X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=2901969d0f9a0a85d4e2263d843dcd84d87d08d5;hb=c8d150be394e2acf91a600a588492b44aa172052;hp=e59c191879b5f8a1e3ff74cdff6c76712de40781;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index e59c191..2901969 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,81 +20,100 @@ 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) {
-        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!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FormatAdapter extends AppletFormatAdapter
+{
+
+    public String formatSequences(String format,
+                                  SequenceI [] seqs,
+                                  String [] omitHiddenColumns)
+    {
+      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());
+
+        seqs = tmp;
+      }
+
+      return formatSequences(format, seqs);
     }
 
-    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);
 
-        try {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param format DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String formatSequences(String format,
+                                  SequenceI [] seqs)
+    {
+
+        try
+        {
             AlignFile afile = null;
 
-            if (format.equals("FASTA")) {
+            if (format.equalsIgnoreCase("FASTA"))
+            {
                 afile = new FastaFile();
-            } else if (format.equals("MSF")) {
-                afile = new MSFfile();
-            } else if (format.equals("PileUp")) {
+                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();
-            } else if (format.equals("CLUSTAL")) {
+                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(s);
+            afile.setSeqs(seqs);
 
             return afile.print();
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             System.err.println("Failed to write alignment as a '" + format +
                 "' file\n");
             e.printStackTrace();