Changeset 20763

Timestamp:

02/03/10 13:50:32 (2 years ago)

Author:

julie

Message:

path fix

File:

• trunk/bio/tools/main/src/org/intermine/bio/logic/OrthologueLinkManager.java (modified) (8 diffs)

trunk/bio/tools/main/src/org/intermine/bio/logic/OrthologueLinkManager.java

@@ -74 +74 @@
 
 /**
+ * @param im intermine api
  * @param webProperties the web properties
  */
@@ -87 +88 @@
 
     /**
+     * @param im intermine api
      * @param webProperties the web properties
      * @return OrthologueLinkManager the link manager
@@ -92 +94 @@
     public static synchronized OrthologueLinkManager getInstance(InterMineAPI im,
             Properties webProperties) {
-        if (orthologueLinkManager == null) {
+        if (orthologueLinkManager == null || DEBUG) {
             orthologueLinkManager = new OrthologueLinkManager(im, webProperties);
         }
@@ -108 +110 @@
         if (timeSinceLastRefresh > ONE_HOUR || DEBUG) {
             lastCacheRefresh = System.currentTimeMillis();
+
             updateMaps();
         }
@@ -294 +297 @@
             QueryClass qcHomologueOrganism = new QueryClass(Organism.class);
             QueryClass qcDataset = new QueryClass(DataSet.class);
+            QueryClass qcGeneHomologue = new QueryClass(Gene.class);
 
             QueryField qfGeneOrganismName = new QueryField(qcOrganism, "shortName");
@@ -303 +307 @@
             q.addToSelect(qfGeneOrganismName);
             q.addToSelect(qfDataset);
-            q.addToOrderBy(qfHomologueOrganismName);
+            q.addToSelect(qfHomologueOrganismName);
 
             q.addFrom(qcGene);
@@ -310 +314 @@
             q.addFrom(qcHomologueOrganism);
             q.addFrom(qcDataset);
+            q.addFrom(qcGeneHomologue);
 
             ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
@@ -325 +330 @@
             cs.addConstraint(new ContainsConstraint(c3, ConstraintOp.CONTAINS, qcDataset));
 
+            // gene.homologues.homologue
+            QueryObjectReference c4 = new QueryObjectReference(qcHomologue, "homologue");
+            cs.addConstraint(new ContainsConstraint(c4, ConstraintOp.CONTAINS, qcGeneHomologue));
+
             // gene.homologues.homologue.organism.shortName
-            QueryObjectReference c4 = new QueryObjectReference(qcHomologue, "organism");
-            cs.addConstraint(new ContainsConstraint(c4, ConstraintOp.CONTAINS,
+            QueryObjectReference c5 = new QueryObjectReference(qcGeneHomologue, "organism");
+            cs.addConstraint(new ContainsConstraint(c5, ConstraintOp.CONTAINS,
                     qcHomologueOrganism));
-
             q.setConstraint(cs);