gmod-apollo-cmts

[Guanming Wu <gua...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26006/apollo/src/java/apollo/dataadapter/chado/jdbc

Modified Files:
	JdbcChadoAdapter.java 
Log Message:
Bug fixes: Use different features for different program or feature types

Index: JdbcChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v
retrieving revision 1.69
retrieving revision 1.70
diff -C2 -d -r1.69 -r1.70
*** JdbcChadoAdapter.java	29 Nov 2004 16:05:47 -0000	1.69
--- JdbcChadoAdapter.java	1 Dec 2004 03:29:53 -0000	1.70
***************
*** 10,13 ****
--- 10,14 ----
  import java.util.HashMap;
  import java.util.Hashtable;
+ import java.util.Iterator;
  import java.util.Map;
  import java.util.Vector;
***************
*** 1020,1031 ****
                                 boolean setAlignSeqs, FeatureLocImplementation featLoc)
      {
- 
        // should make new ones of these for each type if theres multiple types in the query
!       FeatureSet analysisForwardFeatSet = new FeatureSet();
!       analysisForwardFeatSet.setStrand(1);
!       sfs.addFeature(analysisForwardFeatSet);
!       FeatureSet analysisReverseFeatSet = new FeatureSet();
!       analysisReverseFeatSet.setStrand(-1);
!       sfs.addFeature(analysisReverseFeatSet);
        // Count gapped alignments; can't currently display sequences for these
        // JC: The above comment refers to the fact that we don't have the actual 
--- 1021,1033 ----
                                 boolean setAlignSeqs, FeatureLocImplementation featLoc)
      {
        // should make new ones of these for each type if theres multiple types in the query
!       Map forwardFeatMap = new HashMap(); // To sort out FeatureSets based on feature type
!       Map reverseFeatMap = new HashMap(); 
!       //FeatureSet analysisForwardFeatSet = new FeatureSet();
!       //analysisForwardFeatSet.setStrand(1);
!       //sfs.addFeature(analysisForwardFeatSet);
!       //FeatureSet analysisReverseFeatSet = new FeatureSet();
!       //analysisReverseFeatSet.setStrand(-1);
!       //sfs.addFeature(analysisReverseFeatSet);
        // Count gapped alignments; can't currently display sequences for these
        // JC: The above comment refers to the fact that we don't have the actual 
***************
*** 1282,1291 ****
                FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, 
                                                           lastFeatType, lastStrand);
!               if (targetFeatSet.isForwardStrand()) {
!                 analysisForwardFeatSet.addFeature(targetFeatSet);
!               } 
!               else {
!                 analysisReverseFeatSet.addFeature(targetFeatSet);
!               }
                featurePairs.clear();
              }
--- 1284,1300 ----
                FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, 
                                                           lastFeatType, lastStrand);
!               FeatureSet featureSet = getFeatureSetForType(lastFeatType,
!                                                            targetFeatSet.isForwardStrand(),
!                                                            forwardFeatMap,
!                                                            reverseFeatMap);
!               featureSet.addFeature(targetFeatSet);
! //              if (targetFeatSet.isForwardStrand()) {
! //                FeatureSet featureSet = getFeatureSetForType(lastFeatType,
! //                                                             true,)
! //                analysisForwardFeatSet.addFeature(targetFeatSet);
! //              } 
! //              else {
! //                analysisReverseFeatSet.addFeature(targetFeatSet);
! //              }
                featurePairs.clear();
              }
***************
*** 1316,1327 ****
            FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, 
                                                       lastFeatType, lastStrand);
!           if (targetFeatSet.isForwardStrand()) {
!             analysisForwardFeatSet.addFeature(targetFeatSet);
!           } 
!           else {
!             analysisReverseFeatSet.addFeature(targetFeatSet);
!           }
            featurePairs.clear();
          }
        } catch (SQLException sqle) {
          System.err.println(this.getClass() + ": SQLException retrieving analysisfeatures for sequence with feature_id = " + srcSeqId);
--- 1325,1343 ----
            FeatureSet targetFeatSet = _makeFeatureSet(featurePairs, lastTargetSp, 
                                                       lastFeatType, lastStrand);
!           FeatureSet featureSet = getFeatureSetForType(lastFeatType,
!                                                        targetFeatSet.isForwardStrand(),
!                                                        forwardFeatMap,
!                                                        reverseFeatMap);
!           featureSet.addFeature(targetFeatSet);
! //          if (targetFeatSet.isForwardStrand()) {
! //            analysisForwardFeatSet.addFeature(targetFeatSet);
! //          } 
! //          else {
! //            analysisReverseFeatSet.addFeature(targetFeatSet);
! //          }
            featurePairs.clear();
          }
+         addFeatureToParents(sfs, forwardFeatMap);
+         addFeatureToParents(sfs, reverseFeatMap);
        } catch (SQLException sqle) {
          System.err.println(this.getClass() + ": SQLException retrieving analysisfeatures for sequence with feature_id = " + srcSeqId);
***************
*** 1334,1337 ****
--- 1350,1379 ----
  //     }
      } // end of addSearchHits()
+   
+   private FeatureSet getFeatureSetForType(String featureType, 
+                                           boolean isForward, 
+                                           Map forwardMap,
+                                           Map reverseMap) {
+     FeatureSet feature = null;
+     if (isForward) {
+       feature = (FeatureSet) forwardMap.get(featureType);
+       if (feature == null) {
+         feature = new FeatureSet();
+         feature.setStrand(1);
+         feature.setType(featureType);
+         forwardMap.put(featureType, feature);
+       }
+     }
+     else {
+       feature = (FeatureSet) reverseMap.get(featureType);
+       if (feature == null) {
+         feature = new FeatureSet();
+         feature.setStrand(-1);
+         feature.setType(featureType);
+         reverseMap.put(featureType, feature);
+       }
+     }
+     return feature;
+   }
  
  
***************
*** 1530,1533 ****
--- 1572,1577 ----
        String lastProgram = null;
        FeatureSet transcriptFeatSet=null;
+       Map forwardMap = new HashMap();
+       Map reverseMap = new HashMap();
        while (rs.next()) {
          int transcriptId = rs.getInt("transId");
***************
*** 1563,1567 ****
            transcriptFeatSet = _makeFeatureSet(featType,strand);
            transcriptFeatSet.setProgramName(program);
!           parentFeatSet.addFeature(transcriptFeatSet);
            //lastTranscriptName = transcriptName;
            lastTranscriptId = transcriptId;
--- 1607,1616 ----
            transcriptFeatSet = _makeFeatureSet(featType,strand);
            transcriptFeatSet.setProgramName(program);
!           FeatureSet programFeature = getFeatureSetForType(program, 
!                                                            transcriptFeatSet.isForwardStrand(), 
!                                                            forwardMap,
!                                                            reverseMap);
!           programFeature.addFeature(transcriptFeatSet);
!           //parentFeatSet.addFeature(transcriptFeatSet);
            //lastTranscriptName = transcriptName;
            lastTranscriptId = transcriptId;
***************
*** 1574,1578 ****
        String rng = transcriptFeatSet.getStart()+"-"+transcriptFeatSet.getEnd();
        transcriptFeatSet.setName(lastProgram+":"+rng);
! 
      } catch (SQLException sqle) {
        System.err.println(this.getClass() + ": SQLException retrieving gene predictions "
--- 1623,1628 ----
        String rng = transcriptFeatSet.getStart()+"-"+transcriptFeatSet.getEnd();
        transcriptFeatSet.setName(lastProgram+":"+rng);
!       addFeatureToParents(parentFeatSet, forwardMap);
!       addFeatureToParents(parentFeatSet, reverseMap);
      } catch (SQLException sqle) {
        System.err.println(this.getClass() + ": SQLException retrieving gene predictions "
***************
*** 1582,1585 ****
--- 1632,1643 ----
    }
    
+   private void addFeatureToParents(StrandedFeatureSet parentFeatSet, Map forwardMap) {
+     for (Iterator it = forwardMap.keySet().iterator(); it.hasNext();) {
+       String program = (String) it.next();
+       FeatureSet fs = (FeatureSet) forwardMap.get(program);
+       parentFeatSet.addFeature(fs);
+     }
+   }
+ 
  
    private AnalysisTable analysisTable;