Merge branch 'develop' into menard

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index ee24238..d55bab5 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,13 +1,13 @@
 /*
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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 
@@ -38,7 +38,7 @@ 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
@@ -52,7 +52,7 @@ 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,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
@@ -66,8 +66,8 @@ public class AppletFormatAdapter
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "sto" }; // ,
+  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk","xml" }; // ,
 
   // ".blast"
   // };
@@ -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 +227,7 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(inFile, type);
+        afile = new MCview.PDBfile(inFile, type);        
       }
       else if (format.equals("STH"))
       {
@@ -222,7 +237,11 @@ 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);
@@ -329,6 +348,10 @@ 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);
@@ -436,12 +459,17 @@ public class AppletFormatAdapter
       {
         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 +491,18 @@ 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;
@@ -597,11 +637,14 @@ public class AppletFormatAdapter
       if (!fp.isValid())
       {
         fp = null;
-      } else {
-      if (debug)
+      }
+      else
       {
-        System.out.println("Successful.");
-      }}
+        if (debug)
+        {
+          System.out.println("Successful.");
+        }
+      }
     } catch (Exception e)
     {
       if (debug)