[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter AbstractApolloAdapter.java,1.34,1.35 ApolloDataAdapterI.java,1.20,1.21 GFFAdapterGUI.java,1.11,1.12 SerialAdapterGUI.java,1.3,1.4 SerialDiskAdapter.java,1.22,1.23

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

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26788/src/java/apollo/dataadapter

Modified Files:
	AbstractApolloAdapter.java ApolloDataAdapterI.java 
	GFFAdapterGUI.java SerialAdapterGUI.java 
	SerialDiskAdapter.java 
Log Message:
fixed bug reported by sima where save wasnt working from synteny
viewer even from single species. changed comp data holder
getSpeciesCuration to getCuration - lose the species connotation.


Index: AbstractApolloAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/AbstractApolloAdapter.java,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** AbstractApolloAdapter.java	25 Aug 2004 22:52:03 -0000	1.34
--- AbstractApolloAdapter.java	26 Aug 2004 18:12:51 -0000	1.35
***************
*** 150,154 ****
    public boolean rollbackAnnotations(CompositeDataHolder cdh) {
      if (!isComposite())
!       return rollbackAnnotations(cdh.getSpeciesCurationSet(0));
      else // composite/SyntenyAdapter doesnt deal with this yet
        return true;
--- 150,154 ----
    public boolean rollbackAnnotations(CompositeDataHolder cdh) {
      if (!isComposite())
!       return rollbackAnnotations(cdh.getCurationSet(0));
      else // composite/SyntenyAdapter doesnt deal with this yet
        return true;
***************
*** 214,220 ****
      throw new NotImplementedException();
    }
!   /** Only SyntenyAdapter and SerialDiskAdapter actually implements this */
    public void commitChanges(CompositeDataHolder cdh) throws DataAdapterException {
!     throw new NotImplementedException();
    }
  
--- 214,228 ----
      throw new NotImplementedException();
    }
!   /** SyntenyAdapter and SerialDiskAdapter override this */
    public void commitChanges(CompositeDataHolder cdh) throws DataAdapterException {
!     if (!isComposite())
!       commitChanges(cdh.getCurationSet(0));
!   }
! 
!   public void commitChanges(Object values) throws DataAdapterException {
!     if (values instanceof CurationSet)
!       commitChanges((CurationSet)values);
!     else if (values instanceof CompositeDataHolder)
!       commitChanges((CompositeDataHolder)values);
    }
  

Index: ApolloDataAdapterI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/ApolloDataAdapterI.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** ApolloDataAdapterI.java	25 Aug 2004 22:52:03 -0000	1.20
--- ApolloDataAdapterI.java	26 Aug 2004 18:12:53 -0000	1.21
***************
*** 52,55 ****
--- 52,58 ----
    public void commitChanges(CompositeDataHolder cdh) throws DataAdapterException;
  
+   /** Straight from DataAdapterGUI.doOp. Could be cur set or comp data holder */
+   public void commitChanges(Object values) throws DataAdapterException;
+ 
    public Properties getStateInformation();
    public void setStateInformation(Properties props);

Index: GFFAdapterGUI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/GFFAdapterGUI.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** GFFAdapterGUI.java	2 Apr 2004 19:50:36 -0000	1.11
--- GFFAdapterGUI.java	26 Aug 2004 18:12:53 -0000	1.12
***************
*** 170,174 ****
          CompositeDataHolder cdh = apolloData.getCompositeDataHolder();
          // assume its the 1st species - presumptious but what else can we do
!         curSet = cdh.getSpeciesCurationSet(0);
        }
        else {
--- 170,174 ----
          CompositeDataHolder cdh = apolloData.getCompositeDataHolder();
          // assume its the 1st species - presumptious but what else can we do
!         curSet = cdh.getCurationSet(0);
        }
        else {

Index: SerialAdapterGUI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/SerialAdapterGUI.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** SerialAdapterGUI.java	20 Dec 2003 00:04:05 -0000	1.3
--- SerialAdapterGUI.java	26 Aug 2004 18:12:53 -0000	1.4
***************
*** 37,41 ****
          // even recieve a compo data and have to get its cur set - it should
          // get just a CurationSet (or a niftier ApolloDataI)
!         curSet = apolloData.getCompositeDataHolder().getSpeciesCurationSet(0);
        }
        ((ApolloDataAdapterI) driver).commitChanges(curSet);
--- 37,41 ----
          // even recieve a compo data and have to get its cur set - it should
          // get just a CurationSet (or a niftier ApolloDataI)
!         curSet = apolloData.getCompositeDataHolder().getCurationSet(0);
        }
        ((ApolloDataAdapterI) driver).commitChanges(curSet);

Index: SerialDiskAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/SerialDiskAdapter.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** SerialDiskAdapter.java	25 Aug 2004 22:52:03 -0000	1.22
--- SerialDiskAdapter.java	26 Aug 2004 18:12:53 -0000	1.23
***************
*** 112,120 ****
    public void commitChanges(CompositeDataHolder cdh) throws DataAdapterException {
      if (!cdh.isMultiSpecies())
!       commitChanges(cdh.getSpeciesCurationSet(0));
      else {
        for (int i=0; i<cdh.getNumberOfSpecies(); i++) 
          // append curset/species name to file name
!         commitChanges(cdh.getSpeciesCurationSet(i),filename+cdh.getSpecies(i));
      }
    }
--- 112,120 ----
    public void commitChanges(CompositeDataHolder cdh) throws DataAdapterException {
      if (!cdh.isMultiSpecies())
!       commitChanges(cdh.getCurationSet(0));
      else {
        for (int i=0; i<cdh.getNumberOfSpecies(); i++) 
          // append curset/species name to file name
!         commitChanges(cdh.getCurationSet(i),filename+cdh.getSpecies(i));
      }
    }