X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=c855672df94480bebd68ab5c0803b0b34dc6349b;hb=1b1a1007c534a02fdbae76df0c084f215c7c4c21;hp=6710ed49ad262ffdf8087a9f896fe3f1b9f7d004;hpb=be9cbda993c0cb66255c0eb8274ee2bfa9199220;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 6710ed4..c855672 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -25,7 +25,7 @@ import java.awt.event.*;
 
 
 public class FeatureSettings extends Panel implements ItemListener,
-    MouseListener, MouseMotionListener
+    MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
 {
   FeatureRenderer fr;
   AlignmentPanel ap;
@@ -35,13 +35,35 @@ public class FeatureSettings extends Panel implements ItemListener,
   Panel featurePanel = new Panel();
   ScrollPane scrollPane;
   boolean alignmentHasFeatures = false;
+  Image linkImage;
+  Scrollbar transparency ;
 
-  public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
+  public FeatureSettings(final AlignmentPanel ap)
   {
     this.ap = ap;
-    this.av = av;
+    this.av = ap.av;
     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
 
+    transparency = new Scrollbar(Scrollbar.HORIZONTAL,
+     100 - (int)(fr.transparency*100), 1, 1, 100);
+
+    if(fr.transparencySetter!=null)
+    {
+      transparency.addAdjustmentListener(this);
+    }
+    else
+      transparency.setEnabled(false);
+
+    java.net.URL url = getClass().getResource("/images/link.gif");
+    if (url != null)
+    {
+      linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+    }
+
+
+    if(av.featuresDisplayed==null)
+      fr.findAllFeatures();
+
     setTableData();
 
     this.setLayout(new BorderLayout());
@@ -50,6 +72,28 @@ public class FeatureSettings extends Panel implements ItemListener,
     if (alignmentHasFeatures)
       add(scrollPane, BorderLayout.CENTER);
 
+    Button invert = new Button("Invert Selection");
+    invert.addActionListener(this);
+
+    Panel lowerPanel = new Panel(new GridLayout(2,1,5,10));
+    lowerPanel.add(invert);
+
+    Panel tPanel = new Panel(new BorderLayout());
+
+    if(fr.transparencySetter!=null)
+    {
+      tPanel.add(transparency, BorderLayout.CENTER);
+      tPanel.add(new Label("Transparency"), BorderLayout.EAST);
+    }
+    else
+      tPanel.add(new Label("Transparency not available in this web browser"), BorderLayout.CENTER);
+
+    lowerPanel.add(tPanel, BorderLayout.SOUTH);
+
+    add(lowerPanel, BorderLayout.SOUTH);
+
+
+
     if(groupPanel!=null)
     {
       groupPanel.setLayout(
@@ -60,9 +104,10 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     frame = new Frame();
     frame.add(this);
-    int height = featurePanel.getComponentCount()*50 +30;
+    int height = featurePanel.getComponentCount()*50 +60;
+
 
-    height = Math.max(100, height);
+    height = Math.max(200, height);
     height = Math.min(400, height);
 
     jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,
@@ -73,6 +118,8 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     g.setColor(Color.black);
     g.drawString("No Features added to this alignment!!", 10, 20);
+    g.drawString("(Features can be added from searches or", 10, 40);
+    g.drawString("from Jalview / GFF features files)", 10, 60);
   }
 
   void setTableData()
@@ -119,7 +166,14 @@ public class FeatureSettings extends Panel implements ItemListener,
                groupPanel = new Panel();
              }
 
-             Checkbox check = new Checkbox(group, visible);
+             Checkbox check =  new MyCheckbox(
+                group,
+                visible,
+                (fr.featureLinks!=null && fr.featureLinks.containsKey(group))
+                 );
+
+
+             check.addMouseListener(this);
              check.setFont(new Font("Serif", Font.BOLD, 12));
              check.addItemListener(this);
              groupPanel.add(check);
@@ -206,6 +260,7 @@ public class FeatureSettings extends Panel implements ItemListener,
        // now add checkboxes which should be visible,
        // if they have not already been added
        Enumeration en = visibleChecks.elements();
+
        while(en.hasMoreElements())
        {
          addCheck(groupsChanged, en.nextElement().toString());
@@ -246,7 +301,11 @@ public class FeatureSettings extends Panel implements ItemListener,
         selected = true;
       }
 
-      check = new Checkbox(type, selected);
+      check = new MyCheckbox(type,
+                             selected,
+          (fr.featureLinks!=null && fr.featureLinks.containsKey(type))
+           );
+
       check.addMouseListener(this);
       check.addMouseMotionListener(this);
       check.setBackground(fr.getColour(type));
@@ -255,6 +314,16 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  public void actionPerformed(ActionEvent evt)
+  {
+    for(int i=0; i<featurePanel.getComponentCount(); i++)
+    {
+      Checkbox check = (Checkbox)featurePanel.getComponent(i);
+      check.setState(!check.getState());
+    }
+    selectionChanged();
+  }
+
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt != null)
@@ -272,7 +341,11 @@ public class FeatureSettings extends Panel implements ItemListener,
         return;
       }
     }
+    selectionChanged();
+  }
 
+  void selectionChanged()
+  {
       Component[] comps = featurePanel.getComponents();
       int cSize = comps.length;
 
@@ -296,28 +369,46 @@ public class FeatureSettings extends Panel implements ItemListener,
         ap.overviewPanel.updateOverviewImage();
   }
 
-  Checkbox selectedCheck;
+  MyCheckbox selectedCheck;
   boolean dragging = false;
 
   public void mousePressed(MouseEvent evt)
   {
-    selectedCheck = (Checkbox)evt.getSource();
+
+    selectedCheck = (MyCheckbox)evt.getSource();
+
+    if(fr.featureLinks!=null
+       && fr.featureLinks.containsKey(selectedCheck.getLabel() )
+        )
+      {
+        if(evt.getX()>selectedCheck.stringWidth+20)
+        {
+          evt.consume();
+        }
+      }
+
   }
 
   public void mouseDragged(MouseEvent evt)
   {
+    if(((Component)evt.getSource()).getParent()!=featurePanel)
+      return;
       dragging = true;
   }
 
   public void mouseReleased(MouseEvent evt)
   {
+    if(((Component)evt.getSource()).getParent()!=featurePanel)
+      return;
+
     Component comp = null;
     Checkbox  target = null;
 
     int height = evt.getY()+evt.getComponent().getLocation().y;
 
-    if(height > this.getSize().height)
+    if(height > featurePanel.getSize().height)
      {
+
        comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);
      }
      else if(height < 0)
@@ -364,7 +455,23 @@ public class FeatureSettings extends Panel implements ItemListener,
   public void mouseExited(MouseEvent evt){}
   public void mouseClicked(MouseEvent evt)
   {
-    Checkbox check = (Checkbox) evt.getSource();
+    MyCheckbox check = (MyCheckbox) evt.getSource();
+
+    if (fr.featureLinks!=null
+        && fr.featureLinks.containsKey(check.getLabel()))
+    {
+      if (evt.getX() > check.stringWidth + 20)
+      {
+        evt.consume();
+        String link = fr.featureLinks.get(check.getLabel()).toString();
+        ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
+                              link.substring(0, link.indexOf("|")));
+      }
+    }
+
+    if(check.getParent()!=featurePanel)
+      return;
+
     if(evt.getClickCount()>1)
     {
        new UserDefinedColours(this, check.getLabel(),
@@ -372,4 +479,35 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
   public void mouseMoved(MouseEvent evt){}
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
+    ap.seqPanel.seqCanvas.repaint();
+
+  }
+
+  class MyCheckbox extends Checkbox
+  {
+    public int stringWidth;
+    boolean hasLink;
+    public MyCheckbox(String label, boolean checked, boolean haslink)
+    {
+      super(label, checked);
+
+      FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
+      stringWidth = fm.stringWidth(label);
+      this.hasLink = haslink;
+    }
+
+    public void paint(Graphics g)
+    {
+      if (hasLink)
+        g.drawImage(linkImage, stringWidth + 25,(
+        getSize().height-linkImage.getHeight(this))/2,
+                    this);
+    }
+  }
 }
+
+