X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=3cd93458dcc58e2423a2920f43f7919abc92e32d;hb=4dd44779e0d1ffa07b52b67bd8178ad45801bb4f;hp=0484bdddf7424fbaf24390b7004f4436a00f5e6a;hpb=b5dceeaf4112cd63aa1642dd8851b3ec19a7c81e;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0484bdd..3cd9345 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,74 +1,124 @@
+/*
+ * 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.util.Vector;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class FormatAdapter
+    extends AppletFormatAdapter
 {
 
-  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");
-  }
-
-  public static SequenceI[] readFile(String inFile, String type, String format)
+  public String formatSequences(String format,
+                                SequenceI[] seqs,
+                                String[] omitHiddenColumns)
   {
-
-    try
+    if (omitHiddenColumns != null)
     {
-      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();
+      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());
+        tmp[i].setDescription(seqs[i].getDescription());
+      }
+      seqs = tmp;
     }
-    catch (Exception e)  {}
 
-    return null;
+    return formatSequences(format, seqs);
   }
 
-
-  public static String formatSequences(String format, Vector seqs)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param format DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String formatSequences(String format,
+                                SequenceI[] seqs)
   {
-    SequenceI [] s = new SequenceI[seqs.size()];
-
-    for (int i = 0; i < seqs.size(); i++)
-      s[i] = (SequenceI) seqs.elementAt(i);
 
     try
     {
       AlignFile afile = null;
-      if (format.equals("FASTA"))
+
+      if (format.equalsIgnoreCase("FASTA"))
+      {
         afile = new FastaFile();
-      else if (format.equals("MSF"))
+        afile.addJVSuffix(
+            jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
+      }
+      else if (format.equalsIgnoreCase("MSF"))
+      {
         afile = new MSFfile();
-      else if (format.equals("CLUSTAL"))
+        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();
-      else if (format.equals("BLC"))
+        afile.addJVSuffix(
+            jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+      }
+      else if (format.equalsIgnoreCase("BLC"))
+      {
         afile = new BLCFile();
-      else if (format.equals("PIR"))
+        afile.addJVSuffix(
+            jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));
+      }
+      else if (format.equalsIgnoreCase("PIR"))
+      {
         afile = new PIRFile();
-      else if (format.equals("PFAM"))
+        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));
+      }
+
+      afile.setSeqs(seqs);
 
-      afile.setSeqs(s);
       return afile.print();
     }
-    catch (Exception e)  {}
+    catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '" + format +
+                         "' file\n");
+      e.printStackTrace();
+    }
 
     return null;
   }