X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=3cd93458dcc58e2423a2920f43f7919abc92e32d;hb=1c6e3aa5ffd0d3fbbfe5bffbdeaa9c4f54a61cd3;hp=0c8554af6ece5dc20c7aa59d3fdf9254fcc7b9be;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0c8554a..3cd9345 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,109 +1,125 @@
 /*
-* 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
-*/
+ * 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 class FormatAdapter
+    extends AppletFormatAdapter
 {
-    /**
-     * DOCUMENT ME!
-     *
-     * @param format DOCUMENT ME!
-     * @param seqs DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String formatSequences(String format, Vector seqs)
+
+  public String formatSequences(String format,
+                                SequenceI[] seqs,
+                                String[] omitHiddenColumns)
+  {
+    if (omitHiddenColumns != null)
     {
-        SequenceI[] s = new SequenceI[seqs.size()];
+      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;
+    }
 
-        for (int i = 0; i < seqs.size(); i++)
-            s[i] = (SequenceI) seqs.elementAt(i);
+    return formatSequences(format, seqs);
+  }
 
-        try
-        {
-            AlignFile afile = null;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param format DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String formatSequences(String format,
+                                SequenceI[] seqs)
+  {
 
-            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;
 
-            afile.setSeqs(s);
+      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));
+      }
 
-            return afile.print();
-        }
-        catch (Exception e)
-        {
-            System.err.println("Failed to write alignment as a '" + format +
-                "' file\n");
-            e.printStackTrace();
-        }
+      afile.setSeqs(seqs);
 
-        return null;
+      return afile.print();
     }
+    catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '" + format +
+                         "' file\n");
+      e.printStackTrace();
+    }
+
+    return null;
+  }
 }