[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc FlybaseChadoInstance.java,1.21,1.22

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

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7431/apollo/src/java/apollo/dataadapter/chado/jdbc

Modified Files:
	FlybaseChadoInstance.java 
Log Message:
Refactoring for querying by range

Index: FlybaseChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** FlybaseChadoInstance.java	3 Nov 2004 19:29:54 -0000	1.21
--- FlybaseChadoInstance.java	5 Nov 2004 21:42:37 -0000	1.22
***************
*** 48,52 ****
        "WHERE cdsloc.srcfeature_id = "+featLocImp.getContainingFeatureId()+" "+
        "AND cdsloc.feature_id = cds.feature_id AND cds.type_id = "+protCvId+
!       "AND cds.feature_id = cds2trans.subject_id "+
        "AND cds2trans.object_id = trans.feature_id "+
        "AND cds2trans.type_id = "+producedByCvId+" AND trans.type_id = "+mrnaCvId+
--- 48,52 ----
        "WHERE cdsloc.srcfeature_id = "+featLocImp.getContainingFeatureId()+" "+
        "AND cdsloc.feature_id = cds.feature_id AND cds.type_id = "+protCvId+
!       " AND cds.feature_id = cds2trans.subject_id "+
        "AND cds2trans.object_id = trans.feature_id "+
        "AND cds2trans.type_id = "+producedByCvId+" AND trans.type_id = "+mrnaCvId+
***************
*** 76,80 ****
    private int getPaddingForTopLevelSeqType(String seqType) {
      if (seqType.equals("gene")) {
!       if (jdbcChadoAdapter.debug) return 200; // keep small for debug
        return 25000;
      }
--- 76,80 ----
    private int getPaddingForTopLevelSeqType(String seqType) {
      if (seqType.equals("gene")) {
!       if (JdbcChadoAdapter.debug) return 200; // keep small for debug
        return 25000;
      }
***************
*** 113,116 ****
--- 113,134 ----
      return false;
    }
+   
+   public CurationSet getCurationSetInRange(ChadoAdapter adapter,
+                                            String seqType,
+                                            String chromosomeName,
+                                            int start,
+                                            int end,
+                                            Connection conn) {
+     if (conn == null) {
+       return null;
+     }
+ 
+     debugPrintTime();
+     // Query for the Chado feature.feature_id of the requested sequence
+     long seqFeatId = jdbcChadoAdapter.getFeatureId(conn, seqType, chromosomeName);
+     FeatureLocImplementation featLocImp = new ChromosomeFeatureLocImp(seqFeatId, start, end);
+     return getCurationSet(adapter, seqType, chromosomeName, featLocImp, conn);
+   }
+   
  
    /**
***************
*** 127,130 ****
--- 145,164 ----
  
      debugPrintTime();
+     // Query for the Chado feature.feature_id of the requested sequence
+     long seqFeatId = jdbcChadoAdapter.getFeatureId(conn, seqType, topFeatName);
+ 
+     // padding not fully implemented - all queries need to pad - and cur set
+     int padding = getPaddingForTopLevelSeqType(seqType);
+ 
+     FeatureLocImplementation featLocImp = 
+       new FeatureLocImplementation(seqFeatId,haveRedundantFeatureLocs(),conn,padding);
+     return getCurationSet(adapter, seqType, topFeatName, featLocImp, conn);
+   }
+   
+   private CurationSet getCurationSet(ChadoAdapter adapter, 
+                                      String seqType,
+                                      String topFeatName,
+                                      FeatureLocImplementation featLocImp,
+                                      Connection conn) {
      CurationSet cset = null;
      StrandedFeatureSet results = new StrandedFeatureSet(new FeatureSet(), new FeatureSet());
***************
*** 148,159 ****
      cset = new CurationSet();
  
!     // Query for the Chado feature.feature_id of the requested sequence
!     long seqFeatId = jdbcChadoAdapter.getFeatureId(conn, seqType, topFeatName);
! 
!     // padding not fully implemented - all queries need to pad - and cur set
!     int padding = getPaddingForTopLevelSeqType(seqType);
! 
!     FeatureLocImplementation featLocImp = 
!       new FeatureLocImplementation(seqFeatId,haveRedundantFeatureLocs(),conn,padding);
  
      adapter.fireProgressEvent(new ProgressEvent(this, new Double(50.0), "Retrieving " + seqType + " sequence " + topFeatName));
--- 182,193 ----
      cset = new CurationSet();
  
! //    // Query for the Chado feature.feature_id of the requested sequence
! //    long seqFeatId = jdbcChadoAdapter.getFeatureId(conn, seqType, topFeatName);
! //
! //    // padding not fully implemented - all queries need to pad - and cur set
! //    int padding = getPaddingForTopLevelSeqType(seqType);
! //
! //    FeatureLocImplementation featLocImp = 
! //      new FeatureLocImplementation(seqFeatId,haveRedundantFeatureLocs(),conn,padding);
  
      adapter.fireProgressEvent(new ProgressEvent(this, new Double(50.0), "Retrieving " + seqType + " sequence " + topFeatName));
***************
*** 164,173 ****
      // gene seq has to be padded out and retrieved from parent as substring 
      // this should be configged or something
!     if (seqType.equals("gene")) {
        // should just take feat loc imp
!       seq = jdbcChadoAdapter.getSequenceFromParent(featLocImp,true); 
      }
      else {
!       seq = jdbcChadoAdapter.getSequence(conn, seqFeatId, false, true);
      }
      //ChadoFeatureLoc featLoc = new ChadoFeatureLoc((int)seqFeatId,conn);
--- 198,207 ----
      // gene seq has to be padded out and retrieved from parent as substring 
      // this should be configged or something
!     if (seqType.equals("gene") || seqType.equals("chromosome")) {
        // should just take feat loc imp
!       seq = jdbcChadoAdapter.getSequenceFromParent(featLocImp, true); 
      }
      else {
!       seq = jdbcChadoAdapter.getSequence(conn, featLocImp.getFeatureId(), false, true);
      }
      //ChadoFeatureLoc featLoc = new ChadoFeatureLoc((int)seqFeatId,conn);
***************
*** 214,221 ****
      // Features located directly on the reference sequence
      // ------------------------------------------------    
! 
!     adapter.fireProgressEvent(
!       new ProgressEvent(this, z, "Retrieving piecegenie and genscan results"));
!     String[] predictionPrograms = new String[] {"genscan","piecegenie"};
      if (!skipData) 
        jdbcChadoAdapter.addGenePredictionResults(conn, predictionPrograms, results, featLocImp);
--- 248,258 ----
      // Features located directly on the reference sequence
      // ------------------------------------------------    
!     String[] predictionPrograms = getPredictionPrograms();
!     //adapter.fireProgressEvent(
!     //  new ProgressEvent(this, z, "Retrieving piecegenie and genscan results"));
!     adapter.fireProgressEvent(new ProgressEvent(this, 
!                                                 z, 
!                                                 "Retrieving " + concatProgramNames(predictionPrograms) + " results"));
!     //String[] predictionPrograms = new String[] {"genscan","piecegenie"};
      if (!skipData) 
        jdbcChadoAdapter.addGenePredictionResults(conn, predictionPrograms, results, featLocImp);
***************
*** 234,240 ****
  
      // sim4, blastx, and tblastx
!     ProgressEvent p = new ProgressEvent(this, z,"Retrieving sim4 and blastx results");
      adapter.fireProgressEvent(p);
!     String[] hitProgs = new String[] {"sim4","%blastx%"};
      if (!skipData)
        jdbcChadoAdapter.addSearchHits(conn, hitProgs, 0, 1, getTargetSeqs,getTgtSqSep,
--- 271,281 ----
  
      // sim4, blastx, and tblastx
!     String[] hitProgs = getHitPrograms();
!     //ProgressEvent p = new ProgressEvent(this, z,"Retrieving sim4 and blastx results");
!     ProgressEvent p = new ProgressEvent(this, 
!                                         z,
!                                         "Retrieving " + concatProgramNames(hitProgs) + " results");
      adapter.fireProgressEvent(p);
!     //String[] hitProgs = new String[] {"sim4","%blastx%"};
      if (!skipData)
        jdbcChadoAdapter.addSearchHits(conn, hitProgs, 0, 1, getTargetSeqs,getTgtSqSep,
***************
*** 287,290 ****
--- 328,353 ----
      this.jdbcChadoAdapter = jdbcAdapter;
    }
+   
+   protected String[] getHitPrograms() {
+     return new String[] {"sim4","%blastx%"};
+   }
+   
+   protected String[] getPredictionPrograms() {
+     return new String[] {"genscan","piecegenie"};
+   }
+   
+   private String concatProgramNames(String[] names) {
+     String msg = "";
+     int size = names.length;
+     for (int i = 0; i < size; i++) {
+       msg += names[i];
+       if (i < size - 2)
+         msg += ", ";
+       else if (i < size - 1)
+         msg += " and ";
+     }
+     return msg;
+   }
+   
    private void debugPrintTime() { JdbcChadoAdapter.debugPrintTime(); }
  }