[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc ChadoInstance.java,1.10,1.11 FlybaseChadoInstance.java,1.28,1.29 JdbcChadoAdapter.java,1.79,1.80 RiceChadoInstance.java,1.5,1.6 TigrSybilChadoInstance.java,1.16,1.17

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24715/src/java/apollo/dataadapter/chado/jdbc

Modified Files:
	ChadoInstance.java FlybaseChadoInstance.java 
	JdbcChadoAdapter.java RiceChadoInstance.java 
	TigrSybilChadoInstance.java 
Log Message:
added ability to configure gene prediction programs from
chado-adapter.xml:

    <chadoInstance id="riceInstance" default="true">
        <genePredictionPrograms>
            <program>FgenesH</program>
        </genePredictionPrograms>

can add more than one program. Scott is configuring up a a new chado
database so this ability is pretty important so ya he doesnt have to
write java code. need to do the same with alignment programs - but im
out of time - when i get back. im sure their will be more that needs
to come out in the config file out of the Chado instances.



Index: ChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/ChadoInstance.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** ChadoInstance.java	9 Feb 2005 22:55:05 -0000	1.10
--- ChadoInstance.java	19 Feb 2005 00:42:29 -0000	1.11
***************
*** 114,116 ****
--- 114,119 ----
     */
    public void setThreeLevelFeatures(List features);
+ 
+   public void setPredictionPrograms(String[] predictionPrograms);
+   public String[] getPredictionPrograms();
  }

Index: FlybaseChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** FlybaseChadoInstance.java	9 Feb 2005 22:55:05 -0000	1.28
--- FlybaseChadoInstance.java	19 Feb 2005 00:42:29 -0000	1.29
***************
*** 16,19 ****
--- 16,22 ----
  import apollo.datamodel.Transcript;
  
+ /** we need an AbstractChadoInstance super class for generic stuff, like
+     gene prediction programs. */
+ 
  public class FlybaseChadoInstance implements ChadoInstance {
  
***************
*** 21,24 ****
--- 24,28 ----
    private List oneLevelFeatures;
    private List threeLevelFeatures;
+   private String[] predictionPrograms;
  
    public FlybaseChadoInstance() {
***************
*** 348,352 ****
    }
    
!   protected String[] getPredictionPrograms() {
      return new String[] {"genscan","piecegenie"};
    }
--- 352,362 ----
    }
    
!   public void setPredictionPrograms(String[] predictionPrograms) {
!     this.predictionPrograms = predictionPrograms;
!   }
! 
!   public String[] getPredictionPrograms() {
!     if (predictionPrograms != null)
!       return predictionPrograms;
      return new String[] {"genscan","piecegenie"};
    }
***************
*** 390,394 ****
      threeLevelFeatures = new ArrayList(features);
    }
!   
    private void debugPrintTime() { JdbcChadoAdapter.debugPrintTime(); }
  }
--- 400,404 ----
      threeLevelFeatures = new ArrayList(features);
    }
! 
    private void debugPrintTime() { JdbcChadoAdapter.debugPrintTime(); }
  }

Index: JdbcChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v
retrieving revision 1.79
retrieving revision 1.80
diff -C2 -d -r1.79 -r1.80
*** JdbcChadoAdapter.java	18 Feb 2005 21:34:07 -0000	1.79
--- JdbcChadoAdapter.java	19 Feb 2005 00:42:29 -0000	1.80
***************
*** 1697,1700 ****
--- 1697,1705 ----
      // "in(...)" clause of anlaysis ids - postgres7.3 speeds up by a factor of 2 if 
      // i take analysis out of the join - 7.3 is lame lame lame
+     
+     debugPrint("Querying programs for gene prediction: ");
+     for (int i=0;i<programStr.length;i++)
+       debugPrint(programStr[i]+"\n");
+ 
      String analysisWhereClause = getAnalysisTable().getAnalysisIdWhereClause(programStr);
  
***************
*** 1821,1824 ****
--- 1826,1830 ----
        // presently only need id,prog and source - add more as needed
        String sql = "SELECT analysis_id, program, sourcename FROM analysis ";
+       debugMsgAndTime(sql);
        try {
          if (programToAnalysisRow == null)
***************
*** 1861,1867 ****
        String inAnalysisWhereClause = "in (";
        for (int i=0; i<programs.length; i++) {
          if (i > 0) // if not first row, put in comma before id
              inAnalysisWhereClause += ",";
-         int analysis_id = getId(programs[i]);
          inAnalysisWhereClause += analysis_id;
        }
--- 1867,1878 ----
        String inAnalysisWhereClause = "in (";
        for (int i=0; i<programs.length; i++) {
+         int analysis_id = getId(programs[i]);
+         if (analysis_id == -1) {
+           // throw exception???
+           System.out.println("Analysis program "+programs[i]+" not found in analysis"+
+                              " table. Please update conf/chado-adapter.xml");
+         }
          if (i > 0) // if not first row, put in comma before id
              inAnalysisWhereClause += ",";
          inAnalysisWhereClause += analysis_id;
        }

Index: RiceChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/RiceChadoInstance.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** RiceChadoInstance.java	9 Feb 2005 22:55:05 -0000	1.5
--- RiceChadoInstance.java	19 Feb 2005 00:42:30 -0000	1.6
***************
*** 50,55 ****
    
    /** These should come from config - chado-adapter.xml */
!   protected String[] getPredictionPrograms() {
!     return new String[]{"FgenesH"};
    }
  
--- 50,58 ----
    
    /** These should come from config - chado-adapter.xml */
!   public String[] getPredictionPrograms() {
!     if (super.getPredictionPrograms() != null)
!       return super.getPredictionPrograms();
!     //return new String[]{"FgenesH"};
!     return null;
    }
  

Index: TigrSybilChadoInstance.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/TigrSybilChadoInstance.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** TigrSybilChadoInstance.java	9 Feb 2005 22:55:05 -0000	1.16
--- TigrSybilChadoInstance.java	19 Feb 2005 00:42:30 -0000	1.17
***************
*** 272,274 ****
--- 272,279 ----
      throw new UnsupportedOperationException("TigrSybilChadoInstance.setThreeLevelFeatures(): Not supported.");
    }
+   
+   // need abstract super class!
+   private String[] predictionProgs;
+   public String[] getPredictionPrograms() { return predictionProgs; }
+   public void setPredictionPrograms(String[] progs) { this.predictionProgs = progs; }
  }