[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/datamodel FeaturePair.java,1.10.2.2,1.10.2.3 FeatureSet.java,1.29.2.19,1.29.2.20 GenericAnnotationSet.java,1.13.2.3,1.13.2.4 SeqFeature.java,1.33.2.17,1.33.2.18 SeqFeatureI.java,1.15.2.9,1.15.2.10

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

Update of /cvsroot/gmod/apollo/src/java/apollo/datamodel
In directory usw-pr-cvs1:/tmp/cvs-serv12179/datamodel

Modified Files:
      Tag: sanger_branch
	FeaturePair.java FeatureSet.java GenericAnnotationSet.java 
	SeqFeature.java SeqFeatureI.java 
Log Message:
DetailInfo.getName now calls feature.getDisplayName().
SeqFeature.getDisplayName just returns getName.
FeatureSet.getDisplayName returns its first childs name,
unless the first child is a FeaturePair, then it returns the
FeaturePairs Hname.
GenericAnnotationSet overrides FeatureSets behaviour and just returns 
its name.
FeaturePair returns its sequences display id if it has one,
otherwise it returns its hit name.

This code is drawn from what was previously in DetailInfo.getName.
I am trying to make it so ensembls stuff doesnt break, which needs
the FeatureSet and FeaturePair stuff. My fear here is that this logic
is specific to ensembl's data and not to others. If this is in fact true
then this naming issue has to be dealt with in the data adapter or the 
data itself. I guess I'm also wondering why isnt the FeaturePair name
and FeatureSet name given these names to begin with? In other words why
not put these names in the data or have the data adapters figure them?
Unless these solutions are general, then its fine of course.




Index: FeaturePair.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/FeaturePair.java,v
retrieving revision 1.10.2.2
retrieving revision 1.10.2.3
diff -C2 -d -r1.10.2.2 -r1.10.2.3
*** FeaturePair.java	6 Nov 2001 14:23:39 -0000	1.10.2.2
--- FeaturePair.java	1 Mar 2002 02:17:31 -0000	1.10.2.3
***************
*** 59,62 ****
--- 59,74 ----
      return f1.getName();
    }
+ 
+   /** Code taken from DetailInfo.getName() */
+   public String getDisplayName() {
+     SeqFeatureI hit = getHitFeature();
+     SequenceI seq = (SequenceI) hit.getRefSequence();
+     if (seq != null && seq.getDisplayId() != null) {
+       return seq.getDisplayId();
+     } else {
+       return hit.getName() != null ? hit.getName() : "";
+     }
+   }
+ 
    public void        setId(String id) {
      f1.setId(id);

Index: FeatureSet.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/FeatureSet.java,v
retrieving revision 1.29.2.19
retrieving revision 1.29.2.20
diff -C2 -d -r1.29.2.19 -r1.29.2.20
*** FeatureSet.java	28 Feb 2002 21:29:52 -0000	1.29.2.19
--- FeatureSet.java	1 Mar 2002 02:17:31 -0000	1.29.2.20
***************
*** 287,290 ****
--- 287,303 ----
    }
  
+   /** Code taken from DetailInfo.getName. The default behavior for a FeatureSet
+    * is to get your name from your first kid, but why doesnt the FeatureSet have a name
+    * itself? And if the first kid is a FeaturePair then getHname from kid
+    */
+   public String getDisplayName() {
+     if (getFeatureAt(0) instanceof FeaturePair) { 
+       FeaturePair fp = (FeaturePair)getFeatureAt(0);
+       return fp.getHname();
+     } else {
+       return getFeatureAt(0).getName();
+     }
+   }
+ 
    // Internal methods
    public void _setEnds() {

Index: GenericAnnotationSet.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/GenericAnnotationSet.java,v
retrieving revision 1.13.2.3
retrieving revision 1.13.2.4
diff -C2 -d -r1.13.2.3 -r1.13.2.4
*** GenericAnnotationSet.java	7 Nov 2001 22:45:47 -0000	1.13.2.3
--- GenericAnnotationSet.java	1 Mar 2002 02:17:31 -0000	1.13.2.4
***************
*** 75,78 ****
--- 75,84 ----
        return null;
    }
+ 
+   /** Have to override FeatureSets displayName stuff and just return the name */
+   public String getDisplayName() {
+     return getName();
+   }
+ 
    public void       setDescription(String desc) {
      id.setDescription(desc);

Index: SeqFeature.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/SeqFeature.java,v
retrieving revision 1.33.2.17
retrieving revision 1.33.2.18
diff -C2 -d -r1.33.2.17 -r1.33.2.18
*** SeqFeature.java	28 Feb 2002 21:25:52 -0000	1.33.2.17
--- SeqFeature.java	1 Mar 2002 02:17:31 -0000	1.33.2.18
***************
*** 250,253 ****
--- 250,260 ----
    }
  
+   /** getDisplayName defaults to getName(), subclasses can override to 
+    * change display name
+    */
+   public String getDisplayName() {
+     return getName();
+   }
+ 
    public void setId(String id) {
      this.id = id;

Index: SeqFeatureI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/SeqFeatureI.java,v
retrieving revision 1.15.2.9
retrieving revision 1.15.2.10
diff -C2 -d -r1.15.2.9 -r1.15.2.10
*** SeqFeatureI.java	28 Feb 2002 21:25:52 -0000	1.15.2.9
--- SeqFeatureI.java	1 Mar 2002 02:17:31 -0000	1.15.2.10
***************
*** 21,25 ****
    public String      getName();
    public void        setName(String name);
! 
    public long        getStart();
    public void        setStart(long start);
--- 21,27 ----
    public String      getName();
    public void        setName(String name);
!   /** The name of the feature is not necasarily the name that should be displayed */
!   public String  getDisplayName();
!   
    public long        getStart();
    public void        setStart(long start);