[Genoviz-cmts] SF.net SVN: genoviz:[8690] trunk/genometryImpl/src/com/affymetrix/ genometryImpl/SeqSymSummarizer.java

[<hi...@us...>]

Revision: 8690
          http://genoviz.svn.sourceforge.net/genoviz/?rev=8690&view=rev
Author:   hiralv
Date:     2011-08-17 17:32:00 +0000 (Wed, 17 Aug 2011)

Log Message:
-----------
Fixing bug in mismatch graph when length was greater than buffer size.

Modified Paths:
--------------
    trunk/genometryImpl/src/com/affymetrix/genometryImpl/SeqSymSummarizer.java

Modified: trunk/genometryImpl/src/com/affymetrix/genometryImpl/SeqSymSummarizer.java
===================================================================
--- trunk/genometryImpl/src/com/affymetrix/genometryImpl/SeqSymSummarizer.java	2011-08-17 17:19:28 UTC (rev 8689)
+++ trunk/genometryImpl/src/com/affymetrix/genometryImpl/SeqSymSummarizer.java	2011-08-17 17:32:00 UTC (rev 8690)
@@ -78,16 +78,24 @@
 				}
 			}
 
-			for (int j = 0; j < length; j++) {
-				ch = cur_residues[j];
-				if (seq_residues[offset + j] != ch && ch != intron) {
-					y[offset - y_offset + j] += 1;
-				}
+			for (int j = 0; j < length; ) {
+				for(int l = 0; l < BUFFSIZE & j < length; l++, j++){
+					ch = cur_residues[j];
+					if (seq_residues[offset + j] != ch && ch != intron) {
+						y[offset - y_offset + j] += 1;
+					}
 
-				k = ResiduesChars.getValue((char)ch);
-				if(k > -1){
-					yR[k][offset - y_offset + j] += 1;
+					k = ResiduesChars.getValue((char)ch);
+					if(k > -1){
+						yR[k][offset - y_offset + j] += 1;
+					}
 				}
+				
+				if(length > BUFFSIZE){
+					minmax = MisMatchGraphSym.updateY(index, y_offset, BUFFSIZE, y, yR);
+					y = new int[BUFFSIZE];
+					y_offset = offset+BUFFSIZE;
+				}
 			}
 
 		}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.