrix[cellType][target] = 0;
             }
             matrix[cellType][target]++;
         });
     return matrix;
     }
 
     function tableHeaderOut($table, antibodyGroups, antibodyTargetExps) {
         // Generate table header and add to document
 
         var $tableHeader, $thead;
         var maxLen;  // for resizing header cells to accomodate label lengths
         var antibodyTarget;
 
         // fill in column headers from antibody targets returned by server
         $tableHeader = $('#columnHeaders');
         $thead = $('thead');
 
         // 1st column is row headers
         // colgroups are needed to support cross-hair hover effect
         $thead.before('<colgroup></colgroup>');
 
         $.each(antibodyGroups, function (i, group) {
             $tableHeader.append('<th class="groupType"><div class="verticalText">' + 
                                 group.label + '</div></th>');
             maxLen = Math.max(maxLen, group.label.length);
             $thead.before('<colgroup></colgroup>');
+
             $.each(group.targets, function (i, target) {
                 // prune out targets with no experiments 
                 if (antibodyTargetExps[target] === undefined) {
                     return true;
                 }
                 antibodyTarget = encodeProject.getAntibodyTarget(target);
                 $tableHeader.append('<th class="elementType" title="' +
                                 antibodyTarget.description +
                                 '"><div class="verticalText">' + target + '</div></th>');
                 // add colgroup element to support cross-hair hover effect
                 $thead.before('<colgroup class="experimentCol"></colgroup>');
                 maxLen = Math.max(maxLen, target.length);
             });
         });
         // adjust size of headers based on longest label length
         // empirically len/2 em's is right
         $('#columnHeaders th').css('height', (String((maxLen/2 + 2)).concat('em')));
         $('#columnHeaders th').css('width', '1em');
     }
 
     function rowAddCells($row, antibodyGroups, antibodyTargetExps, matrix, cellType) {
         // populate a row in the matrix with cells for antibody target groups and the targets
         // null cellType indicates this is a row for a cell group (tier)
 
         var $td;
 
         $.each(antibodyGroups, function (i, group) {
             // skip group header
             $td = $('<td></td>');
             $td.addClass('matrixCell');
             $row.append($td);
 
             $.each(group.targets, function (i, target) {
                 // prune out targets with no experiments
                 if (antibodyTargetExps[target] === undefined) {
                     return true;
                 }
                 $td = $('<td></td>');
                 $td.addClass('matrixCell');
                 $row.append($td);
 
                 if (cellType === null) {
                     return true;
                 }
                 if (!matrix[cellType][target]) {
                     $td.addClass('todoExperiment');
                     return true;
                 }
                 // this cell represents experiments that
                 // fill in count, mouseover and selection by click
                 $td.addClass('experiment');
                 $td.text(matrix[cellType][target]);
                 $td.data({
                     'target' : target,
                     'cellType' : cellType
                 });
                 $td.mouseover(function() {
                     $(this).attr('title', 'Click to select: ' +
                                 ($(this).data().target) + ' ' + ' in ' + 
                                 $(this).data().cellType +' cells');
                 });
                 $td.click(function() {
                     var url, antibodyTarget;
 
                     // TODO: encapsulate var names
                     // TODO: search on antibody
                     url = encodeMatrix.getSearchUrl(encodeProject.getAssembly());
                     url +=
                        ('&hgt_mdbVar1=dataType&hgt_mdbVal1=' + 'ChipSeq' +
                        '&hgt_mdbVar2=cell&hgt_mdbVal2=' + $(this).data().cellType +
                        '&hgt_mdbVar3=antibody');
                     // TODO: html encode ?
                     antibodyTarget = encodeProject.getAntibodyTarget($(this).data().target);
                     $.each(antibodyTarget.antibodies, function (i, antibody) {
                         url += ('&hgt_mdbVal3=' + antibody);
                     });
                     url += '&hgt_mdbVar4=view&hgt_mdbVal4=Any';
                         // TODO: open search window 
                     window.open(url, "searchWindow");
                 });
             });
         });
     }
 
-    function tableMatrixOut($table, matrix, cellTiers, antibodyGroups, antibodyTargetExps) {
-        // Fill in matrix --
-        // add rows with cell type labels (column 1) and cells for experiments
-        // add sections for each Tier of cell type
-
-        var maxLen, karyotype, cellType;
-        var $row;
-
-        // add sections for each Tier of cells
-        $.each(cellTiers, function (i, tier) {
-            //skip bogus 4th tier (not my property ?)
-            if (tier === undefined) {
-                return true;
-            }
-
-            $row = $('<tr class="matrix"><th class="groupType">' +
-                                "Tier " + tier.term + '</th></td></tr>');
-            rowAddCells($row, antibodyGroups, antibodyTargetExps, matrix, null);
-            $table.append($row);
-            maxLen = 0;
-
-            $.each(tier.cellTypes, function (i, term) {
-                if (!term) {
-                    return true;
-                }
-                if (!matrix[term]) {
-                    return true;
-                }
-                cellType = encodeProject.getCellType(term);
-                karyotype = cellType.karyotype;
-                if (karyotype !== 'cancer' && karyotype !== 'normal') {
-                    karyotype = 'unknown';
-                }
-                // note karyotype bullet layout requires non-intuitive placement
-                // in code before the span that shows to it's left
-                $row = $('<tr>' + 
-                    '<th class="elementType">' +
-                    '<span style="float:right; text-align: right;" title="karyotype: ' + karyotype + '" class="karyotype ' + karyotype + '">&bull;</span>' +
-                    '<span title="' + cellType.description + '"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=' + cellType.term + '">' + cellType.term + '</a>' +
-                    '</th>'
-                    );
-                maxLen = Math.max(maxLen, cellType.term.length);
-
-                rowAddCells($row, antibodyGroups, antibodyTargetExps, matrix, cellType.term);
-                $table.append($row); 
-            });
-            // adjust size of row headers based on longest label length
-            $('tbody th').css('height', '1em');
-            $('tbody th').css('width', (String((maxLen/2 + 2)).concat('em')));
-        });
-        $('body').append($table);
-    }
-
-    function tableOut($table, matrix, cellTiers, antibodyGroups, antibodyTargetExps) {
-        // Create table with rows for each cell type and columns for each antibody target
-
-        tableHeaderOut($table, antibodyGroups, antibodyTargetExps);
-        tableMatrixOut($table, matrix, cellTiers, antibodyGroups, antibodyTargetExps);
-
-        encodeMatrix.addTableFloatingHeader($table);
-        encodeMatrix.rotateTableCells($table);
-        encodeMatrix.hoverTableCrossHair($table);
-    }
-
     // initialize
     encodeMatrix.start($matrixTable);
 
     // load data from server and set up callback
     encodeProject.loadAllFromServer(requests, handleServerData);
 });