X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FClustalFile.java;h=2ea1d2f3017c8588b0fe60745fd4cf153ba70520;hb=424a0faf266f649090f17dc65246cdfb4111217e;hp=71e86b354208977ef26825e91032fe0e8e055155;hpb=bacb105d85f7d068c8cd643cd337b832aeb80343;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 71e86b3..2ea1d2f 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -27,7 +27,6 @@ import jalview.util.*;
 public class ClustalFile
     extends AlignFile
 {
-  Vector ids;
 
   public ClustalFile()
   {
@@ -47,18 +46,18 @@ 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 +65,13 @@ 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 +79,6 @@ public class ClustalFile
             {
               if (flag)
               {
-                StringBuffer tempseq;
-
                 if (seqhash.containsKey(id))
                 {
                   tempseq = (StringBuffer) seqhash.get(id);
@@ -105,6 +101,8 @@ public class ClustalFile
               }
             }
           }
+          else
+            flag = true;
         }
       }
     }
@@ -121,9 +119,6 @@ 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()
@@ -133,40 +128,16 @@ public class ClustalFile
                 .length();
           }
 
-          String head = headers.elementAt(i).toString();
-
-          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);
         }
@@ -185,7 +156,7 @@ public class ClustalFile
     return print(getSeqsAsArray());
   }
 
-  public static String print(SequenceI[] s)
+  public String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer("CLUSTAL\n\n");
 
@@ -196,8 +167,7 @@ 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)
       {
@@ -228,8 +198,7 @@ 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;