JAL-1479 added basic support for SIFTs mapping - more work to follow

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 527b1ff..3e4a82b 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -580,17 +580,15 @@ public class AlignSeq
     int nochunks = ((aseq1.length - count) / len) + 1;
     pid = 0;
 
-    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("Sequence \u27f7 Structure mapping details: ")
+            .append(NEWLINE);
     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()));
@@ -598,6 +596,7 @@ 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
@@ -661,10 +660,16 @@ 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");
     try
     {
       os.print(output.toString());