[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/main CommandLine.java,1.32,1.33

[Nomi H. <no...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/main
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1621/apollo/main

Modified Files:
	CommandLine.java 
Log Message:

Added input/output type "das[2]".


Index: CommandLine.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/main/CommandLine.java,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** CommandLine.java	22 Nov 2005 14:34:56 -0000	1.32
--- CommandLine.java	30 Jan 2006 23:03:25 -0000	1.33
***************
*** 31,34 ****
--- 31,35 ----
  import apollo.dataadapter.gamexml.GAMEAdapter;
  import apollo.dataadapter.genbank.GenbankAdapter;
+ import apollo.dataadapter.das2.DAS2Adapter;
  import apollo.datamodel.GenomicRange;
  
***************
*** 45,48 ****
--- 46,50 ----
    private final static String GFF = GFFAdapter.class.getName();
    private final static String GENBANK = GenbankAdapter.class.getName();
+   private final static String DAS2 = DAS2Adapter.class.getName();
  
    //private DataAdapterRegistry adapterRegistry;
***************
*** 239,243 ****
  
    
-   
    /**
     * Return the IOOptions which has a db dataadapter. For now only test if the dataAdapter is a ChadoAdapter
--- 241,244 ----
***************
*** 251,256 ****
      
      //First, get sure that the IOOptions have their dataadapter. 
-     //
-     // 
      if (!getReadOptions().hasAdapter())
        getReadOptions().setAdapter(inputFmtOption.getAdapter());
--- 252,255 ----
***************
*** 265,273 ****
      
       throw new Exception("Unable to find a database (ie chadoDB) for either input or output");
-         
    }
    
-   
-   
  
    private ApolloDataAdapterI getAdapterForFile(IOOptions options)
--- 264,269 ----
***************
*** 305,308 ****
--- 301,306 ----
      if (suffix.matches("backup|ser"))
        return getDataAdapter(SERIALIZED);
+     if (suffix.matches(".*das2.*"))
+       return getDataAdapter(DAS2);
      // configuration can specify what to do with .xml suffix (game or chado)
      else if (suffix.equals("xml") && xmlSuffixIsConfigged())
***************
*** 333,336 ****
--- 331,337 ----
        return getDataAdapter(GENBANK);
      }
+     else if (adapString.toLowerCase().startsWith("das")) {
+       return getDataAdapter(DAS2);
+     }
      else {
        error("Don't recognize input format "+adapString);
***************
*** 382,386 ****
  
      private final static String help =
!     "Specify input format. [chadoDB|game|chadoxml|genbank|gff|backup]";
  
      private InputFormatCommandOption() {
--- 383,387 ----
  
      private final static String help =
!     "Specify input format. [chadoDB|game|chadoxml|genbank|gff|das2|backup]";
  
      private InputFormatCommandOption() {
***************
*** 406,410 ****
  
      private final static String help =
!     "Specify output format. [chadoDB|game|chadoxml|genbank|gff|backup]";
  
      private OutputFormatCommandOption() { 
--- 407,411 ----
  
      private final static String help =
!     "Specify output format. [chadoDB|game|chadoxml|genbank|gff|das2|backup]";
  
      private OutputFormatCommandOption() { 
***************
*** 975,979 ****
      private BatchInputFile(String batchFilename) throws FileNotFoundException, IOException {
        super(batchFilename);
-      
      }
      
--- 976,979 ----
***************
*** 1033,1119 ****
        }
      }
-     
    }
- 
  }
  
- 
- 
- 
- // delete...
- //   class ReadOptions extends IOOptions {
- //     //boolean forRead() { return true; }
- //     ApolloDataAdapterI getAdapter() throws Exception {
- //       if (adapter == null) {
- //         adapter = inputFmtOption.getAdapter();
- //       }
- //       return adapter;
- //     }
- //     boolean haveSequenceFilename() {
- //       return getSequenceFilename() != null;
- //     }
- //     String getSequenceFilename() {
- //       return seqFileOption.getArg(); // if not "matched" will be null
- //     }
- //   }
- //   class WriteOptions extends IOOptions {
- //     //boolean forRead() { return false; }
- //     ApolloDataAdapterI getAdapter() throws Exception {
- //     //if (adapter == null && outputFmtOption.getMatched())
- //     //  adapter = outputFmtOption.getWriteAdapter();
- //       return adapter;
- 
- //     }
- //   }
- 
- // }
- 
- 
- 
- //       // throws exception if no format
- //       ApolloDataAdapterI readAdapter = getAdapter();
- //       setReadAdapter(readAdapter);
- //       DataInput di = new DataInput(DataInputType.FILE,getFilename());
- //       // gff input may have seq file.
- //       if (haveSequenceFilename())
- //         di.setSequenceFilename(getSequenceFilename());
- //       readAdapter.setDataInput(di);
- //       setReadSpecifiedState(true);
- //     }
- 
- //     private ApolloDataAdapterI getAdapter() throws Exception {
- //       ApolloDataAdapterI adapter; // class var/cache?
- //       // first see if input format explicitly specified
- //       if (haveReadAdapter()) {
- //         adapter = getReadAdapter();
- //       }
- //       // if nothing specified try to get format from file suffix
- //       else {
- //         adapter = getDataAdapterFromSuffix();
- //         if (adapter != null)
- //           System.out.println("No input format specified. Based on suffix "+getFileSuffix()
- //                              +", using data adapter " + adapter.getClass());
- //       }
-       
- //       if (adapter == null) {
- //         error("\nNo input format specified and can't determine it from suffix "
- //               +getFileSuffix());
- //       }
- //       return adapter;
- //     }
- 
-       
- //  } // end of InputFileCommandOption inner class
- 
- //   private void setReadAdapter(ApolloDataAdapterI readAdapter) {
- //     this.readAdapter = readAdapter;
- //   }
- 
-   
- 
- //   private ApolloDataAdapterI getAdapter(boolean forRead) throws Exception {
- //     if (forRead)
- //       return getReadAdapter();
- //     return getWriteAdapter();
- //   }
- 
--- 1033,1037 ----