X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=f3c3a4e9827af72700e11bfb32286cd39fe51b35;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=3e4a82b6ca34724d3a69455499fa535e3866236d;hpb=08cc3b53619f49a365d7346c3cc8d7a5ddd1b455;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3e4a82b..f3c3a4e 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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 +662,8 @@ 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")
-            .form(pid));
-
-    output.append(NEWLINE).append(
-            "Mapping method: Needleman & Wunsch Alignment");
+    output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
     try
     {
       os.print(output.toString());