X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=8958f7b9d5259d60b28173db9f6010ce65b968e0;hb=7157dfd20efd2e1db47db1ac12e879eb51c67b92;hp=8db0a9ad177152cb4d5fc1e903b8c4259d2e49e4;hpb=2bb0a2c4156ec75795c595df0c6300411557b066;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 8db0a9a..8958f7b 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,5 +1,6 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
@@ -13,55 +14,76 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
 import java.util.*;
-import java.net.*;
-import java.awt.Font;
 
-public class BLCFile extends AlignFile {
+import jalview.datamodel.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BLCFile
+    extends AlignFile
+{
   Vector titles;
 
+  /**
+   * Creates a new BLCFile object.
+   */
   public BLCFile()
-  {}
+  {
+  }
 
-  public BLCFile(String inStr) {
-    super(inStr);
+  /**
+   * Creates a new BLCFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public BLCFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
   }
 
-  public void initData() {
+  /**
+   * DOCUMENT ME!
+   */
+  public void initData()
+  {
     super.initData();
     titles = new Vector();
   }
 
-  public BLCFile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
-
-
+  /**
+   * DOCUMENT ME!
+   */
   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{
+    boolean idsFound = false;
+    StringBuffer[] seqstrings;
+
+    String line = null;
+
+    do
+    {
       line = nextLine();
 
       // seek end of ids
       if (line.indexOf("*") > -1)
       {
-        idsFound=true;
+        idsFound = true;
+
         break;
       }
 
@@ -69,80 +91,118 @@ public class BLCFile extends AlignFile {
 
       if (abracket > -1)
       {
+        line = line.substring(abracket + 1);
 
-        if(line.indexOf(" ")>-1)
-        {
-          ids.addElement(line.substring(abracket+1, line.indexOf(" ", abracket+1)));
-          starts.addElement("0");
-          ends.addElement("0");
-        }
-        else
-        {
-          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));
-        }
+        Sequence seq = parseId(line);
+        seqs.addElement(seq);
       }
-    }while(!idsFound);
+    }
+    while (!idsFound);
 
     int starCol = line.indexOf("*");
-    seqstrings = new StringBuffer[ids.size()];
-    for(int i=0; i<ids.size(); i++)
+    seqstrings = new StringBuffer[seqs.size()];
+
+    for (int i = 0; i < seqs.size(); i++)
     {
-      if(seqstrings[i]==null)
+      if (seqstrings[i] == null)
+      {
         seqstrings[i] = new StringBuffer();
+      }
     }
 
-    while ((line = nextLine()).indexOf("*")==-1)
+    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)
+        if (line.length() > (i + starCol))
+        {
           seqstrings[i].append(line.charAt(i + starCol));
+        }
       }
     }
 
-    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);
+
+      newSeq.setSequence(seqstrings[i].toString());
     }
 
-   }catch(Exception ex){ex.printStackTrace();}
   }
 
-  public String print() {
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
     return print(getSeqsAsArray());
   }
-  public static String print(SequenceI[] s) {
-    StringBuffer out = new StringBuffer();
 
-    int i=0;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  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");
-      if (s[i].getSequence().length() > max) { max = s[i].getSequence().length();}
+
+    while ( (i < s.length) && (s[i] != null))
+    {
+      out.append(">" + printId(s[i]));
+      if (s[i].getDescription() != null)
+      {
+        out.append(" " + s[i].getDescription());
+      }
+
+      out.append("\n");
+
+      if (s[i].getSequence().length > max)
+      {
+        max = s[i].getSequence().length;
+      }
+
       i++;
     }
 
-      out.append("* iteration 1\n");
-      for (int j = 0; j < max; j++) {
-        i=0;
-        while (i < s.length && s[i] != null) {
-          if(s[i].getSequence().length()>j )
-            out.append(s[i].getSequence().substring(j,j+1));
-          else
-            out.append("-");
-          i++;
+    out.append("* iteration 1\n");
+
+    for (int j = 0; j < max; j++)
+    {
+      i = 0;
+
+      while ( (i < s.length) && (s[i] != null))
+      {
+        if (s[i].getSequence().length > j)
+        {
+          out.append(s[i].getSequenceAsString(j, j + 1));
+        }
+        else
+        {
+          out.append("-");
         }
-        out.append("\n");
+
+        i++;
       }
+
+      out.append("\n");
+    }
+
     out.append("*\n");
-    return out.toString();
 
+    return out.toString();
   }
 }