X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=e4475ab2408918db7194f8c25990c26ee61e7802;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=2e4ddc4438700055fb745beb09d299c093e0b2fc;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2e4ddc4..e4475ab 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,234 +1,240 @@
-    /*
-    * Jalview - A Sequence Alignment Editor and Viewer
-    * Copyright (C) 2006 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.*;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @author $author$
-     * @version $Revision$
-     */
-    public class AppletFormatAdapter
+/*
+ * 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.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AppletFormatAdapter
+{
+  /** DOCUMENT ME!! */
+  public static final String[] READABLE_FORMATS = new String[]
+      {
+      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
+  };
+
+  public static final String[] WRITEABLE_FORMATS = new String[]
+      {
+      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"
+  };
+
+  public static String INVALID_CHARACTERS = "Contains invalid characters";
+
+  public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
+      "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
+
+  public static String FILE = "File";
+  public static String URL = "URL";
+  public static String PASTE = "Paste";
+  public static String CLASSLOADER = "ClassLoader";
+
+  AlignFile afile = null;
+  String inFile;
+
+  public static final boolean isValidFormat(String format)
+  {
+    boolean valid = false;
+    for (int i = 0; i < READABLE_FORMATS.length; i++)
     {
-        /** DOCUMENT ME!! */
-        public static final String [] READABLE_FORMATS = new String[]
-        {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
-        };
-
-        public static final String [] WRITEABLE_FORMATS = new String[]
-        {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"  //, "AMSA"
-        };
-
-
-        public static String INVALID_CHARACTERS = "Contains invalid characters";
-
-        public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
-                                                 "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
-
-
-        public static String FILE = "File";
-        public static String URL = "URL";
-        public static String PASTE = "Paste";
-        public static String CLASSLOADER = "ClassLoader";
-
-
-        AlignFile afile = null;
-        String inFile;
+      if (READABLE_FORMATS[i].equalsIgnoreCase(format))
+      {
+        return true;
+      }
+    }
 
-        public static final boolean isValidFormat(String format)
+    return valid;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param format DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Alignment readFile(String inFile, String type, String format)
+      throws java.io.IOException
+  {
+    this.inFile = inFile;
+    try
+    {
+      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);
+      }
+      else if (format.equals("JnetFile"))
+      {
+        afile = new JPredFile(inFile, type);
+        ( (JPredFile) afile).removeNonSequences();
+      }
+      else if (format.equals("PDB"))
+      {
+        afile = new MCview.PDBfile(inFile, type);
+      }
+      else if (format.equals("STH"))
+      {
+        afile = new StockholmFile(inFile, type);
+      }
+
+      Alignment al = new Alignment(afile.getSeqsAsArray());
+
+      afile.addAnnotations(al);
+
+      return al;
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      System.err.println("Failed to read alignment using the '" + format +
+                         "' reader.\n" + e);
+
+      if (e.getMessage() != null &&
+          e.getMessage().startsWith(INVALID_CHARACTERS))
+      {
+        throw new java.io.IOException(e.getMessage());
+      }
+
+      // Finally test if the user has pasted just the sequence, no id
+      if (type.equalsIgnoreCase("Paste"))
+      {
+        try
         {
-          boolean valid = false;
-          for(int i=0; i<READABLE_FORMATS.length; i++)
-            if(READABLE_FORMATS[i].equalsIgnoreCase(format))
-              return true;
+          // Possible sequence is just residues with no label
+          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+          Alignment al = new Alignment(afile.getSeqsAsArray());
+          afile.addAnnotations(al);
+          return al;
 
-          return valid;
         }
-
-        /**
-         * DOCUMENT ME!
-         *
-         * @param inFile DOCUMENT ME!
-         * @param type DOCUMENT ME!
-         * @param format DOCUMENT ME!
-         *
-         * @return DOCUMENT ME!
-         */
-        public Alignment readFile(String inFile, String type, String format)
-            throws java.io.IOException
+        catch (Exception ex)
         {
-            this.inFile = inFile;
-            try
-            {
-              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);
-              }
-              else if (format.equals("JnetFile"))
-              {
-                afile = new JPredFile(inFile, type);
-                ( (JPredFile) afile).removeNonSequences();
-              }
-              else if (format.equals("PDB"))
-              {
-                afile = new MCview.PDBfile(inFile, type);
-              }
-              else if (format.equals("STH"))
-              {
-                afile = new StockholmFile(inFile, type);
-              }
-
-              Alignment al = new Alignment(afile.getSeqsAsArray());
-
-              afile.addAnnotations(al);
-
-              return al;
-            }
-            catch (Exception e)
-            {
-              e.printStackTrace();
-              System.err.println("Failed to read alignment using the '" + format +
-                                 "' reader.\n"+e);
-
-              if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))
-                throw new java.io.IOException(e.getMessage());
-
-              // Finally test if the user has pasted just the sequence, no id
-              if(type.equalsIgnoreCase("Paste"))
-              {
-                try{
-                  // Possible sequence is just residues with no label
-                  afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-                  Alignment al = new Alignment(afile.getSeqsAsArray());
-                  afile.addAnnotations(al);
-                  return al;
-
-                }
-                catch(Exception ex)
-                {
-                  if(ex.toString().startsWith(INVALID_CHARACTERS))
-                    throw new java.io.IOException(e.getMessage());
-
-                  ex.printStackTrace();
-                }
-              }
-
-              // If we get to this stage, the format was not supported
-              throw new java.io.IOException(SUPPORTED_FORMATS);
-            }
-        }
-
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new java.io.IOException(e.getMessage());
+          }
 
-        /**
-         * DOCUMENT ME!
-         *
-         * @param format DOCUMENT ME!
-         * @param seqs DOCUMENT ME!
-         *
-         * @return DOCUMENT ME!
-         */
-        public String formatSequences(String format,
-                                      AlignmentI alignment,
-                                      boolean jvsuffix)
-        {
-            try
-            {
-                AlignFile afile = null;
-
-                if (format.equalsIgnoreCase("FASTA"))
-                {
-                    afile = new FastaFile();
-                }
-                else if (format.equalsIgnoreCase("MSF"))
-                {
-                    afile = new MSFfile();
-                }
-                else if (format.equalsIgnoreCase("PileUp"))
-                {
-                    afile = new PileUpfile();
-                }
-                else if (format.equalsIgnoreCase("CLUSTAL"))
-                {
-                    afile = new ClustalFile();
-                }
-                else if (format.equalsIgnoreCase("BLC"))
-                {
-                    afile = new BLCFile();
-                }
-                else if (format.equalsIgnoreCase("PIR"))
-                {
-                    afile = new PIRFile();
-                }
-                else if (format.equalsIgnoreCase("PFAM"))
-                {
-                    afile = new PfamFile();
-                }
-                else if (format.equalsIgnoreCase("STH"))
-                {
-                  afile = new StockholmFile();
-                }
-                else if (format.equals("AMSA"))
-                {
-                  afile = new AMSAFile(alignment);
-                }
-
-                afile.addJVSuffix(jvsuffix);
-
-                afile.setSeqs( alignment.getSequencesArray() );
-
-                return afile.print();
-            }
-            catch (Exception e)
-            {
-                System.err.println("Failed to write alignment as a '" + format +
-                    "' file\n");
-                e.printStackTrace();
-            }
-
-            return null;
+          ex.printStackTrace();
         }
+      }
+
+      // If we get to this stage, the format was not supported
+      throw new java.io.IOException(SUPPORTED_FORMATS);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param format DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String formatSequences(String format,
+                                AlignmentI alignment,
+                                boolean jvsuffix)
+  {
+    try
+    {
+      AlignFile afile = null;
+
+      if (format.equalsIgnoreCase("FASTA"))
+      {
+        afile = new FastaFile();
+      }
+      else if (format.equalsIgnoreCase("MSF"))
+      {
+        afile = new MSFfile();
+      }
+      else if (format.equalsIgnoreCase("PileUp"))
+      {
+        afile = new PileUpfile();
+      }
+      else if (format.equalsIgnoreCase("CLUSTAL"))
+      {
+        afile = new ClustalFile();
+      }
+      else if (format.equalsIgnoreCase("BLC"))
+      {
+        afile = new BLCFile();
+      }
+      else if (format.equalsIgnoreCase("PIR"))
+      {
+        afile = new PIRFile();
+      }
+      else if (format.equalsIgnoreCase("PFAM"))
+      {
+        afile = new PfamFile();
+      }
+      else if (format.equalsIgnoreCase("STH"))
+      {
+        afile = new StockholmFile();
+      }
+      else if (format.equals("AMSA"))
+      {
+        afile = new AMSAFile(alignment);
+      }
+
+      afile.addJVSuffix(jvsuffix);
+
+      afile.setSeqs(alignment.getSequencesArray());
+
+      return afile.print();
     }
+    catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '" + format +
+                         "' file\n");
+      e.printStackTrace();
+    }
+
+    return null;
+  }
+}