[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/util SeqFeatureUtil.java, 1.33, 1.34

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

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

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



Index: SeqFeatureUtil.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/util/SeqFeatureUtil.java,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** SeqFeatureUtil.java	8 Jun 2006 14:46:30 -0000	1.33
--- SeqFeatureUtil.java	26 Jun 2006 23:41:38 -0000	1.34
***************
*** 77,81 ****
      if (feature == null) {
        if (apollo.config.Config.DEBUG) {
!         System.err.println("DEBUG null feature for SeqFeatureUtil.getFeaturesOfClass");
          new Throwable().printStackTrace();
        }
--- 77,81 ----
      if (feature == null) {
        if (apollo.config.Config.DEBUG) {
!         debug("DEBUG null feature for SeqFeatureUtil.getFeaturesOfClass");
          new Throwable().printStackTrace();
        }
***************
*** 92,96 ****
      if (feature == null) {// shouldnt happen
        if (apollo.config.Config.DEBUG) {
!         System.err.println("null feature for SeqFeatureUtil.populateFeaturesOfClass");
          new Throwable().printStackTrace();
        }
--- 92,96 ----
      if (feature == null) {// shouldnt happen
        if (apollo.config.Config.DEBUG) {
!         debug("null feature for SeqFeatureUtil.populateFeaturesOfClass");
          new Throwable().printStackTrace();
        }
***************
*** 162,166 ****
  
    public static boolean equals(CurationSet a, CurationSet b) {
!     System.err.println("Results:");
      /*
      Vector a_features = getFeatureVector(a);
--- 162,166 ----
  
    public static boolean equals(CurationSet a, CurationSet b) {
!     //debug("Results:");
      /*
      Vector a_features = getFeatureVector(a);
***************
*** 394,398 ****
      for (int i=0; i<prop.getAnalysisTypesSize(); i++) {
        String analysisType = prop.getAnalysisType(i);
!       System.out.println("SFU getting leaves for analysis type "+analysisType+" prop "+prop);
        FeatureList anFeats = cur.getAnalysisFeatureList(analysisType);
        tierFeats.addAllFeatures(anFeats); // gets leaves below
--- 394,398 ----
      for (int i=0; i<prop.getAnalysisTypesSize(); i++) {
        String analysisType = prop.getAnalysisType(i);
!       debug("SFU getting leaves for analysis type "+analysisType+" prop "+prop);
        FeatureList anFeats = cur.getAnalysisFeatureList(analysisType);
        tierFeats.addAllFeatures(anFeats); // gets leaves below
***************
*** 430,433 ****
--- 430,438 ----
    }
  
+   public static void debug(String m) {
+     if (apollo.config.Config.DEBUG)
+       System.out.println(m);
+   }
+ 
  }