Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 6ae3a37..7168744 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -39,15 +39,14 @@ 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
    * method
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "AMSA" };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
@@ -71,10 +70,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar,jvp",
-      "sto,stk" }; // ,
-
-  // ".blast"
-  // };
+    "sto,stk", "xml,rnaml" }; // ".blast"
 
   /**
    * List of readable formats by application in order corresponding to
@@ -82,7 +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"
   // };
@@ -231,7 +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"))
       {
@@ -241,7 +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);
@@ -296,7 +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
@@ -348,6 +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);
@@ -455,6 +461,11 @@ public class AppletFormatAdapter
       {
         afile = new AMSAFile(alignment);
       }
+      else if (format.equalsIgnoreCase("RNAML"))
+      {
+        afile = new RnamlFile();
+      }
+      
       else
       {
         throw new Exception(
@@ -506,47 +517,43 @@ public class AppletFormatAdapter
         {
           System.out.println("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
-          String fName = f.getName();
+          Runtime r = Runtime.getRuntime();
+          System.gc();
+          long memf = -r.totalMemory() + r.freeMemory();
+          long t1 = -System.currentTimeMillis();
+          Alignment al = afa.readFile(args[i], FILE,
+                  new IdentifyFile().Identify(args[i], FILE));
+          t1 += System.currentTimeMillis();
+          System.gc();
+          memf += r.totalMemory() - r.freeMemory();
+          if (al != null)
           {
-            Runtime r = Runtime.getRuntime();
-            System.gc();
-            long memf = -r.totalMemory() + r.freeMemory();
-            long t1 = -System.currentTimeMillis();
-            Alignment al = afa.readFile(args[i], FILE,
-                    new IdentifyFile().Identify(args[i], FILE));
-            t1 += System.currentTimeMillis();
-            System.gc();
-            memf += r.totalMemory() - r.freeMemory();
-            if (al != null)
+            System.out.println("Alignment contains " + al.getHeight()
+                    + " sequences and " + al.getWidth() + " columns.");
+            try
             {
-              System.out.println("Alignment contains " + al.getHeight()
-                      + " sequences and " + al.getWidth() + " columns.");
-              try
-              {
-                System.out.println(new AppletFormatAdapter()
-                        .formatSequences("FASTA", al, true));
-              } catch (Exception e)
-              {
-                System.err
-                        .println("Couln't format the alignment for output as a FASTA file.");
-                e.printStackTrace(System.err);
-              }
-            }
-            else
+              System.out.println(new AppletFormatAdapter().formatSequences(
+                      "FASTA", al, true));
+            } catch (Exception e)
             {
-              System.out.println("Couldn't read alignment");
+              System.err
+                      .println("Couln't format the alignment for output as a FASTA file.");
+              e.printStackTrace(System.err);
             }
-            System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-            System.out
-                    .println("Difference between free memory now and before is "
-                            + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
           }
+          else
+          {
+            System.out.println("Couldn't read alignment");
+          }
+          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+          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
                   + "'th argument: " + args[i] + "\n" + e);
         }
-
       }
       else
       {
@@ -727,5 +734,4 @@ public class AppletFormatAdapter
     }
     return null;
   }
-
 }