Merge branch 'JAL-1587_promotedisorder' into develop

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d3b19fa..505f609 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -47,7 +47,9 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FORMATS = new String[]
           { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-    "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC }; // , "SimpleBLAST" };
+      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" }; // ,
+                                                                              // "SimpleBLAST"
+                                                                              // };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -79,7 +81,8 @@ 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", "xml,rnaml", PhylipFile.FILE_EXT }; // ".blast"
+      "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT,
+ "html" }; // ".blast"
 
   /**
    * List of readable formats by application in order corresponding to
@@ -87,7 +90,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
           { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-    "Stockholm", "RNAML", PhylipFile.FILE_DESC };// ,
+      "Stockholm", "RNAML", PhylipFile.FILE_DESC, "HTML" };// ,
 
   // "SimpleBLAST"
   // };
@@ -109,7 +112,7 @@ public class AppletFormatAdapter
     for (int i = 0, iSize = els.length - 1; i < iSize; i++)
     {
       list.append(els[i]);
-      list.append(",");
+      list.append(", ");
     }
     list.append(" and " + els[els.length - 1] + ".");
     return list.toString();
@@ -268,6 +271,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(inFile, type);
       }
+      // else if (format.equals(HtmlFile.FILE_DESC))
+      // {
+      // afile = new HtmlFile(inFile, type);
+      // }
       else if (format.equals("RNAML"))
       {
         afile = new RnamlFile(inFile, type);
@@ -392,6 +399,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(source);
       }
+      // else if (format.equals(HtmlFile.FILE_DESC))
+      // {
+      // afile = new HtmlFile(source);
+      // }
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -527,6 +538,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile();
       }
+      // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC))
+      // {
+      // afile = new HtmlFile();
+      // }
       else if (format.equalsIgnoreCase("RNAML"))
       {
         afile = new RnamlFile();