X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FPfamFile.java;h=7cb381daa99eb59e8a114b774d5351e87ba285bb;hb=811f68c1dc1e4c409751b785203ed0a7289529b3;hp=a6c7a4f3e4edbe66718502f825a7ab6adaf27a40;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index a6c7a4f..7cb381d 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -27,17 +27,11 @@ import jalview.util.*;
 public class PfamFile
     extends AlignFile
 {
-  Vector ids;
 
   public PfamFile()
   {
   }
 
-  public PfamFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public PfamFile(String inFile, String type)
       throws IOException
   {
@@ -47,11 +41,9 @@ public class PfamFile
   public void initData()
   {
     super.initData();
-    ids = new Vector();
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     int i = 0;
     String line;
@@ -113,65 +105,16 @@ public class PfamFile
               .length();
         }
 
-        String head = headers.elementAt(i).toString();
-        int start = 1;
-        int end = seqhash.get(headers.elementAt(i)).toString().length();
-
-        if (head.indexOf("/") > 0)
-        {
-          StringTokenizer st = new StringTokenizer(head, "/");
-
-          if (st.countTokens() == 2)
-          {
-            ids.addElement(st.nextToken());
-
-            String tmp = st.nextToken();
-            st = new StringTokenizer(tmp, "-");
-
-            if (st.countTokens() == 2)
-            {
-              start = Integer.valueOf(st.nextToken()).intValue();
-              end = Integer.valueOf(st.nextToken()).intValue();
-            }
-            else
-            {
-              start = -1;
-              end = -1;
-            }
-          }
-          else
-          {
-            ids.addElement(headers.elementAt(i));
-          }
-        }
-        else
-        {
-          ids.addElement(headers.elementAt(i));
-        }
-
-        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);
-        }
+        Sequence newSeq = parseId(headers.elementAt(i).toString());
+        newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());
+        seqs.addElement(newSeq);
 
         if (!isValidProteinSequence(newSeq.getSequence()))
         {
-          throw new IOException(
-              "Not a valid protein sequence - (PFAM input)");
+          throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                                +" : "+ newSeq.getName()
+                                +" : "+invalidCharacter);
         }
       }
       else
@@ -182,7 +125,7 @@ public class PfamFile
     }
   }
 
-  public static String print(SequenceI[] s)
+  public String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer("");
 
@@ -193,12 +136,11 @@ public class PfamFile
 
     while ( (i < s.length) && (s[i] != null))
     {
-      String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
-          s[i].getEnd();
+      String tmp = printId(s[i]);
 
-      if (s[i].getSequence().length() > max)
+      if (s[i].getSequence().length > max)
       {
-        max = s[i].getSequence().length();
+        max = s[i].getSequence().length;
       }
 
       if (tmp.length() > maxid)
@@ -218,10 +160,9 @@ public class PfamFile
 
     while ( (j < s.length) && (s[j] != null))
     {
-      out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
-          "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
+      out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));
 
-      out.append(s[j].getSequence() + "\n");
+      out.append(s[j].getSequenceAsString() + "\n");
       j++;
     }