From bacb105d85f7d068c8cd643cd337b832aeb80343 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 29 Jul 2005 09:53:09 +0000
Subject: [PATCH] use 1 & -1 if start/end not specified

---
 src/jalview/io/BLCFile.java     |    4 +--
 src/jalview/io/ClustalFile.java |    4 +--
 src/jalview/io/MSFfile.java     |    2 +-
 src/jalview/io/PIRFile.java     |   51 +++++++++++++++++++++++++++------------
 src/jalview/io/PfamFile.java    |   28 +++++----------------
 src/jalview/io/PileUpfile.java  |    2 +-
 6 files changed, 46 insertions(+), 45 deletions(-)

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 074e6ce..ab41f08 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -155,8 +155,8 @@ public class BLCFile extends AlignFile
                         else
                         {
                             ids.addElement(line.substring(abracket + 1));
-                            starts.addElement("0");
-                            ends.addElement("0");
+                            starts.addElement("1");
+                            ends.addElement("-1");
                         }
                     }
                 }
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 74cb2d0..71e86b3 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -121,7 +121,7 @@ public class ClustalFile
       //Add sequences to the hash
       for (i = 0; i < headers.size(); i++)
       {
-        int start = -1;
+        int start = 1;
         int end = -1;
 
         if (seqhash.get(headers.elementAt(i)) != null)
@@ -134,8 +134,6 @@ public class ClustalFile
           }
 
           String head = headers.elementAt(i).toString();
-          start = 1;
-          end = seqhash.get(headers.elementAt(i)).toString().length();
 
           if (head.indexOf("/") > 0)
           {
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 5f81215..8e452e6 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -151,7 +151,7 @@ public class MSFfile extends AlignFile
                 String seq = seqhash.get(head).toString();
 
                 int start = 1;
-                int end = seq.length();
+                int end =  -1;
 
                 if (maxLength < head.length())
                 {
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index a15a4cb..0a24601 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -56,19 +56,33 @@ public class PIRFile
 
       while ( (line = nextLine()) != null)
       {
-        try
+        if(line.length()==0)
         {
-          id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
-          line = line.substring(line.indexOf("/") + 1);
-          start = line.substring(0, line.indexOf("-"));
-          end = line.substring(line.indexOf("-") + 1);
+          //System.out.println("blank line");
+          continue;
         }
-        catch (Exception ex)
+
+        id = "No id";
+        start = "1";
+        end = "-1";
+
+        try
         {
-          id = "No id";
-          start = "0";
-          end = "0";
+          int slashIndex = line.indexOf("/");
+          if(slashIndex!=-1)
+          {
+            id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
+            line = line.substring(line.indexOf("/") + 1);
+            start = line.substring(0, line.indexOf("-"));
+            end = line.substring(line.indexOf("-") + 1);
+          }
+          else
+          {
+            id = line.substring(line.indexOf(";")+1);
+          }
         }
+        catch (Exception ex)
+        {    }// Default id, start and end unchanged
 
         sequence = new StringBuffer();
 
@@ -76,24 +90,29 @@ public class PIRFile
 
         boolean starFound = false;
 
-        do
+        while(!starFound)
         {
           line = nextLine();
           sequence.append(line);
 
+          if (line == null)
+            break;
+
           if (line.indexOf("*") > -1)
           {
             starFound = true;
           }
         }
-        while (!starFound);
 
-        sequence.setLength(sequence.length() - 1);
+        if(sequence.length()>0)
+        {
+          sequence.setLength(sequence.length() - 1);
 
-        Sequence newSeq = new Sequence(id, sequence.toString(),
-                                       Integer.parseInt(start),
-                                       Integer.parseInt(end));
-        seqs.addElement(newSeq);
+          Sequence newSeq = new Sequence(id, sequence.toString(),
+                                         Integer.parseInt(start),
+                                         Integer.parseInt(end));
+          seqs.addElement(newSeq);
+        }
       }
     }
     catch (Exception ex)
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index a6c7a4f..9a6ca54 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -115,7 +115,7 @@ public class PfamFile
 
         String head = headers.elementAt(i).toString();
         int start = 1;
-        int end = seqhash.get(headers.elementAt(i)).toString().length();
+        int end = -1;
 
         if (head.indexOf("/") > 0)
         {
@@ -133,11 +133,6 @@ public class PfamFile
               start = Integer.valueOf(st.nextToken()).intValue();
               end = Integer.valueOf(st.nextToken()).intValue();
             }
-            else
-            {
-              start = -1;
-              end = -1;
-            }
           }
           else
           {
@@ -151,22 +146,11 @@ public class PfamFile
 
         Sequence newSeq = null;
 
-        if ( (start != -1) && (end != -1))
-        {
-          newSeq = new Sequence(ids.elementAt(i).toString(),
-                                seqhash.get(headers.elementAt(i).toString())
-                                .toString(), start, end);
-          seqs.addElement(newSeq);
-        }
-        else
-        {
-          newSeq = new Sequence(ids.elementAt(i).toString(),
-                                seqhash.get(headers.elementAt(i).toString())
-                                .toString(), 1,
-                                seqhash.get(headers.elementAt(i).toString())
-                                .toString().length());
-          seqs.addElement(newSeq);
-        }
+        newSeq = new Sequence(ids.elementAt(i).toString(),
+                              seqhash.get(headers.elementAt(i).toString())
+                              .toString(), start, end);
+        seqs.addElement(newSeq);
+
 
         if (!isValidProteinSequence(newSeq.getSequence()))
         {
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index c200c5e..728d1c6 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -131,7 +131,7 @@ public class PileUpfile
         String seq = seqhash.get(head).toString();
 
         int start = 1;
-        int end = seq.length();
+        int end = -1;
 
         if (maxLength < head.length())
         {
-- 
1.7.10.2