X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=84940a8b88c936537c29c13875f15e33d062e7d3;hb=4f24ef0848cf3c43ba0467f31fce1baa5c57aad5;hp=6ac110d47e041b89534ff1b4f278f0f3bb8ec759;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 6ac110d..84940a8 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,8 +20,6 @@ package jalview.io;
 
 import jalview.datamodel.*;
 
-import java.util.Vector;
-
 
 /**
  * DOCUMENT ME!
@@ -29,77 +27,24 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public class FormatAdapter
+public class FormatAdapter extends AppletFormatAdapter
 {
-    /** DOCUMENT ME!! */
-    public static Vector formats = new Vector();
 
-    static
+    public String formatSequences(String format,
+                                  SequenceI [] seqs,
+                                  String [] omitHiddenColumns)
     {
-        formats.addElement("FASTA");
-        formats.addElement("MSF");
-        formats.addElement("PileUp");
-        formats.addElement("CLUSTAL");
-        formats.addElement("BLC");
-        formats.addElement("PIR");
-        formats.addElement("PFAM");
+      if(omitHiddenColumns!=null)
+      {
+        for(int i=0; i<seqs.length; i++)
+          seqs [i] = new Sequence(
+              seqs[i].getName(), omitHiddenColumns[i],
+              seqs[i].getStart(), seqs[i].getEnd());
+      }
+
+      return formatSequences(format, seqs);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     * @param format DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static SequenceI[] readFile(String inFile, String type, String format)
-    {
-        try
-        {
-            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);
-            }
-
-            return afile.getSeqsAsArray();
-        }
-        catch (Exception e)
-        {
-            System.err.println("Failed to read alignment using the '" + format +
-                "' reader.");
-            e.printStackTrace();
-        }
-
-        return null;
-    }
 
     /**
      * DOCUMENT ME!
@@ -109,12 +54,9 @@ public class FormatAdapter
      *
      * @return DOCUMENT ME!
      */
-    public static String formatSequences(String format, Vector seqs)
+    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
         {
@@ -123,33 +65,47 @@ public class FormatAdapter
             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 = 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));
             }
 
-            afile.setSeqs(s);
+            afile.setSeqs(seqs);
 
             return afile.print();
         }