From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 28 Oct 2015 11:45:20 +0000 (+0000)
Subject: JAL-1952 bugfix
X-Git-Tag: Release_2_10_0~341^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=5f2df50328b5b4e3ca082b8bf27360aaabc69e3a;p=jalview.git

JAL-1952 bugfix
---

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3e4a82b..369721d 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -577,18 +577,21 @@ public class AlignSeq
       }
     }
     int len = 72 - maxid - 1;
-    int nochunks = ((aseq1.length - count) / len) + 1;
+    int nochunks = ((aseq1.length - count) / len)
+            + ((aseq1.length - count) % len > 0 ? 1 : 0);
     pid = 0;
 
-    output.append("Sequence \u27f7 Structure mapping details: ")
-            .append(NEWLINE);
+    output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
+    output.append("Length of alignment = ")
+            .append(String.valueOf(aseq1.length - count)).append(NEWLINE);
+    output.append("Sequence ");
     output.append(new Format("%" + maxid + "s").form(s1.getName()));
     output.append(" :  ").append(String.valueOf(s1.getStart()))
             .append(" - ").append(String.valueOf(s1.getEnd()));
     output.append(" (Sequence length = ")
             .append(String.valueOf(s1str.length())).append(")")
             .append(NEWLINE);
-    // output.append("Sequence ");
+    output.append("Sequence ");
     output.append(new Format("%" + maxid + "s").form(s2.getName()));
     output.append(" :  ").append(String.valueOf(s2.getStart()))
             .append(" - ").append(String.valueOf(s2.getEnd()));
@@ -596,7 +599,6 @@ public class AlignSeq
             .append(String.valueOf(s2str.length())).append(")")
             .append(NEWLINE).append(NEWLINE);
 
-    // output mappings
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
@@ -660,16 +662,9 @@ public class AlignSeq
       output.append(NEWLINE).append(NEWLINE);
     }
 
-    output.append("Length of alignment = ")
-            .append(String.valueOf(aseq1.length - count)).append(NEWLINE);
-    output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
-
     pid = pid / (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n\n")
+    output = output.append(new Format("Percentage ID = %2.2f\n")
             .form(pid));
-
-    output.append(NEWLINE).append(
-            "Mapping method: Needleman & Wunsch Alignment");
     try
     {
       os.print(output.toString());