X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=417dabad168f86c4927a3d4b02d5d7fa57f320dc;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=b1952a9fc66e060730fa6a936a09f5db844b1c62;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b1952a9..417daba 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -38,7 +39,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FORMATS = new String[]
   { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile" }; // , "SimpleBLAST" };
+      "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -52,25 +53,24 @@ public class AppletFormatAdapter
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa, 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, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "sto" }; // ,
-
-  // ".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 +78,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm" };// ,
+      "Stockholm","RNAML" };// ,
 
   // "SimpleBLAST"
   // };
@@ -119,6 +119,21 @@ public class AppletFormatAdapter
   String inFile;
 
   /**
+   * 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
    * 
    * @param format
@@ -212,7 +227,9 @@ 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"))
       {
@@ -222,7 +239,11 @@ public class AppletFormatAdapter
       {
         afile = new SimpleBlastFile(inFile, type);
       }
-
+      else if (format.equals("RNAML"))
+      {
+        afile = new RnamlFile(inFile, type);
+      }
+      
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -277,7 +298,7 @@ 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
@@ -329,6 +350,10 @@ public class AppletFormatAdapter
       {
         afile = new StockholmFile(source);
       }
+      else if (format.equals("RNAML"))
+      {
+        afile = new RnamlFile(source);
+      }
       else if (format.equals("SimpleBLAST"))
       {
         afile = new SimpleBlastFile(source);
@@ -430,18 +455,23 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
         afile = new AMSAFile(alignment);
       }
+      else if (format.equalsIgnoreCase("RNAML"))
+      {
+        afile = new RnamlFile();
+      }
+      
       else
       {
         throw new Exception(
                 "Implementation error: Unknown file format string");
       }
-
+      afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());
@@ -463,6 +493,18 @@ public class AppletFormatAdapter
     return null;
   }
 
+  public static String checkProtocol(String file)
+  {
+    String protocol = FILE;
+    String ft = file.toLowerCase().trim();
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
+    {
+      protocol = URL;
+    }
+    return protocol;
+  }
+
   public static void main(String[] args)
   {
     int i = 0;
@@ -507,7 +549,6 @@ 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