9a49290fedc8b4f9c7a631dedcfe8ac3aa2b4cee
chinhli
  Thu Oct 20 14:10:43 2011 -0700
merge conflict resolved
diff --git src/hg/js/encodeProject.js src/hg/js/encodeProject.js
index 25c2113..e61ab10 100644
--- src/hg/js/encodeProject.js
+++ src/hg/js/encodeProject.js
@@ -1,214 +1,213 @@
-// encodeProject - javascript utilities for ENCODE-specific things 
-// such as controlled vocabulary and experiment table
+/* encodeProject - javascript utilities for ENCODE-specific things 
+ such as controlled vocabulary and experiment table
 
-// Formatted: jsbeautify.py -j
-// Syntax checked: jslint --indent=4 --plusplus=true --strict=false --browser=true
+ Formatted: jsbeautify.py -j -k
+ Syntax checked: jslint --indent=4 --plusplus=true --strict=false --browser=true
+*/
 /*global $ */
 
 var encodeProject = (function () {
     var server = "genome.ucsc.edu",
         assembly = "hg19",
         cgi = "/cgi-bin/hgApi?";
 
     function cmpNoCase(a, b) {
         // Helper function for case-insensitive sort
         var A, B;
         A = a.toUpperCase();
         B = b.toUpperCase();
         if (A < B) {
             return -1;
         }
         if (A > B) {
             return 1;
         }
         return 0;
     }
 
     // TODO: modularize by extending Array.sort ?
+
+
     function cmpCV(a, b) {
         // Helper function for case-insensitive sort of CV objects
         //  Use label if any, otherwise the term
         A = (a.label !== undefined ? a.label.toUpperCase() : a.term.toUpperCase());
         B = (b.label !== undefined ? b.label.toUpperCase() : b.term.toUpperCase());
         if (A < B) {
             return -1;
         }
         if (A > B) {
             return 1;
         }
         return 0;
     }
 
     return {
         setup: function (settings) {
             // Change defaults
             if (settings.server) {
                 server = settings.server;
             }
             if (settings.assembly) {
                 server = settings.assembly;
             }
         },
 
         getServer: function () {
             // Get currently set server 
             return server;
         },
 
         getDataGroups: function (dataTypes) {
             // Return sorted array of dataGroup objects each having a .label,
             // .dataTypes, 
             // and an array of dataTypes, alphasorted, with 'Other' last
             var dataGroupHash = {},
                 dataGroups = [],
-                otherGroup,
-                group;
+                otherGroup, group;
             $.each(dataTypes, function (i, dataType) {
                 group = dataType.dataGroup;
                 if (!group) {
                     return true;
                 }
                 if (!dataGroupHash[group]) {
                     dataGroupHash[group] = {
                         label: group,
                         dataTypes: []
                     };
                 }
                 dataGroupHash[group].dataTypes.push(dataType.label);
             });
             $.each(dataGroupHash, function (key, item) {
                 if (key === "Other") {
                     otherGroup = item;
                 } else {
                     dataGroups.push(item);
                 }
             });
             dataGroups.sort(cmpCV);
             dataGroups.push(otherGroup);
             $.each(dataGroups, function (i, group) {
                 if (!dataGroups[i]) {
                     // for some reason there's  __ element here (not my property)
                     return true;
                 }
                 dataGroups[i].dataTypes.sort(cmpNoCase);
             });
             return dataGroups;
         },
 
         getCellTiers: function (cellTypes) {
             // Return sorted array of cellTier objects each having a .term,
             // with tier number, .celltypes, 
             // and an array of cell types, alphasorted
             var cellTiers = [],
                 tier;
             $.each(cellTypes, function (i, cellType) {
                 tier = cellType.tier;
                 // ignore untiered cell types (all human should have a tier)
                 if (!tier) {
                     return true;
                 }
                 if (!cellTiers[tier]) {
                     cellTiers[tier] = {
                         term: tier,
                         cellTypes: []
                     };
                 }
                 cellTiers[tier].cellTypes.push(cellType.term);
             });
             cellTiers.sort(cmpCV);
             $.each(cellTiers, function (i, tier) {
                 if (!cellTiers[i]) {
                     // for some reason there's  __ element here (not my property)
                     return true;
                 }
                 cellTiers[i].cellTypes.sort(cmpNoCase);
             });
             return cellTiers;
         },
 
         isHistone: function (target) {
             // Helper function, returns true if antibody target histone modification
-
             return target.match(/^H[234]/);
         },
 
         antibodyFromExp: function (experiment) {
             // Get antibody from expVars field of experiment
             var match = experiment.expVars.match(/antibody=(\S+)/);
             if (match) {
                 return match[1];
             }
         },
 
         targetFromAntibody: function (antibody, antibodyCV) {
             // Get target for antibody from antibody controlled vocab
             if (antibodyCV[antibody]) {
                 return antibodyCV[antibody].target;
             }
         },
 
         getAntibodyGroups: function (antibodies) {
             // Return sorted array of antibodyGroup objects each having a .label
             // with group name (Histone Modification or Transcription Factor), 
             // and an array of antibody targets, alphasorted
             var antibodyGroups = [],
                 antibodyGroupHash = {},
-                group,
-                target;
+                group, target;
             $.each(antibodies, function (i, antibody) {
-                group = encodeProject.isHistone(antibody.target) ? 
-                        "Histone Modification" : "Transcription Factor";
+                group = encodeProject.isHistone(antibody.target) ? "Histone Modification" : "Transcription Factor";
                 if (!antibodyGroupHash[group]) {
                     antibodyGroupHash[group] = {
                         label: group,
                         targets: [],
                         targetHash: {}
                     };
                 }
                 target = antibody.target;
                 if (antibodyGroupHash[group].targetHash[target] === undefined) {
                     antibodyGroupHash[group].targetHash[target] = target;
                     antibodyGroupHash[group].targets.push(target);
                 }
             });
             $.each(antibodyGroupHash, function (key, item) {
                 antibodyGroups.push(item);
             });
             antibodyGroups.sort(cmpCV);
             $.each(antibodyGroups, function (i, group) {
                 if (!antibodyGroups[i]) {
                     // for some reason there's  __ element here (not my property)
                     return true;
                 }
                 antibodyGroups[i].targets.sort(cmpNoCase);
             });
             return antibodyGroups;
         },
 
         serverRequests: {
             // Requests for data from server API
             experiment: "cmd=encodeExperiments",
 
             dataType: "cmd=cv&type=dataType",
 
             cellType: "cmd=cv&type=cellType",
 
             antibody: "cmd=cv&type=antibody"
         },
 
         loadAllFromServer: function (requests, handler) {
             // Execute requests to server via ajax
             var serverData = [],
                 count = requests.length;
 
             $.each(requests, function (i, request) {
                 $.getJSON("http://" + server + cgi + "db=" + assembly + "&" + request, function (data) {
                     serverData[i] = data;
                     if (--count === 0) {
                         handler(serverData);
                     }
                 });
             });
         }
     };
 }());