Load data file added

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a4f5e4d..b2c8901 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -360,6 +360,27 @@ public class AlignFrame
     thread.start();\r
   }\r
 \r
+  public void associatedData_actionPerformed(ActionEvent e)\r
+  {\r
+    // Pick the tree file\r
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+        getProperty(\r
+            "LAST_DIRECTORY"));\r
+    chooser.setFileView(new JalviewFileView());\r
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");\r
+    chooser.setToolTipText("Load Jalview Annotations / Features file");\r
+\r
+    int value = chooser.showOpenDialog(null);\r
+\r
+    if (value == JalviewFileChooser.APPROVE_OPTION)\r
+    {\r
+      String choice = chooser.getSelectedFile().getPath();\r
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+      loadJalviewDataFile(choice);\r
+    }\r
+\r
+  }\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -685,6 +706,10 @@ public class AlignFrame
         AlignFrame af = new AlignFrame(alignment);\r
         String newtitle = new String("Copied sequences");\r
 \r
+        //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+        FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+        fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+\r
         if (title.startsWith("Copied sequences"))\r
         {\r
           newtitle = title;\r
@@ -2608,8 +2633,7 @@ public boolean parseGroupsFile(String file)
             alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
           }\r
 \r
-          sf = new SequenceFeature(type, desc, "", start, end);\r
-          sf.setFeatureGroup(featureGroup);\r
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
 \r
           seq.getDatasetSequence().addSequenceFeature(sf);\r
         }\r
@@ -2683,57 +2707,68 @@ public void drop(DropTargetDropEvent evt)
     {\r
       e.printStackTrace();\r
     }\r
-\r
     if (files != null)\r
     {\r
       try\r
       {\r
-        boolean isAnnotation = false;\r
 \r
         for (int i = 0; i < files.size(); i++)\r
         {\r
-          String file = files.get(i).toString();\r
-\r
-          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);\r
-\r
-          if( !isAnnotation )\r
-          {\r
-            boolean isGroupsFile = parseGroupsFile(file);\r
-            if (!isGroupsFile)\r
-            {\r
-              String protocol = "File";\r
-              String format = new IdentifyFile().Identify(file, protocol);\r
-              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);\r
-\r
-              FastaFile ff = new FastaFile();\r
-              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
-              c.setContents(new StringSelection(ff.print(sequences)), this);\r
-\r
-              this.paste(false);\r
-\r
-            }\r
-          }\r
+          loadJalviewDataFile(files.get(i).toString());\r
         }\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
+    }\r
+}\r
+\r
+  // This method will attempt to load a "dropped" file first by testing\r
+  // whether its and Annotation file, then group file. If both are\r
+  // false then the user may have dropped an alignment file onto this\r
+  // AlignFrame\r
+   void loadJalviewDataFile(String file)\r
+  {\r
+    try{\r
+      boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.\r
+          alignment, file);\r
 \r
-        if(isAnnotation)\r
+      if (!isAnnotation)\r
+      {\r
+        boolean isGroupsFile = parseGroupsFile(file);\r
+        if (!isGroupsFile)\r
         {\r
-          int height = alignPanel.annotationPanel.adjustPanelHeight();\r
-          alignPanel.annotationScroller.setPreferredSize(\r
-              new Dimension(alignPanel.annotationScroller.getWidth(),\r
-                            height));\r
+          String protocol = "File";\r
+          String format = new IdentifyFile().Identify(file, protocol);\r
+          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,\r
+              format);\r
 \r
-          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
-              alignPanel.annotationSpaceFillerHolder.getWidth(),\r
-              height));\r
+          FastaFile ff = new FastaFile();\r
+          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+          c.setContents(new StringSelection(ff.print(sequences)), this);\r
 \r
-          alignPanel.addNotify();\r
+          this.paste(false);\r
         }\r
       }\r
-      catch (Exception ex)\r
+\r
+      if (isAnnotation)\r
       {\r
-        ex.printStackTrace();\r
+        int height = alignPanel.annotationPanel.adjustPanelHeight();\r
+        alignPanel.annotationScroller.setPreferredSize(\r
+            new Dimension(alignPanel.annotationScroller.getWidth(),\r
+                          height));\r
+\r
+        alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
+            alignPanel.annotationSpaceFillerHolder.getWidth(),\r
+            height));\r
+\r
+        alignPanel.addNotify();\r
       }\r
-    }\r
-}\r
 \r
+    }catch(Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+  }\r
 }\r