JAL-1355

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b22b8d3..ce15f0e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -22,8 +22,11 @@ package jalview.io;
 
 import java.io.File;
 import java.io.InputStream;
+import java.util.List;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting
@@ -41,22 +44,22 @@ 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
    * method
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH" };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jvp",
-      "sto,stk", "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
@@ -71,8 +74,8 @@ public class AppletFormatAdapter
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar,jvp",
-    "sto,stk", "xml,rnaml" }; // ".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
@@ -80,7 +83,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm","RNAML" };// ,
+      "Stockholm", "RNAML" };// ,
 
   // "SimpleBLAST"
   // };
@@ -229,7 +232,7 @@ 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);
       }
@@ -245,7 +248,7 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile(inFile, type);
       }
-      
+
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -405,6 +408,35 @@ public class AppletFormatAdapter
     }
   }
 
+
+  /**
+   * create an alignment flatfile from a Jalview alignment view 
+   * @param format
+   * @param jvsuffix
+   * @param av
+   * @param selectedOnly
+   * @return flatfile in a string
+   */
+  public String formatSequences(String format, boolean jvsuffix,
+          AlignViewportI av, boolean selectedOnly)
+  {
+
+    AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
+    AlignmentI aselview = selvew.getVisibleAlignment(av
+            .getGapCharacter());
+    List<AlignmentAnnotation> ala = (av
+            .getVisibleAlignmentAnnotation(selectedOnly));
+    if (ala != null)
+    {
+      for (AlignmentAnnotation aa : ala)
+      {
+        aselview.addAnnotation(aa);
+      }
+    }
+    
+    return formatSequences(format, aselview, jvsuffix);
+  }
+  
   /**
    * Construct an output class for an alignment in a particular filetype TODO:
    * allow caller to detect errors and warnings encountered when generating
@@ -467,11 +499,10 @@ public class AppletFormatAdapter
       {
         afile = new RnamlFile();
       }
-      
+
       else
       {
-        throw new Exception(
-                "Implementation error: Unknown file format string");
+        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);