X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=7dc11c1d6bac662f25fa0e77db2e8cc8079c4a7c;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=30d57e0a3326e6837761655f27963a0ec3d90e9c;hpb=449001e7a8c9aad77117daa36567f3e8313646ea;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 30d57e0..7dc11c1 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) 2007 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
@@ -18,110 +18,330 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import java.awt.*;
 import java.util.*;
+
+import java.awt.*;
 import java.awt.event.*;
 
+import jalview.datamodel.*;
 
-public class FeatureSettings extends Panel implements ItemListener,
-    MouseListener, MouseMotionListener
+public class FeatureSettings
+    extends Panel implements ItemListener,
+    MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
 {
-  final FeatureRenderer fr;
-  final AlignmentPanel ap;
-  final AlignViewport av;
-  final Frame frame;
+  FeatureRenderer fr;
+  AlignmentPanel ap;
+  AlignViewport av;
+  Frame frame;
   Panel groupPanel;
   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());
-    ScrollPane sp = new ScrollPane();
-    sp.add(featurePanel);
-    add(sp, BorderLayout.CENTER);
-    if(groupPanel!=null)
+    scrollPane = new ScrollPane();
+    scrollPane.add(featurePanel);
+    if (alignmentHasFeatures)
     {
-      sp = new ScrollPane();
-      sp.add(groupPanel);
+      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());
 
-      add(sp, BorderLayout.NORTH);
-      sp.validate();
-      sp.setSize( 100, 55);
+    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(
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+      groupPanel.validate();
+
+      add(groupPanel, BorderLayout.NORTH);
     }
     frame = new Frame();
     frame.add(this);
-    int height = featurePanel.getComponentCount()*50 ;
-    if (height>400)
-      height = 400;
+    int height = featurePanel.getComponentCount() * 50 + 60;
+
+    height = Math.max(200, height);
+    height = Math.min(400, height);
 
-    jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 200,
+    jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,
                                      height);
   }
 
+  public void paint(Graphics g)
+  {
+    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()
   {
-    if(fr.featureGroups==null)
+    alignmentHasFeatures = false;
+
+    if (fr.featureGroups == null)
+    {
       fr.featureGroups = new Hashtable();
-    else
-      fr.featureGroups.clear();
+    }
 
     Vector allFeatures = new Vector();
-    Enumeration tmpfeatures;
-    SequenceFeature sf;
+    Vector allGroups = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
 
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
       if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      {
         continue;
+      }
+
+      alignmentHasFeatures = true;
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures().elements();
-      while (tmpfeatures.hasMoreElements())
+      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      int index = 0;
+      while (index < tmpfeatures.length)
       {
-        sf = (SequenceFeature) tmpfeatures.nextElement();
-        if (!allFeatures.contains(sf.getType()))
+        if (tmpfeatures[index].getFeatureGroup() != null)
         {
-          allFeatures.addElement(sf.getType());
-          Color col = fr.getColour(sf.getType());
-          boolean displayed = true;
-          if (fr.featuresDisplayed != null)
-            displayed = fr.featuresDisplayed.contains(sf.getType());
-
-          Checkbox check = new Checkbox(sf.getType(), displayed);
-          check.addMouseListener(this);
-          check.addMouseMotionListener(this);
-          check.setBackground(col);
-          check.addItemListener(this);
-          featurePanel.add(check);
+          group = tmpfeatures[index].featureGroup;
+          if (!allGroups.contains(group))
+          {
+            allGroups.addElement(group);
+
+            boolean visible = true;
+            if (fr.featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+            }
+
+            fr.featureGroups.put(group, new Boolean(visible));
+
+            if (groupPanel == null)
+            {
+              groupPanel = new Panel();
+            }
+
+            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);
+          }
         }
-        if(sf.getFeatureGroup()!=null
-           && !fr.featureGroups.containsKey(sf.getFeatureGroup()))
+
+        if (!allFeatures.contains(tmpfeatures[index].getType()))
+        {
+          allFeatures.addElement(tmpfeatures[index].getType());
+        }
+        index++;
+      }
+    }
+
+    resetTable(false);
+  }
+
+  //This routine adds and removes checkboxes depending on
+  //Group selection states
+  void resetTable(boolean groupsChanged)
+  {
+    SequenceFeature[] tmpfeatures;
+    String group = null, type;
+    Vector visibleChecks = new Vector();
+
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      {
+        continue;
+      }
+
+      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        group = tmpfeatures[index].featureGroup;
+
+        if (group == null || fr.featureGroups.get(group) == null ||
+            ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+        {
+          type = tmpfeatures[index].getType();
+          if (!visibleChecks.contains(type))
+          {
+            visibleChecks.addElement(type);
+          }
+        }
+        index++;
+      }
+    }
+
+    Component[] comps;
+    int cSize = featurePanel.getComponentCount();
+    Checkbox check;
+    //This will remove any checkboxes which shouldn't be
+    //visible
+    for (int i = 0; i < cSize; i++)
+    {
+      comps = featurePanel.getComponents();
+      check = (Checkbox) comps[i];
+      if (!visibleChecks.contains(check.getLabel()))
+      {
+        featurePanel.remove(i);
+        cSize--;
+        i--;
+      }
+    }
+
+    if (fr.renderOrder != null)
+    {
+      //First add the checks in the previous render order,
+      //in case the window has been closed and reopened
+      for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
+      {
+        String item = fr.renderOrder[ro];
+
+        if (!visibleChecks.contains(item))
         {
-          fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));
-          if(groupPanel==null)
-            groupPanel = new Panel();
-
-          Checkbox check = new Checkbox(sf.getFeatureGroup(), true);
-          check.setFont(new Font("Serif", Font.BOLD, 12));
-          check.addItemListener(this);
-          groupPanel.add(check);
+          continue;
         }
+
+        visibleChecks.removeElement(item);
+
+        addCheck(false, item);
       }
     }
 
-    featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5));
+    // 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());
+    }
+
+    featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,
+                                          10, 5));
     featurePanel.validate();
+
+    if (scrollPane != null)
+    {
+      scrollPane.validate();
+    }
+
+    itemStateChanged(null);
+  }
+
+  void addCheck(boolean groupsChanged, String type)
+  {
+    boolean addCheck;
+    Component[] comps = featurePanel.getComponents();
+    Checkbox check;
+    addCheck = true;
+    for (int i = 0; i < featurePanel.getComponentCount(); i++)
+    {
+      check = (Checkbox) comps[i];
+      if (check.getLabel().equals(type))
+      {
+        addCheck = false;
+        break;
+      }
+    }
+
+    if (addCheck)
+    {
+      boolean selected = false;
+      if (groupsChanged || av.featuresDisplayed.containsKey(type))
+      {
+        selected = true;
+      }
+
+      check = new MyCheckbox(type,
+                             selected,
+                             (fr.featureLinks != null &&
+                              fr.featureLinks.containsKey(type))
+          );
+
+      check.addMouseListener(this);
+      check.addMouseMotionListener(this);
+      check.setBackground(fr.getColour(type));
+      check.addItemListener(this);
+      featurePanel.add(check);
+    }
+  }
+
+  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)
+    if (evt != null)
     {
       //Is the source a top level featureGroup?
       Checkbox source = (Checkbox) evt.getSource();
@@ -130,80 +350,117 @@ public class FeatureSettings extends Panel implements ItemListener,
         fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
         ap.seqPanel.seqCanvas.repaint();
         if (ap.overviewPanel != null)
+        {
           ap.overviewPanel.updateOverviewImage();
+        }
 
+        resetTable(true);
         return;
       }
     }
+    selectionChanged();
+  }
 
-      Component[] comps = featurePanel.getComponents();
-      int cSize = comps.length;
+  void selectionChanged()
+  {
+    Component[] comps = featurePanel.getComponents();
+    int cSize = comps.length;
+
+    Object[][] tmp = new Object[cSize][3];
+    int tmpSize = 0;
+    for (int i = 0; i < cSize; i++)
+    {
+      Checkbox check = (Checkbox) comps[i];
+      tmp[tmpSize][0] = check.getLabel();
+      tmp[tmpSize][1] = fr.getColour(check.getLabel());
+      tmp[tmpSize][2] = new Boolean(check.getState());
+      tmpSize++;
+    }
 
-      Object[][] data = new Object[cSize][3];
+    Object[][] data = new Object[tmpSize][3];
+    System.arraycopy(tmp, 0, data, 0, tmpSize);
 
-      for (int i = 0; i < cSize; i++)
-      {
-        Checkbox check = (Checkbox) comps[i];
-        data[i][0] = check.getLabel();
-        data[i][1] = fr.getColour(check.getLabel());
-        data[i][2] = new Boolean(check.getState());
-      }
+    fr.setFeaturePriority(data);
 
-      fr.setFeaturePriority(data);
-      ap.seqPanel.seqCanvas.repaint();
-      if (ap.overviewPanel != null)
-        ap.overviewPanel.updateOverviewImage();
+    ap.paintAlignment(true);
   }
 
-  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)
   {
-      dragging = true;
+    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;
+    Checkbox target = null;
 
-    int height = evt.getY()+evt.getComponent().getLocation().y;
+    int height = evt.getY() + evt.getComponent().getLocation().y;
 
+    if (height > featurePanel.getSize().height)
+    {
 
-    if(height > this.getSize().height)
-     {
-       comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);
-     }
-     else if(height < 0)
-     {
-       comp = featurePanel.getComponent(0);
-     }
-     else
-     {
-       comp = featurePanel.getComponentAt(evt.getX(),
-                                  evt.getY() +
-                                  evt.getComponent().getLocation().y);
-     }
+      comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);
+    }
+    else if (height < 0)
+    {
+      comp = featurePanel.getComponent(0);
+    }
+    else
+    {
+      comp = featurePanel.getComponentAt(evt.getX(),
+                                         evt.getY() +
+                                         evt.getComponent().getLocation().y);
+    }
 
-    if(comp!=null && comp instanceof Checkbox)
-      target = (Checkbox)comp;
+    if (comp != null && comp instanceof Checkbox)
+    {
+      target = (Checkbox) comp;
+    }
 
-    if (selectedCheck != null && target != null && selectedCheck != target)
+    if (selectedCheck != null
+        && target != null
+        && selectedCheck != target)
     {
       int targetIndex = -1;
-      for(int i=0; i<featurePanel.getComponentCount(); i++)
+      for (int i = 0; i < featurePanel.getComponentCount(); i++)
       {
-          if(target==featurePanel.getComponent(i))
-          { targetIndex = i; break; }
+        if (target == featurePanel.getComponent(i))
+        {
+          targetIndex = i;
+          break;
+        }
       }
 
-
       featurePanel.remove(selectedCheck);
       featurePanel.add(selectedCheck, targetIndex);
       featurePanel.validate();
@@ -211,9 +468,80 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  public void setUserColour(String feature, Color col)
+  {
+    fr.setColour(feature, col);
+    featurePanel.removeAll();
+    resetTable(false);
+    ap.paintAlignment(true);
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {
+    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(),
+                             fr.getColour(check.getLabel()));
+    }
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {}
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
+    ap.seqPanel.seqCanvas.repaint();
+
+  }
 
-  public void mouseEntered(MouseEvent evt){}
-  public void mouseExited(MouseEvent evt){}
-  public void mouseClicked(MouseEvent evt){}
-  public void mouseMoved(MouseEvent evt){}
+  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);
+      }
+    }
+  }
 }