documentation and proxy call to util.MapList.getToWord(mpos)

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0484bdd..3cd9345 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,74 +1,124 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.io;\r
 \r
 import jalview.datamodel.*;\r
-import java.util.Vector;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
 public class FormatAdapter\r
+    extends AppletFormatAdapter\r
 {\r
 \r
-  public static Vector formats = new Vector();\r
-  static{\r
-    formats.addElement("FASTA");\r
-    formats.addElement("MSF");\r
-    formats.addElement("CLUSTAL");\r
-    formats.addElement("BLC");\r
-    formats.addElement("PIR");\r
-    formats.addElement("PFAM");\r
-  }\r
-\r
-  public static SequenceI[] readFile(String inFile, String type, String format)\r
+  public String formatSequences(String format,\r
+                                SequenceI[] seqs,\r
+                                String[] omitHiddenColumns)\r
   {\r
-\r
-    try\r
+    if (omitHiddenColumns != null)\r
     {\r
-      AlignFile afile = null;\r
-      if (format.equals("FASTA"))\r
-        afile = new FastaFile(inFile, type);\r
-      else if (format.equals("MSF"))\r
-        afile = new MSFfile(inFile, type);\r
-      else if (format.equals("CLUSTAL"))\r
-        afile = new ClustalFile(inFile, type);\r
-      else if (format.equals("BLC"))\r
-        afile = new BLCFile(inFile, type);\r
-      else if (format.equals("PIR"))\r
-        afile = new PIRFile(inFile, type);\r
-      else if (format.equals("PFAM"))\r
-        afile = new PfamFile(inFile, type);\r
-\r
-      return afile.getSeqsAsArray();\r
+      SequenceI[] tmp = new SequenceI[seqs.length];\r
+      for (int i = 0; i < seqs.length; i++)\r
+      {\r
+        tmp[i] = new Sequence(\r
+            seqs[i].getName(), omitHiddenColumns[i],\r
+            seqs[i].getStart(), seqs[i].getEnd());\r
+        tmp[i].setDescription(seqs[i].getDescription());\r
+      }\r
+      seqs = tmp;\r
     }\r
-    catch (Exception e)  {}\r
 \r
-    return null;\r
+    return formatSequences(format, seqs);\r
   }\r
 \r
-\r
-  public static String formatSequences(String format, Vector seqs)\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param format DOCUMENT ME!\r
+   * @param seqs DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public String formatSequences(String format,\r
+                                SequenceI[] seqs)\r
   {\r
-    SequenceI [] s = new SequenceI[seqs.size()];\r
-\r
-    for (int i = 0; i < seqs.size(); i++)\r
-      s[i] = (SequenceI) seqs.elementAt(i);\r
 \r
     try\r
     {\r
       AlignFile afile = null;\r
-      if (format.equals("FASTA"))\r
+\r
+      if (format.equalsIgnoreCase("FASTA"))\r
+      {\r
         afile = new FastaFile();\r
-      else if (format.equals("MSF"))\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
+      }\r
+      else if (format.equalsIgnoreCase("MSF"))\r
+      {\r
         afile = new MSFfile();\r
-      else if (format.equals("CLUSTAL"))\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
+      }\r
+      else if (format.equalsIgnoreCase("PileUp"))\r
+      {\r
+        afile = new PileUpfile();\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
+      }\r
+      else if (format.equalsIgnoreCase("CLUSTAL"))\r
+      {\r
         afile = new ClustalFile();\r
-      else if (format.equals("BLC"))\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
+      }\r
+      else if (format.equalsIgnoreCase("BLC"))\r
+      {\r
         afile = new BLCFile();\r
-      else if (format.equals("PIR"))\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
+      }\r
+      else if (format.equalsIgnoreCase("PIR"))\r
+      {\r
         afile = new PIRFile();\r
-      else if (format.equals("PFAM"))\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
+      }\r
+      else if (format.equalsIgnoreCase("PFAM"))\r
+      {\r
         afile = new PfamFile();\r
+        afile.addJVSuffix(\r
+            jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
+      }\r
+\r
+      afile.setSeqs(seqs);\r
 \r
-      afile.setSeqs(s);\r
       return afile.print();\r
     }\r
-    catch (Exception e)  {}\r
+    catch (Exception e)\r
+    {\r
+      System.err.println("Failed to write alignment as a '" + format +\r
+                         "' file\n");\r
+      e.printStackTrace();\r
+    }\r
 \r
     return null;\r
   }\r