[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter FeatureSetBuilder.java,1.5,1.6 GFFSyntenyAdapter.java,1.3,1.4 SyntenyGFFAdapter.java,1.2,1.3

[Suzanna L. <su...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter
In directory sc8-pr-cvs1:/tmp/cvs-serv6686/apollo/dataadapter

Modified Files:
	FeatureSetBuilder.java GFFSyntenyAdapter.java 
	SyntenyGFFAdapter.java 
Log Message:

well, this is a big commit. waited a long time to proceed with it.

1. holder no longer exists as an inherent aspect of seqfeatures. this
is all handled now within the gui drawables. each drawable has a couple
attributes that determine when to draw the feature it is associated
with. one is the draw-level. this indicates the depth of the feature
hierarchy that the drawable can represent. e.g. a draw_level of 2
means it can draw a seqfeature and its direct parent and a draw_level
of 1 means it can only represent the seqfeature itself. 

2. drawables no longer implement the datamodel interfaces. they are
truly just drawables/glyphs that can represent the model.

3. added 2 more analysis parsers for repeatmasker and trnascan

4. added some gui utilities to reduce duplicated code

5. changed the format of the tiers files to be tag : value. the code
will still read the old format, but will automatically update it to
the new format.

hmmm, think that is it. still doing more testing, but so far so good



Index: FeatureSetBuilder.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/FeatureSetBuilder.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** FeatureSetBuilder.java	27 Feb 2003 18:18:03 -0000	1.5
--- FeatureSetBuilder.java	30 Nov 2003 04:58:18 -0000	1.6
***************
*** 97,101 ****
  
      fs.setType(type);
!     fs.setHolder (true);
      fs.setStrand (strand);
  
--- 97,101 ----
  
      fs.setType(type);
!     // fs.setHolder (true);
      fs.setStrand (strand);
  
***************
*** 125,129 ****
  
      fs.setType(type);
!     fs.setHolder (true);
      fs.setStrand (strand);
  
--- 125,129 ----
  
      fs.setType(type);
!     // fs.setHolder (true);
      fs.setStrand (strand);
  
***************
*** 154,158 ****
  
      fs.setType(type);
!     fs.setHolder (true);
      fs.setStrand (strand);
  
--- 154,158 ----
  
      fs.setType(type);
!     // fs.setHolder (true);
      fs.setStrand (strand);
  
***************
*** 180,184 ****
  
  
!     int sfVectSize = sf_vect.size(); 
      long[]        starts = new long[sfVectSize];
      SeqFeatureI[] f      = new SeqFeatureI[sfVectSize];
--- 180,184 ----
  
  
!     int sfVectSize = sf_vect.size();
      long[]        starts = new long[sfVectSize];
      SeqFeatureI[] f      = new SeqFeatureI[sfVectSize];
***************
*** 215,219 ****
  
          // Puts homols together based on coordinate gaps between them
!         // and also that the hit start coord follows on from 
          // the previous hit end
  
--- 215,219 ----
  
          // Puts homols together based on coordinate gaps between them
!         // and also that the hit start coord follows on from
          // the previous hit end
  

Index: GFFSyntenyAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/GFFSyntenyAdapter.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** GFFSyntenyAdapter.java	25 Nov 2002 22:51:28 -0000	1.3
--- GFFSyntenyAdapter.java	30 Nov 2003 04:58:18 -0000	1.4
***************
*** 109,114 ****
                                                   (int)fp.getHigh(),
                                                   chr2,
!                                                  (int)fp.getHLow(),
!                                                  (int)fp.getHHigh(),
                                                   fp.getStrand());
              regions.addElement(sr);
--- 109,114 ----
                                                   (int)fp.getHigh(),
                                                   chr2,
!                                                  (int)fp.getHlow(),
!                                                  (int)fp.getHhigh(),
                                                   fp.getStrand());
              regions.addElement(sr);

Index: SyntenyGFFAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/SyntenyGFFAdapter.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** SyntenyGFFAdapter.java	10 Sep 2002 15:08:14 -0000	1.2
--- SyntenyGFFAdapter.java	30 Nov 2003 04:58:18 -0000	1.3
***************
*** 136,140 ****
            }
            if (chr1 != null && chr2 != null) {
!             SyntenyRegion sr = new SyntenyRegion(chr1,(int)fp.getLow(),(int)fp.getHigh(),chr2,(int)fp.getHLow(),(int)fp.getHHigh(),fp.getStrand());
  
              regions.addElement(sr);
--- 136,146 ----
            }
            if (chr1 != null && chr2 != null) {
!             SyntenyRegion sr = new SyntenyRegion(chr1,
! 						 fp.getLow(),
! 						 fp.getHigh(),
! 						 chr2,
! 						 fp.getHlow(),
! 						 fp.getHhigh(),
! 						 fp.getStrand());
  
              regions.addElement(sr);