JAL-841; Structure trigger token in jalview.io.Alignmentfile extended

to RNA secondary structure ("S")

Change-Id: If09667335829497fd389d9bc71dfec10a37233df

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fc2fe24..7b6c6af 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4717,6 +4717,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
         alignPanel.paintAlignment(true);
+        System.out.println("Hallo");
       }
     } catch (Exception ex)
     {

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d4284a2..f1a7caf 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1018,7 +1018,7 @@ public class AnnotationFile
         }\r
       }\r
       if (hasSymbols\r
-              && (token.equals("H") || token.equals("E") || token\r
+              && (token.equals("H") || token.equals("E") || token.equals("S") || token\r
                       .equals(" ")))\r
       {\r
         // Either this character represents a helix or sheet\r

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index f24ecbc..e9574fc 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -67,7 +67,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "sto", "stk" }; // ,
+      "stk" }; // ,
 
   // ".blast"
   // };

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index acd24b3..6e15b90 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -80,12 +80,11 @@ public class JalviewFileChooser extends JFileChooser
     // SelectAllFilter needs to be set first before adding further
     // file filters to fix bug on Mac OSX
     setAcceptAllFileFilterUsed(selectAll);
-
+    
     for (int i = 0; i < suffix.length; i++)
     {
       JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);
       addChoosableFileFilter(jvf);
-
       if ((selected != null) && selected.equalsIgnoreCase(desc[i]))
       {
         chosen = jvf;