X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=a23bbba3b665a4a6685fabef14588b76315d06b4;hb=3e5323394ec75b802624d4a7040f7550cf31fdbf;hp=3e5e250c200486f3abafb855b6b779d9c6d7cef5;hpb=128c1c559ce7749ba5a39d30e6108f5ce8f4b99e;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 3e5e250..a23bbba 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,86 +1,124 @@
+/*
+* 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
+*/
 package jalview.io;
 
 import jalview.datamodel.*;
-import java.util.Vector;
-public class FormatAdapter
-{
 
-  public static Vector formats = new Vector();
-  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)
-  {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FormatAdapter extends AppletFormatAdapter
+{
 
-    try
+    public String formatSequences(String format,
+                                  SequenceI [] seqs,
+                                  String [] omitHiddenColumns)
     {
-      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("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);
+      if(omitHiddenColumns!=null)
+      {
+        SequenceI [] tmp = new SequenceI[seqs.length];
+        for(int i=0; i<seqs.length; i++)
+          tmp [i] = new Sequence(
+              seqs[i].getName(), omitHiddenColumns[i],
+              seqs[i].getStart(), seqs[i].getEnd());
 
-      return afile.getSeqsAsArray();
-    }
-    catch (Exception e)  {
-    System.err.println("Failed to read alignment using the '"+format+"' reader.");
-    e.printStackTrace();
+        seqs = tmp;
+      }
+
+      return formatSequences(format, seqs);
     }
 
-    return null;
-  }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param format DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String formatSequences(String format,
+                                  SequenceI [] seqs)
+    {
 
-  public static String formatSequences(String format, Vector seqs)
-  {
-    SequenceI [] s = new SequenceI[seqs.size()];
+        try
+        {
+            AlignFile afile = null;
 
-    for (int i = 0; i < seqs.size(); i++)
-      s[i] = (SequenceI) seqs.elementAt(i);
+            if (format.equalsIgnoreCase("FASTA"))
+            {
+                afile = new FastaFile();
+                afile.addJVSuffix(
+                    jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
+            }
+            else if (format.equalsIgnoreCase("MSF"))
+            {
+              afile = new MSFfile();
+              afile.addJVSuffix(
+                  jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));
+            }
+            else if (format.equalsIgnoreCase("PileUp"))
+            {
+                afile = new PileUpfile();
+                afile.addJVSuffix(
+                    jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));
+            }
+            else if (format.equalsIgnoreCase("CLUSTAL"))
+            {
+                afile = new ClustalFile();
+                afile.addJVSuffix(
+                    jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+            }
+            else if (format.equalsIgnoreCase("BLC"))
+            {
+                afile = new BLCFile();
+                afile.addJVSuffix(
+                    jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));
+            }
+            else if (format.equalsIgnoreCase("PIR"))
+            {
+                afile = new PIRFile();
+                afile.addJVSuffix(
+                    jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));
+            }
+            else if (format.equalsIgnoreCase("PFAM"))
+            {
+                afile = new PfamFile();
+                afile.addJVSuffix(
+                    jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
+            }
 
-    try
-    {
-      AlignFile afile = null;
-      if (format.equals("FASTA"))
-        afile = new FastaFile();
-      else if (format.equals("MSF"))
-        afile = new MSFfile();
-      else if (format.equals("PileUp"))
-        afile = new PileUpfile();
-      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(seqs);
 
-      afile.setSeqs(s);
-      return afile.print();
-    }
-    catch (Exception e)  {
-      System.err.println("Failed to write alignment as a '"+format+"' file\n");
-      e.printStackTrace();
-    }
+            return afile.print();
+        }
+        catch (Exception e)
+        {
+            System.err.println("Failed to write alignment as a '" + format +
+                "' file\n");
+            e.printStackTrace();
+        }
 
-    return null;
-  }
+        return null;
+    }
 }