From 0ad0cc7fe1de5c299363b0dc9b4b032d5d199275 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Mar 2006 15:32:50 +0000
Subject: [PATCH] Load data file added

---
 src/jalview/gui/AlignFrame.java |  111 +++++++++++++++++++++++++--------------
 1 file changed, 73 insertions(+), 38 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a4f5e4d..b2c8901 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -360,6 +360,27 @@ public class AlignFrame
     thread.start();
   }
 
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");
+    chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(choice);
+    }
+
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -685,6 +706,10 @@ public class AlignFrame
         AlignFrame af = new AlignFrame(alignment);
         String newtitle = new String("Copied sequences");
 
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+        fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+
         if (title.startsWith("Copied sequences"))
         {
           newtitle = title;
@@ -2608,8 +2633,7 @@ public boolean parseGroupsFile(String file)
             alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
           }
 
-          sf = new SequenceFeature(type, desc, "", start, end);
-          sf.setFeatureGroup(featureGroup);
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
           seq.getDatasetSequence().addSequenceFeature(sf);
         }
@@ -2683,57 +2707,68 @@ public void drop(DropTargetDropEvent evt)
     {
       e.printStackTrace();
     }
-
     if (files != null)
     {
       try
       {
-        boolean isAnnotation = false;
 
         for (int i = 0; i < files.size(); i++)
         {
-          String file = files.get(i).toString();
-
-          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
-
-          if( !isAnnotation )
-          {
-            boolean isGroupsFile = parseGroupsFile(file);
-            if (!isGroupsFile)
-            {
-              String protocol = "File";
-              String format = new IdentifyFile().Identify(file, protocol);
-              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
-
-              FastaFile ff = new FastaFile();
-              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-              c.setContents(new StringSelection(ff.print(sequences)), this);
-
-              this.paste(false);
-
-            }
-          }
+          loadJalviewDataFile(files.get(i).toString());
         }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
+
+  // This method will attempt to load a "dropped" file first by testing
+  // whether its and Annotation file, then group file. If both are
+  // false then the user may have dropped an alignment file onto this
+  // AlignFrame
+   void loadJalviewDataFile(String file)
+  {
+    try{
+      boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
+          alignment, file);
 
-        if(isAnnotation)
+      if (!isAnnotation)
+      {
+        boolean isGroupsFile = parseGroupsFile(file);
+        if (!isGroupsFile)
         {
-          int height = alignPanel.annotationPanel.adjustPanelHeight();
-          alignPanel.annotationScroller.setPreferredSize(
-              new Dimension(alignPanel.annotationScroller.getWidth(),
-                            height));
+          String protocol = "File";
+          String format = new IdentifyFile().Identify(file, protocol);
+          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,
+              format);
 
-          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              alignPanel.annotationSpaceFillerHolder.getWidth(),
-              height));
+          FastaFile ff = new FastaFile();
+          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+          c.setContents(new StringSelection(ff.print(sequences)), this);
 
-          alignPanel.addNotify();
+          this.paste(false);
         }
       }
-      catch (Exception ex)
+
+      if (isAnnotation)
       {
-        ex.printStackTrace();
+        int height = alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationScroller.setPreferredSize(
+            new Dimension(alignPanel.annotationScroller.getWidth(),
+                          height));
+
+        alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            alignPanel.annotationSpaceFillerHolder.getWidth(),
+            height));
+
+        alignPanel.addNotify();
       }
-    }
-}
 
+    }catch(Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
 }
-- 
1.7.10.2