[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/synteny SyntenyComparaAdapter.java,1.14,1.15

[Vivek I. <vi...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/synteny
In directory sc8-pr-cvs1:/tmp/cvs-serv11563

Modified Files:
	SyntenyComparaAdapter.java 
Log Message:

If you are running a compara-data fetch which only has information for the
range of one species, then you really need to fetch alignments (to infer the
range of the other species). If apollo doesn't get them, then it needs to 
exit gracefully, not with an IllegalState. This change makes Apollo do that.


Index: SyntenyComparaAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/synteny/SyntenyComparaAdapter.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** SyntenyComparaAdapter.java	9 Apr 2003 13:04:29 -0000	1.14
--- SyntenyComparaAdapter.java	28 Apr 2003 15:31:18 -0000	1.15
***************
*** 293,296 ****
--- 293,306 ----
          );
  
+       //
+       //If we ran a one-sided fetch and it yielded no limit information, then 
+       //bug out now.
+       if(list.size() <= 0){
+         throw new apollo.dataadapter.DataAdapterException(
+           "No dna-dna alignments were found for the selected range - "+
+           " I cannot infer the corresponding range on the hit species"
+         );
+       }//end if
+ 
        findLimitsOfAligns(list, curationSet);
  
***************
*** 447,450 ****
--- 457,470 ----
          );
  
+       //
+       //If we ran a one-sided fetch and it yielded no limit information, then 
+       //bug out now.
+       if(list.size() <= 0){
+         throw new apollo.dataadapter.DataAdapterException(
+           "No protein alignments were found for the selected range - "+
+           " I cannot infer the corresponding range on the hit species"
+         );
+       }//end if
+       
        //
        //This so the single-species fetch that follows this compara-fetch