JAL-1641 Re-implemented lost changes after sequenceFeature refactor

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c69a0c7..39b0819 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -47,7 +47,8 @@ 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, "HTML" };
+      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+      "HTML" };
 
   /**
    * List of readable format file extensions by application in order
@@ -55,7 +56,8 @@ public class AppletFormatAdapter
    */
   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" };
+      "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+      "jar,jvp", "html" };
 
   /**
    * List of readable formats by application in order corresponding to
@@ -63,7 +65,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
-      "RNAML", PhylipFile.FILE_DESC, "Jalview", "HTML" };
+      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview", "HTML" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -71,7 +73,7 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
           { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
-    "STH", PhylipFile.FILE_DESC };
+    "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
@@ -79,7 +81,7 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", PhylipFile.FILE_EXT, "jvp" };
+      "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
@@ -87,7 +89,7 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
-      PhylipFile.FILE_DESC, "Jalview" };
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -265,10 +267,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(inFile, type);
       }
-      // else if (format.equals(HtmlFile.FILE_DESC))
-      // {
-      // afile = new HtmlFile(inFile, type);
-      // }
+       else if (format.equals(JSONFile.FILE_DESC))
+       {
+       afile = new JSONFile(inFile, type);
+       }
       else if (format.equals("RNAML"))
       {
         afile = new RnamlFile(inFile, type);
@@ -277,6 +279,7 @@ public class AppletFormatAdapter
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
+      afile.addSeqGroups(al);
 
       return al;
     } catch (Exception e)
@@ -299,6 +302,8 @@ public class AppletFormatAdapter
           // Possible sequence is just residues with no label
           afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
           Alignment al = new Alignment(afile.getSeqsAsArray());
+
+          afile.addSeqGroups(al);
           afile.addAnnotations(al);
           return al;
 
@@ -393,13 +398,14 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(source);
       }
-      // else if (format.equals(HtmlFile.FILE_DESC))
-      // {
-      // afile = new HtmlFile(source);
-      // }
+       else if (format.equals(JSONFile.FILE_DESC))
+       {
+       afile = new JSONFile(source);
+       }
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
+      afile.addSeqGroups(al);
 
       return al;
     } catch (Exception e)
@@ -491,7 +497,6 @@ public class AppletFormatAdapter
     try
     {
       AlignFile afile = null;
-
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
@@ -532,10 +537,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile();
       }
-      // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC))
-      // {
-      // afile = new HtmlFile();
-      // }
+       else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+       {
+       afile = new JSONFile();
+       }
       else if (format.equalsIgnoreCase("RNAML"))
       {
         afile = new RnamlFile();
@@ -549,6 +554,17 @@ public class AppletFormatAdapter
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());
+      afile.addSeqGroups(alignment);
+
+      // Add non auto calculated annotation to AlignFile
+      for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
+      {
+        if (!annot.autoCalculated)
+        {
+          afile.annotations.add(annot);
+        }
+
+      }
 
       String afileresp = afile.print();
       if (afile.hasWarningMessage())