X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=b43e3ead651d9237ab44f18627f9647db41ae572;hb=dad6e1eb4bd44e9f70e4bbb5f3a7da6e25a917bd;hp=74cb2d0b32548f81c6cf86396da0075025cdceef;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 74cb2d0..b43e3ea 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.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 ClustalFile
     extends AlignFile
 {
-  Vector ids;
 
   public ClustalFile()
   {
   }
 
-  public ClustalFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public ClustalFile(String inFile, String type)
       throws IOException
   {
@@ -47,18 +41,18 @@ public class ClustalFile
   public void initData()
   {
     super.initData();
-    ids = new Vector();
   }
 
-  public void parse()
+  public void parse() throws IOException
   {
     int i = 0;
     boolean flag = false;
 
     Vector headers = new Vector();
     Hashtable seqhash = new Hashtable();
-
-    String line;
+    StringBuffer tempseq;
+    String line, id;
+    StringTokenizer str;
 
     try
     {
@@ -66,14 +60,13 @@ public class ClustalFile
       {
         if (line.indexOf(" ") != 0)
         {
-          StringTokenizer str = new StringTokenizer(line, " ");
-          String id = "";
+          str = new StringTokenizer(line, " ");
 
           if (str.hasMoreTokens())
           {
             id = str.nextToken();
 
-            if (id.equals("CLUSTAL"))
+            if (id.equalsIgnoreCase("CLUSTAL"))
             {
               flag = true;
             }
@@ -81,8 +74,6 @@ public class ClustalFile
             {
               if (flag)
               {
-                StringBuffer tempseq;
-
                 if (seqhash.containsKey(id))
                 {
                   tempseq = (StringBuffer) seqhash.get(id);
@@ -105,6 +96,8 @@ public class ClustalFile
               }
             }
           }
+          else
+            flag = true;
         }
       }
     }
@@ -121,9 +114,6 @@ public class ClustalFile
       //Add sequences to the hash
       for (i = 0; i < headers.size(); i++)
       {
-        int start = -1;
-        int end = -1;
-
         if (seqhash.get(headers.elementAt(i)) != null)
         {
           if (maxLength < seqhash.get(headers.elementAt(i)).toString()
@@ -133,42 +123,16 @@ public class ClustalFile
                 .length();
           }
 
-          String head = headers.elementAt(i).toString();
-          start = 1;
-          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, "-");
+          Sequence newSeq = parseId(headers.elementAt(i).toString());
+          newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );
 
-              if (st.countTokens() == 2)
-              {
-                start = Integer.valueOf(st.nextToken())
-                    .intValue();
-                end = Integer.valueOf(st.nextToken()).intValue();
-              }
-            }
-            else
-            {
-              ids.addElement(headers.elementAt(i));
-            }
-          }
-          else
+          if (!isValidProteinSequence(newSeq.getSequence()))
           {
-            ids.addElement(headers.elementAt(i));
+              throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                                    + " : " + newSeq.getName()
+                                    + " : " + invalidCharacter);
           }
 
-          Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                                         seqhash.get(headers.elementAt(i).
-              toString())
-                                         .toString(), start, end);
 
           seqs.addElement(newSeq);
         }
@@ -187,7 +151,7 @@ public class ClustalFile
     return print(getSeqsAsArray());
   }
 
-  public static String print(SequenceI[] s)
+  public String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer("CLUSTAL\n\n");
 
@@ -198,12 +162,11 @@ public class ClustalFile
 
     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)
@@ -230,22 +193,21 @@ public class ClustalFile
 
       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]) + " "));
 
         int start = i * len;
         int end = start + len;
 
-        if ( (end < s[j].getSequence().length()) &&
-            (start < s[j].getSequence().length()))
+        if ( (end < s[j].getSequence().length) &&
+            (start < s[j].getSequence().length))
         {
-          out.append(s[j].getSequence().substring(start, end));
+          out.append(s[j].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length())
+          if (start < s[j].getSequence().length)
           {
-            out.append(s[j].getSequence().substring(start));
+            out.append(s[j].getSequenceAsString().substring(start));
           }
         }