Changeset 22806

Timestamp:

08/09/10 17:43:30 (17 months ago)

Author:

rns

Message:

Compile and checkstyle fixes.

Location:

branches/mnw21/pathquery_refactor

Files:

• bio/postprocess/main/src/org/intermine/bio/postprocess/TransferSequences.java (modified) (4 diffs)
• intermine/api/test/src/org/intermine/api/template/TemplatePopulatorTest.java (modified) (6 diffs)
• modmine/webapp/src/org/modmine/web/FeaturesAction.java (modified) (18 diffs)
• modmine/webapp/src/org/modmine/web/logic/ModMineUtil.java (modified) (2 diffs)

branches/mnw21/pathquery_refactor/bio/postprocess/main/src/org/intermine/bio/postprocess/TransferSequences.java

@@ -17 +17 @@
 
 import org.apache.log4j.Logger;
-import org.biojava.bio.seq.DNATools;
 import org.biojava.bio.symbol.IllegalAlphabetException;
 import org.biojava.bio.symbol.IllegalSymbolException;
-import org.biojava.bio.symbol.SymbolList;
 import org.intermine.bio.util.ClobAccessReverseComplement;
 import org.intermine.bio.util.Constants;
@@ -309 +307 @@
         }
 
-        if (locationOnChr.getStrand().equals("-1")) {
+        if ("-1".equals(locationOnChr.getStrand())) {
             subSeqString = new ClobAccessReverseComplement(subSeqString);
         }
@@ -397 +395 @@
             Transcript transcript =  (Transcript) rr.get(0);
 
-           if (currentTranscript == null || !transcript.equals(currentTranscript)) {
-               if (currentTranscript != null) {
-                   storeNewSequence(currentTranscript,
-                           new PendingClob(currentTranscriptBases.toString()));
-                   i++;
-                   if (i % 100 == 0) {
-                       long now = System.currentTimeMillis();
-                       LOG.info("Set sequences for " + i + " Transcripts"
+            if (currentTranscript == null || !transcript.equals(currentTranscript)) {
+                if (currentTranscript != null) {
+                    storeNewSequence(currentTranscript,
+                            new PendingClob(currentTranscriptBases.toString()));
+                    i++;
+                    if (i % 100 == 0) {
+                        long now = System.currentTimeMillis();
+                        LOG.info("Set sequences for " + i + " Transcripts"
                                 + " (avg = " + ((60000L * i) / (now - start)) + " per minute)");
                     }
@@ -415 +413 @@
             Location  location = (Location) rr.get(3);
 
-            if (location.getStrand() != null && location.getStrand().equals("-1")) {
+            if (location.getStrand() != null && "-1".equals(location.getStrand())) {
                 currentTranscriptBases.insert(0, exonSequence.getResidues());
             } else {

branches/mnw21/pathquery_refactor/intermine/api/test/src/org/intermine/api/template/TemplatePopulatorTest.java

@@ -71 +71 @@
         PathConstraint age = new PathConstraintAttribute("Employee.age", ConstraintOp.EQUALS, "30");
         TemplateValue value = new TemplateValue(age, ConstraintOp.EQUALS, "21", 
-                TemplateValue.ValueType.SIMPLE_VALUE);
+                TemplateValue.ValueType.SIMPLE_VALUE, SwitchOffAbility.LOCKED);
         values.put("Employee.age", Arrays.asList(new TemplateValue[] {value}));
         try {
@@ -83 +83 @@
         PathConstraint nameCon = simple.getEditableConstraints("Employee.name").get(0);
         TemplateValue value1 = new TemplateValue(nameCon, ConstraintOp.EQUALS, "name", 
-                TemplateValue.ValueType.SIMPLE_VALUE);
+                TemplateValue.ValueType.SIMPLE_VALUE, SwitchOffAbility.LOCKED);
         TemplateValue value2 = new TemplateValue(nameCon, ConstraintOp.EQUALS, "other name", 
-                TemplateValue.ValueType.SIMPLE_VALUE);
+                TemplateValue.ValueType.SIMPLE_VALUE, SwitchOffAbility.LOCKED);
         values.put("Employee.name", Arrays.asList(new TemplateValue[] {value1, value2}));
         try {
@@ -97 +97 @@
         PathConstraint ageCon = twoConstraints.getEditableConstraints("Employee.age").get(0);
         TemplateValue value = new TemplateValue(ageCon, ConstraintOp.EQUALS, "21",
-                TemplateValue.ValueType.SIMPLE_VALUE);
+                TemplateValue.ValueType.SIMPLE_VALUE, SwitchOffAbility.LOCKED);
         values.put("Employee.age", Arrays.asList(new TemplateValue[] {value}));
         try {
@@ -109 +109 @@
         PathConstraint nameCon = simple.getEditableConstraints("Employee.name").get(0);
         TemplateValue value = new TemplateValue(nameCon, ConstraintOp.NOT_EQUALS,
-                "Kevin Bacon", TemplateValue.ValueType.SIMPLE_VALUE);
+                "Kevin Bacon", TemplateValue.ValueType.SIMPLE_VALUE, SwitchOffAbility.LOCKED);
         values.put("Employee.name", Arrays.asList(new TemplateValue[] {value}));
         TemplateQuery res = TemplatePopulator.getPopulatedTemplate(simple, values);
@@ -121 +121 @@
         PathConstraint nameCon = simple.getEditableConstraints("Employee.name").get(0);
         TemplateValue value = new TemplateValue(nameCon, ConstraintOp.IN, "bag1",
-                TemplateValue.ValueType.BAG_VALUE);
+                TemplateValue.ValueType.BAG_VALUE, SwitchOffAbility.LOCKED);
         values.put("Employee.name", Arrays.asList(new TemplateValue[] {value}));
         TemplateQuery res = TemplatePopulator.getPopulatedTemplate(simple, values);
@@ -209 +209 @@
         PathConstraint nameCon = simple.getEditableConstraints("Employee.name").get(0);
         TemplateValue value = new TemplateValue(nameCon, ConstraintOp.GREATER_THAN, "bag1",
-                TemplateValue.ValueType.BAG_VALUE);
+                TemplateValue.ValueType.BAG_VALUE, SwitchOffAbility.LOCKED);
         values.put("Employee.name", Arrays.asList(new TemplateValue[] {value}));
         try {

branches/mnw21/pathquery_refactor/modmine/webapp/src/org/modmine/web/FeaturesAction.java

@@ -22 +22 @@
 import javax.servlet.http.HttpSession;
 
-import org.apache.log4j.Logger;
 import org.apache.struts.action.ActionForm;
 import org.apache.struts.action.ActionForward;
@@ -37 +36 @@
 import org.intermine.objectstore.ObjectStore;
 import org.intermine.pathquery.Constraints;
-import org.intermine.pathquery.PathNode;
-import org.intermine.pathquery.OldPathQuery;
+import org.intermine.pathquery.OrderDirection;
+import org.intermine.pathquery.PathQuery;
 import org.intermine.util.StringUtil;
 import org.intermine.web.logic.bag.BagHelper;
@@ -96 +95 @@
         Set<Integer> taxIds = new HashSet<Integer>();
 
-        OldPathQuery q = new OldPathQuery(model);
+        PathQuery q = new PathQuery(model);
 
         boolean hasPrimer = false;
 
-        if (type.equals("experiment")) {
+        if ("experiment".equals(type)) {
             experimentName = (String) request.getParameter("experiment");
             DisplayExperiment exp = MetadataCache.getExperimentByName(os, experimentName);
@@ -118 +117 @@
                 }
 
-                q.addConstraint(rootChoice + ".submissions.experiment.name",
-                        Constraints.eq(experimentName));
+                q.addConstraint(Constraints.eq(rootChoice + ".submissions.experiment.name",
+                        experimentName));
             } else {
 
@@ -145 +144 @@
                 q.addView(featureType + ".primaryIdentifier");
                 q.addView(featureType + ".score");
-                if (action.equals("results")) {
+                if ("results".equals(action)) {
                     // we don't want this field on exports
                     q.addView(featureType + ":scoreProtocol.name");
                 }
-                q.addConstraint(featureType + ".submissions.experiment.name",
-                        Constraints.eq(experimentName));
+                q.addConstraint(Constraints.eq(featureType + ".submissions.experiment.name",
+                        experimentName));
 
                 if (allUnlocated.contains(featureType)) {
@@ -162 +161 @@
         }
 
-        else if (type.equals("submission")) {
+        else if ("submission".equals(type)) {
             dccId = (String) request.getParameter("submission");
             Submission sub = MetadataCache.getSubmissionByDccId(os, new Integer(dccId));
@@ -181 +180 @@
                 }
 
-                q.addConstraint(rootChoice + ".submissions.DCCid",
-                        Constraints.eq(new Integer(dccId)));
+                q.addConstraint(Constraints.eq(rootChoice + ".submissions.DCCid", dccId));
             } else {
 
@@ -210 +208 @@
                 q.addView(featureType + ".primaryIdentifier");
                 q.addView(featureType + ".score");
-                if (action.equals("results")) {
+                if ("results".equals(action)) {
                     q.addView(featureType + ":scoreProtocol.name");
                 }
-                q.addConstraint(featureType + ".submissions.DCCid",
-                        Constraints.eq(new Integer(dccId)));
+                q.addConstraint(Constraints.eq(featureType + ".submissions.DCCid", dccId));
 
                 if (unlocFeatures == null || !unlocFeatures.contains(featureType)) {
@@ -229 +226 @@
 
         // For the expression levels
-        else if (type.equals("subEL")) {
+        else if ("subEL".equals(type)) {
             dccId = (String) request.getParameter("submission");
-            PathNode node = q.addNode("Submission.features");
-            node.setType(featureType);
+            q.addConstraint(Constraints.type("Submission.features", featureType));
+
             String path = "Submission.features.expressionLevels";
-
             q.addView(path + ".name");
             q.addView(path + ".value");
@@ -243 +239 @@
             q.addView(path + ".predictionStatus");
 
-            q.addConstraint("Submission.DCCid",
-                    Constraints.eq(new Integer(dccId)));
-        }
-        else if (type.equals("expEL")) {
+            q.addConstraint(Constraints.eq("Submission.DCCid", dccId));
+        }
+        else if ("expEL".equals(type)) {
             String eName = (String) request.getParameter("experiment");
 
-            PathNode node = q.addNode("Experiment.submissions.features");
-            node.setType(featureType);
+            q.addConstraint(Constraints.type("Experiment.submissions.features", featureType));
+
             String path = "Experiment.submissions.features.expressionLevels";
-
             q.addView(path + ".name");
             q.addView(path + ".value");
@@ -261 +255 @@
             q.addView(path + ".predictionStatus");
 
-            q.addConstraint("Experiment.name",
-                    Constraints.eq(eName));
-        }
-
-        if (action.equals("results")) {
+            q.addConstraint(Constraints.eq("Experiment.name", eName));
+        }
+
+        if ("results".equals(action)) {
             String qid = SessionMethods.startQueryWithTimeout(request, false, q);
             Thread.sleep(200);
@@ -272 +265 @@
                 .addParameter("qid", qid)
                 .forward();
-        } else if (action.equals("export")) {
+        } else if ("export".equals(action)) {
             String format = request.getParameter("format");
 
@@ -293 +286 @@
 
             TableExportForm exportForm = null;
-            if (format.equals("gff3")) {
+            if ("gff3".equals(format)) {
                 exportForm = new GFF3ExportForm();
                 exportForm.setDoGzip(doGzip);
@@ -305 +298 @@
             return null;
 
-        } else if (action.equals("list")) {
+        } else if ("list".equals(action)) {
             // need to select just id of featureType to create list
-            q.setView(featureType + ".id");
+            q.addView(featureType + ".id");
 
             Profile profile = SessionMethods.getProfile(session);
@@ -382 +375 @@
      * @param hasPrimer
      */
-    private void addEFactorToQuery(OldPathQuery q, String featureType,
+    private void addEFactorToQuery(PathQuery q, String featureType,
             boolean hasPrimer) {
         if (!hasPrimer) {
@@ -395 +388 @@
      * @param featureType the feature type
      */
-    private void addLocationToQuery(OldPathQuery q, String featureType) {
+    private void addLocationToQuery(PathQuery q, String featureType) {
         q.addView(featureType + ".chromosome.primaryIdentifier");
         q.addView(featureType + ".chromosomeLocation.start");
@@ -402 +395 @@
         q.addView(featureType + ".submissions.DCCid");
 
-        q.addOrderBy(featureType + ".chromosome.primaryIdentifier");
-        q.addOrderBy(featureType + ".chromosomeLocation.start");
+        q.addOrderBy(featureType + ".chromosome.primaryIdentifier", OrderDirection.ASC);
+        q.addOrderBy(featureType + ".chromosomeLocation.start", OrderDirection.ASC);
     }
 
@@ -431 +424 @@
         return taxIds;
     }
-
-
-
 }
 

branches/mnw21/pathquery_refactor/modmine/webapp/src/org/modmine/web/logic/ModMineUtil.java

@@ -32 +32 @@
  * @author Fengyuan Hu
  */
-public class ModMineUtil
+public final class ModMineUtil
 {
+    private ModMineUtil() {
+    }
+
     /**
      * For a bag of Submission objects, returns a set of Submission objects.
@@ -60 +63 @@
 
         Results r = os.execute(q);
-        Iterator<ResultsRow> it = r.iterator();
+        @SuppressWarnings("unchecked") Iterator<ResultsRow> it = (Iterator) r.iterator();
+
         Set<Submission> subs = new LinkedHashSet<Submission>();