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 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -316,7 +316,11 @@ public class MSFfile extends AlignFile
         i=0;\r
         while ((i < s.length) && (s[i] != null))\r
         {\r
-            nameBlock[i] = new String("  Name: " + s[i].getName() + " ");\r
+\r
+            nameBlock[i] = new String("  Name: " + s[i].getName()\r
+                                      + "/" + s[i].getStart() + "-" + s[i].getEnd()\r
+                                      +" ");\r
+\r
             idBlock[i] = new String("Len: " +\r
                     maxLenpad.form(s[i].getSequence().length()) + "  Check: " +\r
                     maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");\r
@@ -370,7 +374,11 @@ public class MSFfile extends AlignFile
             while ((j < s.length) && (s[j] != null))\r
             {\r
                 String name = s[j].getName();\r
-                out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
+              //  out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
+\r
+                out.append(new Format("%-" + maxid + "s").form(name\r
+                   + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+\r
 \r
                 for (int k = 0; k < 5; k++)\r
                 {\r

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 87a1652..8c8a3ea 100755 (executable)
--- 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))\r
     {\r
       String seq = s[i].getSequence();\r
-      out.append(" Name: " + s[i].getName() + " oo  Len:  " +\r
+      out.append(" Name: " + s[i].getName() +\r
+                   "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+                 " oo  Len:  " +\r
                  s[i].getSequence().length() + "  Check:  " + checksums[i] +\r
                  "  Weight:  1.00\n");\r
 \r
@@ -258,7 +260,10 @@ public class PileUpfile
       while ( (j < s.length) && (s[j] != null))\r
       {\r
         String name = s[j].getName();\r
-        out.append(new Format("%-" + maxid + "s").form(name) + " ");\r
+       // out.append(new Format("%-" + maxid + "s").form(name) + " ");\r
+\r
+         out.append(new Format("%-" + maxid + "s").form(name\r
+          + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
 \r
         for (int k = 0; k < 5; k++)\r
         {\r