X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=288d476ff3fc150f54d95bfdfd6b540c332f5d5f;hb=6a495a81e764c82f9fdfb6b3f990b962a5b85286;hp=637db81b2cf01f4c1512bd841dd29766e2607a7d;hpb=6a609c7e9363f8f057c6dbb5cdcd247fb2efc995;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
old mode 100755
new mode 100644
index 637db81..288d476
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,27 +1,31 @@
 /*
- * 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;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+
 import java.io.File;
 import java.io.InputStream;
 
-import jalview.datamodel.*;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -37,48 +41,49 @@ public class AppletFormatAdapter
    * List of valid format strings used in the isValidFormat method
    */
   public static final String[] READABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
-
+  { "BLC", "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM",
+    "PDB", "JnetFile", "RNAML" }; 
   /**
    * List of valid format strings for use by callers of the formatSequences
    * method
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+  { "BLC", "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM",
+      "STH",
+      "AMSA" };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * 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", "meg", "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", "MEGA", "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,rnaml" }; // ,
-
-  // ".blast"
-  // };
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc", "amsa",
+      "jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
 
   /**
    * List of readable formats by application in order corresponding to
    * READABLE_EXTENSIONS
    */
   public static final String[] READABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm","RNAML" };// ,
+  { "Fasta", "Clustal", "PFAM", "MEGA", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "Stockholm", "RNAML" };
 
   // "SimpleBLAST"
   // };
@@ -227,7 +232,9 @@ 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 +248,11 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile(inFile, type);
       }
-      
+      else if (format.equals("MEGA"))
+      {
+        afile = new MegaFile(inFile, type);
+      }
+
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -356,6 +367,10 @@ public class AppletFormatAdapter
       {
         afile = new SimpleBlastFile(source);
       }
+      else if (format.equals("MEGA"))
+      {
+        afile = new MegaFile(source);
+      }
 
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
@@ -453,7 +468,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -463,7 +478,10 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile();
       }
-      
+      else if (format.equalsIgnoreCase("MEGA"))
+      {
+        afile = new MegaFile();
+      }
       else
       {
         throw new Exception(
@@ -547,7 +565,6 @@ 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