Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 89adead..f316a7e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -46,10 +46,24 @@ public class AppletFormatAdapter
    * List of valid format strings used in the isValidFormat method
    */
   public static final String[] READABLE_FORMATS = new String[]
-          { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" }; // ,
-                                                                              // "SimpleBLAST"
-                                                                              // };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" };
+
+  /**
+   * List of readable format file extensions by application in order
+   * corresponding to READABLE_FNAMES
+   */
+  public static final String[] READABLE_EXTENSIONS = new String[]
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, "jar,jvp", "html" };
+
+  /**
+   * List of readable formats by application in order corresponding to
+   * READABLE_EXTENSIONS
+   */
+  public static final String[] READABLE_FNAMES = new String[]
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
+      "RNAML", PhylipFile.FILE_DESC, "Jalview", "HTML" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -75,26 +89,6 @@ public class AppletFormatAdapter
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
       PhylipFile.FILE_DESC, "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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT,
- "html" }; // ".blast"
-
-  /**
-   * List of readable formats by application in order corresponding to
-   * READABLE_EXTENSIONS
-   */
-  public static final String[] READABLE_FNAMES = new String[]
-          { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm", "RNAML", PhylipFile.FILE_DESC, "HTML" };// ,
-
-  // "SimpleBLAST"
-  // };
-
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
   // TODO: make these messages dynamic