X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFastaFile.java;h=c69b8ce6804530264c3cfe5111cd3342ebad9ddf;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=d5a6a663cb051acc25a7c9e4c0cd4585f4e58a91;hpb=6af1258218f8fdbb2d9d6794e72db4c41ec8bf48;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index d5a6a66..c69b8ce 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,29 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
 
-import java.util.*;
-
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -31,187 +28,190 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class FastaFile extends AlignFile
+public class FastaFile
+    extends AlignFile
 {
-    /**
-     * Creates a new FastaFile object.
-     */
-    public FastaFile()
-    {
-    }
-
-    /**
-     * Creates a new FastaFile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public FastaFile(String inFile, String type) throws IOException
-    {
-        super(inFile, type);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public void parse() throws IOException
+  /**
+   * Length of a sequence line
+   */
+  int len = 72;
+
+  StringBuffer out;
+
+  /**
+   * Creates a new FastaFile object.
+   */
+  public FastaFile()
+  {
+  }
+
+  /**
+   * Creates a new FastaFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public FastaFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public void parse()
+      throws IOException
+  {
+    StringBuffer sb = new StringBuffer();
+    boolean firstLine = true;
+
+    String line;
+    Sequence seq = null;
+
+    boolean annotation = false;
+
+    while ( (line = nextLine()) != null)
     {
-        StringBuffer sb = new StringBuffer();
-        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) == '>')
         {
-            line = line.trim();
-            if (line.length() > 0)
+          if (line.startsWith(">#_"))
+          {
+            if (annotation)
             {
-              if (line.charAt(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);
-                    }
-                    annotation = true;
-                  }
-                  else
-                    annotation = false;
-
-                    if (!firstLine)
-                    {
-                      if (!annotation && !isValidProteinSequence(sb.toString().toCharArray()))
-                      {
-                        throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
-                                              +" : "+seq.getName()
-                                              +" : "+invalidCharacter);
-                      }
-
-                       seq.setSequence(sb.toString());
-
-                       if (!annotation)
-                         seqs.addElement(seq);
-                    }
-
-                    seq = parseId(line.substring(1));
-                    firstLine = false;
-
-                    sb = new StringBuffer();
-                }
-                else
-                {
-                    sb.append(line);
-                }
+              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);
             }
-        }
-
-        if (annotation)
-        {
-          Annotation[] anots = new Annotation[sb.length()];
-          String anotString = sb.toString();
-          for (int i = 0; i < sb.length(); i++)
+          }
+          else
           {
-            anots[i] = new Annotation(anotString.substring(i, i + 1),
-                                      null,
-                                      ' ', 0);
+            annotation = false;
           }
-          AlignmentAnnotation aa = new AlignmentAnnotation(
-              seq.getName().substring(2), seq.getDescription(),
-              anots);
-
-          annotations.addElement(aa);
-        }
 
-        else if (!firstLine)
-        {
+          if (!firstLine)
+          {
+            seq.setSequence(sb.toString());
 
-            if (!isValidProteinSequence(sb.toString().toCharArray()))
+            if (!annotation)
             {
-                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
-                                      +" : "+seq.getName()
-                                      +" : "+invalidCharacter);
+              seqs.addElement(seq);
             }
+          }
 
-            seq.setSequence(sb.toString());
-            seqs.addElement(seq);
+          seq = parseId(line.substring(1));
+          firstLine = false;
+
+          sb = new StringBuffer();
+
+          if (line.startsWith(">#_"))
+          {
+            annotation = true;
+          }
         }
+        else
+        {
+          sb.append(line);
+        }
+      }
     }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param len DOCUMENT ME!
-     * @param gaps DOCUMENT ME!
-     * @param displayId DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print(SequenceI[] s)
+    if (annotation)
     {
-        int len = 72;
-        StringBuffer out = new StringBuffer();
-        int i = 0;
+      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);
+    }
 
-        while ((i < s.length) && (s[i] != null))
-        {
-            out.append(">" + printId(s[i]));
-            if(s[i].getDescription()!=null)
-              out.append(" "+s[i].getDescription());
+    else if (!firstLine)
+    {
+      seq.setSequence(sb.toString());
+      seqs.addElement(seq);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param len DOCUMENT ME!
+   * @param gaps DOCUMENT ME!
+   * @param displayId DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print(SequenceI[] s)
+  {
+    out = new StringBuffer();
+    int i = 0;
+
+    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");
+      out.append("\n");
 
-            int nochunks = (s[i].getLength() / len) + 1;
+      int nochunks = (s[i].getLength() / len) + 1;
 
-            for (int j = 0; j < nochunks; j++)
-            {
-                int start = j * len;
-                int end = start + len;
-
-                if (end < s[i].getLength())
-                {
-                    out.append(s[i].getSequenceAsString(start, end) + "\n");
-                }
-                else if (start < s[i].getLength())
-                {
-                    out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
-                }
-            }
+      for (int j = 0; j < nochunks; j++)
+      {
+        int start = j * len;
+        int end = start + len;
 
-            i++;
+        if (end < s[i].getLength())
+        {
+          out.append(s[i].getSequenceAsString(start, end) + "\n");
+        }
+        else if (start < s[i].getLength())
+        {
+          out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
         }
+      }
 
-        return out.toString();
+      i++;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print()
-    {
-        return print(getSeqsAsArray());
-    }
+    return out.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
 }