X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=04867a2a8b2ab786889c0a21c13c93b30441f433;hb=6af1258218f8fdbb2d9d6794e72db4c41ec8bf48;hp=0edcb63556fc402b41d1a9fdb3f0d9dcbc0b2657;hpb=378126d607a06854e8752d156120462459364586;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 0edcb63..04867a2 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.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
@@ -42,15 +42,6 @@ public class BLCFile extends AlignFile
     {
     }
 
-    /**
-     * Creates a new BLCFile object.
-     *
-     * @param inStr DOCUMENT ME!
-     */
-    public BLCFile(String inStr)
-    {
-        super(inStr);
-    }
 
     /**
      * Creates a new BLCFile object.
@@ -77,18 +68,13 @@ public class BLCFile extends AlignFile
     /**
      * DOCUMENT ME!
      */
-    public void parse()
+    public void parse() throws IOException
     {
         boolean idsFound = false;
-        Vector ids = new Vector();
         StringBuffer[] seqstrings;
-        Vector starts = new Vector();
-        Vector ends = new Vector();
 
         String line = null;
 
-        try
-        {
             do
             {
                 line = nextLine();
@@ -105,68 +91,18 @@ public class BLCFile extends AlignFile
 
                 if (abracket > -1)
                 {
-                    if (line.indexOf(" ") > -1) //
-                    {
-                        ///Colur it be this format?
-                        //>54402046         0             1   137   137:
-                        // or this??
-                        //     1   >L1H14       30539  343
-                        try
-                        {
-                            ids.addElement(line.substring(abracket + 1,
-                                    line.indexOf(" ", abracket + 1)));
-
-                            // remove p Value
-                            line = line.substring(abracket + 1);
-                            line = line.substring(line.indexOf(" ") + 1);
-                            line = line.trim();
-                            line = line.substring(line.indexOf(" ") + 1);
-                            line = line.trim();
-
-                            int value = Integer.parseInt(line.substring(0,
-                                        line.indexOf(" ")));
-                            starts.addElement(value + "");
-                            line = line.substring(line.indexOf(" ") + 1);
-                            line = line.trim();
-                            value = Integer.parseInt(line.substring(0,
-                                        line.indexOf(" ")));
-                            ends.addElement(value + "");
-                        }
-                        catch (Exception ex)
-                        {
-                            System.err.println("Error during blockfile read.");
-                            ex.printStackTrace();
-                            starts.addElement("1");
-                            ends.addElement("-1");
-                        }
-                    }
-                    else
-                    {
-                        if (line.indexOf("/") > -1)
-                        {
-                            ids.addElement(line.substring(abracket + 1,
-                                    line.indexOf("/")));
-                            line = line.substring(line.indexOf("/") + 1);
-                            starts.addElement(line.substring(0,
-                                    line.indexOf("-")));
-                            ends.addElement(line.substring(line.indexOf("-") +
-                                    1));
-                        }
-                        else
-                        {
-                            ids.addElement(line.substring(abracket + 1));
-                            starts.addElement("1");
-                            ends.addElement("-1");
-                        }
-                    }
+                  line = line.substring(abracket+1);
+
+                  Sequence seq = parseId(line);
+                  seqs.addElement(seq);
                 }
             }
             while (!idsFound);
 
             int starCol = line.indexOf("*");
-            seqstrings = new StringBuffer[ids.size()];
+            seqstrings = new StringBuffer[seqs.size()];
 
-            for (int i = 0; i < ids.size(); i++)
+            for (int i = 0; i < seqs.size(); i++)
             {
                 if (seqstrings[i] == null)
                 {
@@ -176,7 +112,7 @@ public class BLCFile extends AlignFile
 
             while ((line = nextLine()).indexOf("*") == -1)
             {
-                for (int i = 0; i < ids.size(); i++)
+                for (int i = 0; i < seqs.size(); i++)
                 {
                     if (line.length() > (i + starCol))
                     {
@@ -185,19 +121,20 @@ public class BLCFile extends AlignFile
                 }
             }
 
-            for (int i = 0; i < ids.size(); i++)
+            for (int i = 0; i < seqs.size(); i++)
             {
-                Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                        seqstrings[i].toString(),
-                        Integer.parseInt(starts.elementAt(i).toString()),
-                        Integer.parseInt(ends.elementAt(i).toString()));
-                seqs.addElement(newSeq);
+              Sequence newSeq = (Sequence) seqs.elementAt(i);
+
+              if (!isValidProteinSequence(newSeq.getSequence()))
+              {
+                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                               +" : "+ newSeq.getName()
+                               +" : "+invalidCharacter);
+              }
+
+              newSeq.setSequence(seqstrings[i].toString());
             }
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+
     }
 
     /**
@@ -217,21 +154,30 @@ public class BLCFile extends AlignFile
      *
      * @return DOCUMENT ME!
      */
-    public static String print(SequenceI[] s)
+    public String print(SequenceI[] s)
     {
         StringBuffer out = new StringBuffer();
-
+        /**
+         * A general parser for ids. Will look for dbrefs in
+         * Uniprot format source|id
+         * And also Jalview /start-end
+         *
+         * @String id Id to be parsed
+     */
         int i = 0;
         int max = -1;
 
         while ((i < s.length) && (s[i] != null))
         {
-            out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +
-                s[i].getEnd() + "\n");
+            out.append(">" + printId(s[i]));
+            if(s[i].getDescription()!=null)
+              out.append(" "+s[i].getDescription());
+
+            out.append("\n");
 
-            if (s[i].getSequence().length() > max)
+            if (s[i].getSequence().length > max)
             {
-                max = s[i].getSequence().length();
+                max = s[i].getSequence().length;
             }
 
             i++;
@@ -245,9 +191,9 @@ public class BLCFile extends AlignFile
 
             while ((i < s.length) && (s[i] != null))
             {
-                if (s[i].getSequence().length() > j)
+                if (s[i].getSequence().length > j)
                 {
-                    out.append(s[i].getSequence().substring(j, j + 1));
+                    out.append(s[i].getSequenceAsString(j, j + 1));
                 }
                 else
                 {