X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=61c2331465e952492f73174cc456fff1376a5ac3;hb=e6d5a919ade2b070a34f40683c8664b684f76cde;hp=dba0c61d3e84677672b8e0d78a53b782d7180d43;hpb=b3f66e3a4fd8d3f24a5a44f8716a41c84c4d1cb3;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index dba0c61..61c2331 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,81 +1,166 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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.util.Vector;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class FormatAdapter
 {
+    /** DOCUMENT ME!! */
+    public static final Vector formats = new Vector();
 
-  public static Vector formats = new Vector();
-  static{
-    formats.addElement("FASTA");
-    formats.addElement("MSF");
-    formats.addElement("CLUSTAL");
-    formats.addElement("BLC");
-    formats.addElement("PIR");
-    formats.addElement("PFAM");
-  }
+    static
+    {
+        formats.addElement("FASTA");
+        formats.addElement("MSF");
+        formats.addElement("PileUp");
+        formats.addElement("CLUSTAL");
+        formats.addElement("BLC");
+        formats.addElement("PIR");
+        formats.addElement("PFAM");
+    }
 
-  public static SequenceI[] readFile(String inFile, String type, String format)
-  {
+    AlignFile afile = null;
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     * @param format DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI[] readFile(String inFile, String type, String format)
     {
-      AlignFile afile = null;
-      if (format.equals("FASTA"))
-        afile = new FastaFile(inFile, type);
-      else if (format.equals("MSF"))
-        afile = new MSFfile(inFile, type);
-      else if (format.equals("CLUSTAL"))
-        afile = new ClustalFile(inFile, type);
-      else if (format.equals("BLC"))
-        afile = new BLCFile(inFile, type);
-      else if (format.equals("PIR"))
-        afile = new PIRFile(inFile, type);
-      else if (format.equals("PFAM"))
-        afile = new PfamFile(inFile, type);
-
-      return afile.getSeqsAsArray();
-    }
-    catch (Exception e)  {
-    System.err.println("Failed to read alignment using the '"+format+"' reader.");
-    e.printStackTrace();
+        try
+        {
+            if (format.equals("FASTA"))
+            {
+                afile = new FastaFile(inFile, type);
+            }
+            else if (format.equals("MSF"))
+            {
+                afile = new MSFfile(inFile, type);
+            }
+            else if (format.equals("PileUp"))
+            {
+                afile = new PileUpfile(inFile, type);
+            }
+            else if (format.equals("CLUSTAL"))
+            {
+                afile = new ClustalFile(inFile, type);
+            }
+            else if (format.equals("BLC"))
+            {
+                afile = new BLCFile(inFile, type);
+            }
+            else if (format.equals("PIR"))
+            {
+                afile = new PIRFile(inFile, type);
+            }
+            else if (format.equals("PFAM"))
+            {
+                afile = new PfamFile(inFile, type);
+            }
+
+            return afile.getSeqsAsArray();
+        }
+        catch (Exception e)
+        {
+            System.err.println("Failed to read alignment using the '" + format +
+                "' reader.");
+            e.printStackTrace();
+        }
+
+        return null;
     }
 
-    return null;
-  }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param format DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String formatSequences(String format, Vector seqs)
+    {
+        SequenceI[] s = new SequenceI[seqs.size()];
 
-  public static String formatSequences(String format, Vector seqs)
-  {
-    SequenceI [] s = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+            s[i] = (SequenceI) seqs.elementAt(i);
 
-    for (int i = 0; i < seqs.size(); i++)
-      s[i] = (SequenceI) seqs.elementAt(i);
+        try
+        {
+            AlignFile afile = null;
 
-    try
-    {
-      AlignFile afile = null;
-      if (format.equals("FASTA"))
-        afile = new FastaFile();
-      else if (format.equals("MSF"))
-        afile = new MSFfile();
-      else if (format.equals("CLUSTAL"))
-        afile = new ClustalFile();
-      else if (format.equals("BLC"))
-        afile = new BLCFile();
-      else if (format.equals("PIR"))
-        afile = new PIRFile();
-      else if (format.equals("PFAM"))
-        afile = new PfamFile();
-
-      afile.setSeqs(s);
-      return afile.print();
-    }
-    catch (Exception e)  {
-      System.err.println("Failed to write alignment as a '"+format+"' file\n");
-      e.printStackTrace();
-    }
+            if (format.equalsIgnoreCase("FASTA"))
+            {
+                afile = new FastaFile();
+            }
+            else if (format.equalsIgnoreCase("MSF"))
+            {
+                afile = new MSFfile();
+            }
+            else if (format.equalsIgnoreCase("PileUp"))
+            {
+                afile = new PileUpfile();
+            }
+            else if (format.equalsIgnoreCase("CLUSTAL"))
+            {
+                afile = new ClustalFile();
+            }
+            else if (format.equalsIgnoreCase("BLC"))
+            {
+                afile = new BLCFile();
+            }
+            else if (format.equalsIgnoreCase("PIR"))
+            {
+                afile = new PIRFile();
+            }
+            else if (format.equalsIgnoreCase("PFAM"))
+            {
+                afile = new PfamFile();
+            }
 
-    return null;
-  }
+            afile.setSeqs(s);
+
+            return afile.print();
+        }
+        catch (Exception e)
+        {
+            System.err.println("Failed to write alignment as a '" + format +
+                "' file\n");
+            e.printStackTrace();
+        }
+
+        return null;
+    }
 }