[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui/evidencepanel SetDetailPanel.java,1.8,1.9

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

Update of /cvsroot/gmod/apollo/src/java/apollo/gui/evidencepanel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7047/src/java/apollo/gui/evidencepanel

Modified Files:
	SetDetailPanel.java 
Log Message:
Fixed gene prediction names in jdbc adapter (thought this was gonna be
totally trivial). jdbc gene predictions are seq features where game
gene predictions are feature pairs (i think all game results are
feature pairs). so the naming/label code acts differently if feature
pair or not - thus the differences. theres code in FlyDisplayPrefs for
non feat pairs (seq feats) labels that was never being called before
because we havent had fly seq feat results.

anyways the names are not like game names as sima suggested the best
names for predictions is just program:start-end
(Genscan:30000-31000). So thats the format for prediction names -
maybe other results should include coords as sima suggests.



Index: SetDetailPanel.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/evidencepanel/SetDetailPanel.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** SetDetailPanel.java	26 May 2004 22:54:22 -0000	1.8
--- SetDetailPanel.java	28 May 2004 23:11:10 -0000	1.9
***************
*** 146,149 ****
--- 146,154 ----
    public void setToFeature (SeqFeatureI feature) {}
  
+   /** sets text for descBox and labelBox. if FeaturePair label comes from type + 
+       hit seq display id or type + hit name, fp desc is hit seq desc or prog+db.
+       If not FeatPair, featureDisplayString(feat) is used which returns 
+       biotype+featname - and if annot feat tacks on gene description.
+       Also tacks on length to label. */
    protected void setupHeader(FeatureSetI fset, SeqFeatureI sf) {
      String desc = "";
***************
*** 151,154 ****
--- 156,160 ----
      int length = 0;
  
+     // FeaturePair
      if (sf.hasHitFeature()) {
        SequenceI seq = fset.getHitSequence();
***************
*** 169,173 ****
          desc = fset.getProgramName()  + " " + fset.getDatabase();
        }
!     } else { // Not a FeaturePair
        if (fset.getRefFeature() != null && fset.getRefFeature().hasType()) {
          name = featureDisplayString(fset.getRefFeature());
--- 175,181 ----
          desc = fset.getProgramName()  + " " + fset.getDatabase();
        }
!     } 
!     // Not a FeaturePair    
!     else { 
        if (fset.getRefFeature() != null && fset.getRefFeature().hasType()) {
          name = featureDisplayString(fset.getRefFeature());
***************
*** 195,198 ****
--- 203,207 ----
    }
  
+   /** return config display prefs bio type display + feat name (if has name) */
    private String featureDisplayString(SeqFeatureI feat) {
      // This is a better type of type