JAL-1260 v2 patch from David Roldán-Martínez

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
old mode 100755 (executable)
new mode 100644 (file)
index d55bab5..ead63c8
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -38,7 +41,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FORMATS = new String[]
   { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
+      "PDB", "JnetFile", "RNAML", "GENBANK" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -52,25 +55,24 @@ public class AppletFormatAdapter
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "jvp", "sto,stk", "jar" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
   public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "STH", "Jalview" };
 
   /**
    * List of readable format file extensions by application in order
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "sto,stk","xml" }; // ,
-
-  // ".blast"
-  // };
+  { "fa,faa,fasta,mfa,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "jar,jvp", "sto,stk", "xml,rnaml", "gb" }; // ".blast"
 
   /**
    * List of readable formats by application in order corresponding to
@@ -78,7 +80,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm","RNAML" };// ,
+      "Stockholm", "RNAML", "GenBank" };
 
   // "SimpleBLAST"
   // };
@@ -227,7 +229,9 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(inFile, type);        
+        afile = new MCview.PDBfile(inFile, type);
+        // Uncomment to test Jmol data based PDB processing: JAL-1213
+        // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
       }
       else if (format.equals("STH"))
       {
@@ -241,7 +245,10 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile(inFile, type);
       }
-      
+      else if (format.equals("GENBANK"))
+      {
+        afile = new GenBankFile(inFile, type);
+      }
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -296,7 +303,7 @@ public class AppletFormatAdapter
    * 
    * @return DOCUMENT ME!
    */
-  public Alignment readFromFile(FileParse source, String format)
+  public AlignmentI readFromFile(FileParse source, String format)
           throws java.io.IOException
   {
     // TODO: generalise mapping between format string and io. class instances
@@ -356,6 +363,10 @@ public class AppletFormatAdapter
       {
         afile = new SimpleBlastFile(source);
       }
+      else if (format.equals("GENBANK"))
+      {
+        afile = new GenBankFile(source);
+      }
 
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
@@ -453,7 +464,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -463,7 +474,10 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile();
       }
-      
+      else if (format.equalsIgnoreCase("GENBANK"))
+      {
+        afile = new GenBankFile();
+      }
       else
       {
         throw new Exception(
@@ -547,7 +561,6 @@ public class AppletFormatAdapter
           System.out
                   .println("Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
-
         } catch (Exception e)
         {
           System.err.println("Exception when dealing with " + i