[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/datamodel CompositeDataHolder.java,1.3,1.4 LinkSet.java,1.1,1.2

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

Update of /cvsroot/gmod/apollo/src/java/apollo/datamodel
In directory sc8-pr-cvs1:/tmp/cvs-serv11723/src/java/apollo/datamodel

Modified Files:
	CompositeDataHolder.java LinkSet.java 
Log Message:
Synteny now working with game! (though a bit crudely) No links are
queried for, rather the links come from the game species data. Things
need to be spruced up a bit - nav bars need to be taken out, need
tiers file entries for the psuedo data(not covered), need a db
chooser, need a link chooser from specifying just one species - also i
need to test more game data than my one example.



Index: CompositeDataHolder.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/CompositeDataHolder.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** CompositeDataHolder.java	26 Sep 2003 20:45:52 -0000	1.3
--- CompositeDataHolder.java	30 Sep 2003 12:37:58 -0000	1.4
***************
*** 5,8 ****
--- 5,10 ----
  import java.util.HashMap;
  
+ import apollo.util.FeatureList;
+ 
  /** Holds multiple curation sets for synteny. Links are stored as curation 
      sets as well for now - change. Should this be called SyntenyDataHolder or 
***************
*** 49,60 ****
    }
  
    public boolean hasLinks() { return hasLinks; }
  
!   /** Eventually return a LinkSet, and have better way of getting at link than
!       through string */
    public LinkSet getLinkSet(String firstSetName, String secondSetName) {
      LinkSet linkSet = getLinkSetFromCache(firstSetName,secondSetName);
      if (linkSet != null) return linkSet;
  
      CurationSet cs = getCurationSet(firstSetName+"-"+secondSetName);
      if (cs != null) {
--- 51,67 ----
    }
  
+   private CurationSet getCurationSet(int i) {
+     return getCurationSet(getSpecies(i));
+   }
+   private String getSpecies(int i) { return (String)species.get(i); }
+ 
    public boolean hasLinks() { return hasLinks; }
  
!   /** Return Link set linking 2 species */
    public LinkSet getLinkSet(String firstSetName, String secondSetName) {
      LinkSet linkSet = getLinkSetFromCache(firstSetName,secondSetName);
      if (linkSet != null) return linkSet;
  
+     // try getting from composite curation set
      CurationSet cs = getCurationSet(firstSetName+"-"+secondSetName);
      if (cs != null) {
***************
*** 76,84 ****
    }
  
    /** Should be phased out */
    public CurationSet getCompositeCurationSet() { return compositeCurationSet; }
  
    public void getLinksFromCurationSet() {
! 
    }
  
--- 83,107 ----
    }
  
+   /** CompDH keeps track of link sets through nameToLinkSet hash */
+   private void addLinkSet(LinkSet linkSet) { 
+     nameToLinkSet.put(linkSet.getName(),linkSet); 
+     hasLinks = true;
+   }
+ 
    /** Should be phased out */
    public CurationSet getCompositeCurationSet() { return compositeCurationSet; }
  
+   /** Gets links from alignments in curation set. Should this go in a util class? */
    public void getLinksFromCurationSet() {
!     CurationSet curSet1 = getCurationSet(0);
!     CurationSet curSet2 = getCurationSet(1);
!     String hitSpecies = curSet2.getName(); // contig id//curSet2.getOrganism();
!     
!     // Should probably try getting links from both?
!     StrandedFeatureSetI results = curSet1.getResults();
!     // Will hitSpecies always work for hit name?
!     FeatureList featPairs = results.findFeaturesByHitName(hitSpecies); 
!     LinkSet linkSet = new LinkSet(featPairs,getSpecies(0),getSpecies(1));
!     addLinkSet(linkSet);
    }
  

Index: LinkSet.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/LinkSet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** LinkSet.java	15 Aug 2003 23:32:04 -0000	1.1
--- LinkSet.java	30 Sep 2003 12:37:58 -0000	1.2
***************
*** 3,6 ****
--- 3,8 ----
  import java.util.Vector;
  
+ import apollo.util.FeatureList;
+ 
  /** Set of links for synteny view */
  
***************
*** 15,18 ****
--- 17,26 ----
    /** non cur set wrapper */
    public LinkSet() {}
+ 
+   LinkSet(FeatureList links,String species1, String species2) {
+     setSpecies1(species1);
+     setSpecies2(species2);
+     feats = links;
+   }
  
    /** Temporary CurationSet wrapper */