Merge branch 'JAL-1347' into develop

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 11f5adb..eac7cf2 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -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
@@ -52,22 +52,24 @@ 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,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk" };
 
   /**
    * 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" };
 
   /**
    * 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,stk" }; // ,
+  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk","xml,rnaml" }; // ,
 
   // ".blast"
   // };
@@ -78,7 +80,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm" };// ,
+      "Stockholm","RNAML" };// ,
 
   // "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"))
       {
@@ -237,7 +241,11 @@ 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);
@@ -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
@@ -344,6 +352,10 @@ 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);
@@ -445,12 +457,17 @@ 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(
@@ -534,7 +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