X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=d7da302962d95a3fdf0af2d5b5a2b2d73a113aab;hb=b3e75fa460d849bf012a901c81b7df2717cfcafa;hp=d4831d721f1dfd21097524c70eee2338d1765551;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d4831d7..d7da302 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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" }; // , "SimpleBLAST" };
 
   /**
    * 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, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "jar,jvp", "sto,stk", "xml,rnaml" }; // ".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" };// ,
 
   // "SimpleBLAST"
   // };
@@ -117,18 +119,22 @@ public class AppletFormatAdapter
   AlignFile afile = null;
 
   String inFile;
+
   /**
-   * character used to write newlines 
+   * character used to write newlines
    */
   protected String newline = System.getProperty("line.separator");
+
   public void setNewlineString(String nl)
   {
     newline = nl;
   }
+
   public String getNewlineString()
   {
     return newline;
   }
+
   /**
    * check that this format is valid for reading
    * 
@@ -223,7 +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"))
       {
@@ -237,7 +245,7 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile(inFile, type);
       }
-      
+
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -292,7 +300,7 @@ 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
@@ -449,7 +457,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -459,7 +467,7 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile();
       }
-      
+
       else
       {
         throw new Exception(
@@ -491,7 +499,8 @@ public class AppletFormatAdapter
   {
     String protocol = FILE;
     String ft = file.toLowerCase().trim();
-    if (ft.indexOf("http:") ==0 || ft.indexOf("https:") ==0 || ft.indexOf("file:") == 0)
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
     {
       protocol = URL;
     }
@@ -542,7 +551,6 @@ 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