[Gmod-schema-cmts] schema/XMLTools/GameChadoConv GTC.java,1.1,1.2

[Frank S. <smu...@us...>]

Update of /cvsroot/gmod/schema/XMLTools/GameChadoConv
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15029/schema/XMLTools/GameChadoConv

Modified Files:
	GTC.java 
Log Message:


Index: GTC.java
===================================================================
RCS file: /cvsroot/gmod/schema/XMLTools/GameChadoConv/GTC.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** GTC.java	9 Oct 2003 18:16:32 -0000	1.1
--- GTC.java	27 Aug 2004 16:47:06 -0000	1.2
***************
*** 15,18 ****
--- 15,19 ----
  		int seqflags = ChadoWriter.SEQOMIT;
  		int tpflags = ChadoWriter.TPOMIT;
+ 		int ulflags = 0;
  		for(int i=0;i<argv.length;i++){
  			if(argv[i]!=null){
***************
*** 21,34 ****
  					if(argv[i].equals("-a")){//ALL
  						parseflags = GameSaxReader.PARSEALL;
! 					}else if(argv[i].equals("-c")){//COMPUTATIONAL_ANALYSIS
  						parseflags = GameSaxReader.PARSECOMP;
! 					}else if(argv[i].equals("-g")){//GENES
  						parseflags = GameSaxReader.PARSEGENES;
! 					}else if(argv[i].equals("-t")){//TRANSACTIONAL CHANGES
  						modeflags = ChadoWriter.WRITECHANGED;
! 					}else if(argv[i].equals("-s")){//INCL SEQ
  						seqflags = ChadoWriter.SEQINCL;
! 					}else if(argv[i].equals("-p")){//INCL Transposable Elements
  						tpflags = ChadoWriter.TPINCL;
  					}
  				}else{
--- 22,46 ----
  					if(argv[i].equals("-a")){//ALL
  						parseflags = GameSaxReader.PARSEALL;
! 					}else if(argv[i].equals("-c")){
! 						//COMPUTATIONAL_ANALYSIS
  						parseflags = GameSaxReader.PARSECOMP;
! 					}else if(argv[i].equals("-g")){
! 						//GENES
  						parseflags = GameSaxReader.PARSEGENES;
! 					}else if(argv[i].equals("-t")){
! 						//TRANSACTIONAL CHANGES
  						modeflags = ChadoWriter.WRITECHANGED;
! 					}else if(argv[i].equals("-s")){
! 						//INCL SEQ
  						seqflags = ChadoWriter.SEQINCL;
! 					}else if(argv[i].equals("-p")){
! 						//INCL Transposable Elements
  						tpflags = ChadoWriter.TPINCL;
+ 					}else if(argv[i].equals("-R")){
+ 						//EXCEPTION FOR REL4 CODE
+ 						ulflags = ChadoWriter.REL4;
+ 					}else if(argv[i].equals("-H")){
+ 						//EXCEPTION FOR HETEROCHROMATIN CODE
+ 						ulflags = ChadoWriter.HET;
  					}
  				}else{
***************
*** 42,46 ****
  		}
  
! 		ChadoWriter rd = new ChadoWriter(infile,outfile,parseflags,modeflags,seqflags,tpflags);
  		rd.GameToChado();
  	}
--- 54,59 ----
  		}
  
! 		ChadoWriter rd = new ChadoWriter(infile,outfile,
! 				parseflags,modeflags,seqflags,tpflags,ulflags);
  		rd.GameToChado();
  	}