From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 5 Oct 2005 12:34:32 +0000 (+0000)
Subject: Sequence start end added for the time being
X-Git-Tag: Release_2_07~66
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2c56ea5abe1fa29c861beb02fb594ad807b307ed;p=jalview.git

Sequence start end added for the time being
---

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 8082ee3..2cef0fe 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -316,7 +316,11 @@ public class MSFfile extends AlignFile
         i=0;
         while ((i < s.length) && (s[i] != null))
         {
-            nameBlock[i] = new String("  Name: " + s[i].getName() + " ");
+
+            nameBlock[i] = new String("  Name: " + s[i].getName()
+                                      + "/" + s[i].getStart() + "-" + s[i].getEnd()
+                                      +" ");
+
             idBlock[i] = new String("Len: " +
                     maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
                     maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
@@ -370,7 +374,11 @@ public class MSFfile extends AlignFile
             while ((j < s.length) && (s[j] != null))
             {
                 String name = s[j].getName();
-                out.append(new Format("%-" + maxid + "s").form(name)+ " ");
+              //  out.append(new Format("%-" + maxid + "s").form(name)+ " ");
+
+                out.append(new Format("%-" + maxid + "s").form(name
+                   + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
+
 
                 for (int k = 0; k < 5; k++)
                 {
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 87a1652..8c8a3ea 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -217,7 +217,9 @@ public class PileUpfile
     while ( (i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequence();
-      out.append(" Name: " + s[i].getName() + " oo  Len:  " +
+      out.append(" Name: " + s[i].getName() +
+                   "/" + s[i].getStart() + "-" + s[i].getEnd() +
+                 " oo  Len:  " +
                  s[i].getSequence().length() + "  Check:  " + checksums[i] +
                  "  Weight:  1.00\n");
 
@@ -258,7 +260,10 @@ public class PileUpfile
       while ( (j < s.length) && (s[j] != null))
       {
         String name = s[j].getName();
-        out.append(new Format("%-" + maxid + "s").form(name) + " ");
+       // out.append(new Format("%-" + maxid + "s").form(name) + " ");
+
+         out.append(new Format("%-" + maxid + "s").form(name
+          + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
 
         for (int k = 0; k < 5; k++)
         {