From 4d85e896a94bc9fe9a8476473a5f2358979a0627 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Jun 2006 08:50:35 +0000
Subject: [PATCH] Fetch DBRefs

---
 src/jalview/gui/AlignFrame.java    |   72 +++++++++++++++++++++++++++++++++---
 src/jalview/jbgui/GAlignFrame.java |   25 +++++++++++--
 2 files changed, 88 insertions(+), 9 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 32a50cf..f426f9c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -35,6 +35,7 @@ import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
 import java.awt.dnd.*;
+import org.biojava.dasobert.eventmodel.*;
 
 
 /**
@@ -44,7 +45,7 @@ import java.awt.dnd.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements DropTargetListener
+    extends GAlignFrame implements DropTargetListener, FeatureListener
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
@@ -169,7 +170,6 @@ public class AlignFrame
       }
       ;
     });
-
   }
 
   public void setGUINucleotide(boolean nucleotide)
@@ -187,6 +187,61 @@ public class AlignFrame
     }
   }
 
+  public void comeBackLater(FeatureEvent evt)
+  {}
+
+  public void newFeatures(FeatureEvent evt)
+  {
+    if (evt.getFeatures().length > 0)
+    {
+      alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
+      alignPanel.repaint();
+    }
+    else
+    {
+      System.out.println("No Features found for " +
+                         evt.getDasSource().getNickname());
+    }
+  }
+
+  Hashtable progressBars;
+  public void setProgressBar(String message, long id)
+  {
+    if(progressBars == null)
+      progressBars = new Hashtable();
+
+    JPanel progressPanel;
+    GridLayout layout = (GridLayout) statusPanel.getLayout();
+    if(progressBars.get( new Long(id) )!=null)
+     {
+       progressPanel = (JPanel)progressBars.get( new Long(id) );
+       statusPanel.remove(progressPanel);
+       progressBars.remove( progressPanel );
+       progressPanel = null;
+       if(message!=null)
+         statusBar.setText(message);
+
+       layout.setRows(layout.getRows() - 1);
+     }
+    else
+    {
+      progressPanel = new JPanel(new BorderLayout(10, 5));
+
+      JProgressBar progressBar = new JProgressBar();
+      progressBar.setIndeterminate(true);
+
+      progressPanel.add(new JLabel(message), BorderLayout.WEST);
+      progressPanel.add(progressBar, BorderLayout.CENTER);
+
+      layout.setRows(layout.getRows() + 1);
+      statusPanel.add(progressPanel);
+
+      progressBars.put(new Long(id), progressPanel);
+    }
+
+    validate();
+  }
+
 
   /*
    Added so Castor Mapping file can obtain Jalview Version
@@ -1400,11 +1455,16 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+
+  public void dbRefs_actionPerformed(ActionEvent e)
+  {
+    new DBRefFetcher(viewport.alignment, this);
+  }
+
   public void fetchSeqFeatures_actionPerformed(ActionEvent e)
   {
-      new DasSequenceFeatureFetcher(viewport.
-                                    alignment,
-                                    alignPanel);
+      new DasSequenceFeatureFetcher(viewport.alignment,
+                                    this);
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
   }
@@ -2638,7 +2698,7 @@ public boolean parseFeaturesFile(String file, String type)
 {
     boolean featuresFile = false;
     try{
-      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment,
+      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
                                          alignPanel.seqPanel.seqCanvas.
                                          getFeatureRenderer().featureColours);
     }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 5a404eb..eafbf12 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;
 
 import jalview.schemes.*;
+import java.awt.BorderLayout;
 
 public class GAlignFrame
     extends JInternalFrame
@@ -130,6 +131,9 @@ public class GAlignFrame
   JMenuItem addFromURL = new JMenuItem();
   JMenuItem exportAnnotations = new JMenuItem();
   JMenuItem exportFeatures = new JMenuItem();
+  JMenuItem dbRefs = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
   public GAlignFrame()
   {
 
@@ -1034,6 +1038,15 @@ public class GAlignFrame
         exportAnnotations_actionPerformed(e);
       }
     });
+    dbRefs.setText("Fetch DB Refs");
+    dbRefs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        dbRefs_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -1090,6 +1103,7 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
+    viewMenu.add(dbRefs);
     viewMenu.add(fetchSeqFeatures);
     viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
@@ -1125,9 +1139,7 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);
     calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-    jMenu1.add(pasteNew);
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1142,6 +1154,8 @@ public class GAlignFrame
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
@@ -1495,4 +1509,9 @@ public class GAlignFrame
   {
 
   }
+
+  public void dbRefs_actionPerformed(ActionEvent e)
+  {
+
+  }
 }
-- 
1.7.10.2