From 0b49125cd94fa3b7ebe7fada108e8b549ffe540e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 22 Aug 2005 15:53:24 +0000
Subject: [PATCH] fixed hanging on job finished bug.

---
 src/jalview/io/JPredFile.java |  142 ++++++++++++++++++++---------------------
 1 file changed, 71 insertions(+), 71 deletions(-)

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 901c204..5483f94 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,26 +1,26 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
 
-/**
- * PredFile.java
- * JalviewX / Vamsas Project
- * JPred.seq.concise reader
+/**
+ * PredFile.java
+ * JalviewX / Vamsas Project
+ * JPred.seq.concise reader
  */
 package jalview.io;
 
@@ -121,8 +121,8 @@ public class JPredFile extends AlignFile
         conf = null;
     }
 
-    /**
- * parse a JPred concise file into a sequence-alignment like object.
+    /**
+ * parse a JPred concise file into a sequence-alignment like object.
  */
     public void parse() throws IOException
     {
@@ -245,7 +245,7 @@ public class JPredFile extends AlignFile
 
                     while (ids.lastIndexOf(name) > -1)
                     {
-                        name = id.substring(id.indexOf(";") + 1) + "_" + 1;
+                        name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
                     }
 
                     ids.addElement(name);
@@ -307,10 +307,10 @@ public class JPredFile extends AlignFile
         }
     }
 
-    /**
- * print
- *
- * @return String
+    /**
+ * print
+ *
+ * @return String
    */
     public String print()
     {
@@ -344,47 +344,47 @@ public class JPredFile extends AlignFile
 }
 
 
-/*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
-  out.append(s[0].sequence.substring(i, i + 1) + " ");
-  out.append(s[1].sequence.substring(i, i + 1) + " ");
-  out.append(s[1].score[0].elementAt(i) + " ");
-  out.append(s[1].score[1].elementAt(i) + " ");
-  out.append(s[1].score[2].elementAt(i) + " ");
-  out.append(s[1].score[3].elementAt(i) + " ");
-
-  out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
-    public static void main(String[] args)
- {
-  try
-  {
-    BLCFile blc = new BLCFile(args[0], "File");
-    DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
-    for (int i = 0; i < blc.seqs.size(); i++)
-    {
-      s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
-    }
-    String out = BLCFile.print(s);
-
-    AlignFrame af = new AlignFrame(null, s);
-    af.resize(700, 500);
-    af.show();
-    System.out.println(out);
-  }
-  catch (java.io.IOException e)
-  {
-    System.out.println("Exception " + e);
-  }
- }
-
- }
+/*
+ StringBuffer out = new StringBuffer();
+
+ out.append("START PRED\n");
+ for (int i = 0; i < s[0].sequence.length(); i++)
+ {
+  out.append(s[0].sequence.substring(i, i + 1) + " ");
+  out.append(s[1].sequence.substring(i, i + 1) + " ");
+  out.append(s[1].score[0].elementAt(i) + " ");
+  out.append(s[1].score[1].elementAt(i) + " ");
+  out.append(s[1].score[2].elementAt(i) + " ");
+  out.append(s[1].score[3].elementAt(i) + " ");
+
+  out.append("\n");
+ }
+ out.append("END PRED\n");
+ return out.toString();
+ }
+
+    public static void main(String[] args)
+ {
+  try
+  {
+    BLCFile blc = new BLCFile(args[0], "File");
+    DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
+    for (int i = 0; i < blc.seqs.size(); i++)
+    {
+      s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
+    }
+    String out = BLCFile.print(s);
+
+    AlignFrame af = new AlignFrame(null, s);
+    af.resize(700, 500);
+    af.show();
+    System.out.println(out);
+  }
+  catch (java.io.IOException e)
+  {
+    System.out.println("Exception " + e);
+  }
+ }
+
+ }
  */
-- 
1.7.10.2