[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/synteny AbstractLinker.java, 1.6, 1.7

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

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/synteny
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv4461/apollo/dataadapter/synteny

Modified Files:
	AbstractLinker.java 
Log Message:
made synteny debug print statements print with debug flag - didnt take
them out as olivier is still working this stuff



Index: AbstractLinker.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/synteny/AbstractLinker.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** AbstractLinker.java	9 Jun 2006 17:23:23 -0000	1.6
--- AbstractLinker.java	26 Jun 2006 23:41:38 -0000	1.7
***************
*** 24,28 ****
      LinkType type = linkedProp.getLinkType();
  
!     System.out.println("link type "+type);
  
      if (type == LinkType.PEPTIDE) {
--- 24,28 ----
      LinkType type = linkedProp.getLinkType();
  
!     //System.out.println("link type "+type);
  
      if (type == LinkType.PEPTIDE) {
***************
*** 65,69 ****
    /** Default behavior is to extract all feats of feature property in cur set */
    protected FeatureList getLinkFeatures(CurationSet curSet) {
!     System.out.println("********is parent linnk type "+getFeatureProperty().getLinkType().isParentLevel());
      if (getFeatureProperty().getLinkType().isParentLevel())
        return SeqFeatureUtil.getFeatPropLeafParentFeats(curSet,getFeatureProperty());
--- 65,69 ----
    /** Default behavior is to extract all feats of feature property in cur set */
    protected FeatureList getLinkFeatures(CurationSet curSet) {
!     dbg("******is parent link type "+getFeatureProperty().getLinkType().isParentLevel());
      if (getFeatureProperty().getLinkType().isParentLevel())
        return SeqFeatureUtil.getFeatPropLeafParentFeats(curSet,getFeatureProperty());
***************
*** 96,99 ****
--- 96,104 ----
    }
  
+   private void dbg(String m) { 
+     if (apollo.config.Config.DEBUG)
+       System.out.println(m);
+   }
+ 
    /** Returns true if 2 feats are linked to each other */
    protected abstract boolean featsAreLinked(SeqFeatureI feat1, SeqFeatureI feat2);
***************
*** 111,115 ****
      adap.setInputType(getInputType());
      adap.setInput(getInputString(link));
!     if (apollo.config.Config.DEBUG) System.out.println("AbsLink adap input "+adap.getInput()+" input string set to data adapter is "+getInputString(link));
      doPadding(adap,link);
      return adap.getCurationSet(); // throws DA exception
--- 116,120 ----
      adap.setInputType(getInputType());
      adap.setInput(getInputString(link));
!     dbg("AbsLink adap input "+adap.getInput()+" input string set to data adapter is "+getInputString(link));
      doPadding(adap,link);
      return adap.getCurationSet(); // throws DA exception