From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Sep 2015 16:20:13 +0000 (+0100)
Subject: JAL-1853 make getVisibleSeqs more memory efficient by clipping sequences as the seque... 
X-Git-Tag: Release_2_10_0~514^2~3^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=29134e3225e8fd45d5c2c3067e79779577997f51;p=jalview.git

JAL-1853 make getVisibleSeqs more memory efficient by clipping sequences as the sequence vector is populated
---

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 7ccd9cf..e089a11 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -474,12 +474,8 @@ public class AlignmentView
     for (int i = 0, j = sequences.length; i < j; i++)
     {
       aln[i] = sequences[i].getSeq(c);
-    }
-    // Remove hidden regions from sequence objects.
-    String seqs[] = getSequenceStrings(c);
-    for (int i = 0, j = aln.length; i < j; i++)
-    {
-      aln[i].setSequence(seqs[i]);
+      // Remove hidden regions from sequence
+      aln[i].setSequence(getASequenceString(c, i));
     }
     return aln;
   }