X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFastaFile.java;h=684f867f0fe28e123bb766a2dfb762629b256820;hb=558597672640984d936ea22409a674293192a09c;hp=37c96f600a5c9b1f34282255b7ad085088b10fd7;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 37c96f6..684f867 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.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
@@ -22,6 +22,8 @@ import jalview.datamodel.*;
 
 import java.io.*;
 
+import java.util.*;
+
 
 /**
  * DOCUMENT ME!
@@ -31,21 +33,18 @@ import java.io.*;
  */
 public class FastaFile extends AlignFile
 {
-    /**
-     * Creates a new FastaFile object.
-     */
-    public FastaFile()
-    {
-    }
+  /**
+   * Length of a sequence line
+   */
+  int len = 72;
+
+  StringBuffer out;
 
     /**
      * Creates a new FastaFile object.
-     *
-     * @param inStr DOCUMENT ME!
      */
-    public FastaFile(String inStr)
+    public FastaFile()
     {
-        super(inStr);
     }
 
     /**
@@ -69,27 +68,57 @@ public class FastaFile extends AlignFile
     public void parse() throws IOException
     {
         StringBuffer sb = new StringBuffer();
-        int count = 0;
+        boolean firstLine = true;
 
         String line;
         Sequence seq = null;
 
+        boolean annotation = false;
+
         while ((line = nextLine()) != null)
         {
+            line = line.trim();
             if (line.length() > 0)
             {
-                if (line.charAt(0)=='>')
+              if (line.charAt(0)=='>')
                 {
-                    if (count != 0)
+                  if (line.startsWith(">#_"))
+                  {
+                    if (annotation)
+                    {
+                      Annotation[] anots = new Annotation[sb.length()];
+                      String anotString = sb.toString();
+                      for (int i = 0; i < sb.length(); i++)
+                      {
+                        anots[i] = new Annotation(anotString.substring(i, i+1),
+                                                  null,
+                                                  ' ', 0);
+                      }
+                      AlignmentAnnotation aa = new AlignmentAnnotation(
+                          seq.getName().substring(2), seq.getDescription(),
+                          anots);
+
+                      annotations.addElement(aa);
+                    }
+                  }
+                  else
+                    annotation = false;
+
+                    if (!firstLine)
                     {
                        seq.setSequence(sb.toString());
-                       seqs.addElement(seq);
+
+                       if (!annotation)
+                         seqs.addElement(seq);
                     }
 
                     seq = parseId(line.substring(1));
+                    firstLine = false;
 
-                    count++;
                     sb = new StringBuffer();
+
+                    if (line.startsWith(">#_"))
+                      annotation = true;
                 }
                 else
                 {
@@ -98,19 +127,30 @@ public class FastaFile extends AlignFile
             }
         }
 
-        if (count > 0)
+        if (annotation)
         {
-            if (!isValidProteinSequence(sb.toString().toUpperCase()))
-            {
-                throw new IOException("Invalid protein sequence");
-            }
+          Annotation[] anots = new Annotation[sb.length()];
+          String anotString = sb.toString();
+          for (int i = 0; i < sb.length(); i++)
+          {
+            anots[i] = new Annotation(anotString.substring(i, i + 1),
+                                      null,
+                                      ' ', 0);
+          }
+          AlignmentAnnotation aa = new AlignmentAnnotation(
+              seq.getName().substring(2), seq.getDescription(),
+              anots);
+
+          annotations.addElement(aa);
+        }
 
+        else if (!firstLine)
+        {
             seq.setSequence(sb.toString());
             seqs.addElement(seq);
         }
     }
 
-
     /**
      * DOCUMENT ME!
      *
@@ -123,8 +163,7 @@ public class FastaFile extends AlignFile
      */
     public String print(SequenceI[] s)
     {
-        int len = 72;
-        StringBuffer out = new StringBuffer();
+        out = new StringBuffer();
         int i = 0;
 
         while ((i < s.length) && (s[i] != null))
@@ -144,11 +183,11 @@ public class FastaFile extends AlignFile
 
                 if (end < s[i].getLength())
                 {
-                    out.append(s[i].getSequence(start, end) + "\n");
+                    out.append(s[i].getSequenceAsString(start, end) + "\n");
                 }
                 else if (start < s[i].getLength())
                 {
-                    out.append(s[i].getSequence(start, s[i].getLength()) + "\n");
+                    out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
                 }
             }