X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=b58d3456e3533e85d338994c56f17fe77bb66320;hb=b169b1a49c078d123feb729db6acb9779f50e7d6;hp=20e4a4d548ed79a6b071c3ac4d5149a6e6440498;hpb=011c92dbea927aa8ae693ae75bf1b42a1c564aef;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 20e4a4d..b58d345 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -25,15 +25,18 @@ import java.awt.event.*;
 
 
 public class FeatureSettings extends Panel implements ItemListener,
-    MouseListener, MouseMotionListener
+    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)
   {
@@ -41,96 +44,163 @@ public class FeatureSettings extends Panel implements ItemListener,
     this.av = 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 = new ScrollPane();
     scrollPane.add(featurePanel);
-    add(scrollPane, BorderLayout.CENTER);
+    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(
-          new GridLayout(groupPanel.getComponentCount() / 4, 4));
+          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;
+
 
-    jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 250,
+    height = Math.max(200, height);
+    height = Math.min(400, height);
+
+    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()
   {
+    alignmentHasFeatures = false;
+
     if(fr.featureGroups==null)
       fr.featureGroups = new Hashtable();
-    else
-      fr.featureGroups.clear();
 
     Vector allFeatures = new Vector();
+    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();
       int index = 0;
       while (index < tmpfeatures.length)
       {
-        if(tmpfeatures[index].getFeatureGroup()!=null
-           && tmpfeatures[index].getFeatureGroup().length()>0
-           && !fr.featureGroups.containsKey(tmpfeatures[index].getFeatureGroup()))
+        if(tmpfeatures[index].getFeatureGroup()!=null)
         {
-          fr.featureGroups.put(tmpfeatures[index].getFeatureGroup(), new Boolean(true));
-          if(groupPanel==null)
-          {
-            groupPanel = new Panel();
-          }
-
-          Checkbox check = new Checkbox(tmpfeatures[index].getFeatureGroup(), true);
-          check.setFont(new Font("Serif", Font.BOLD, 12));
-          check.addItemListener(this);
-          groupPanel.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 (!allFeatures.contains(tmpfeatures[index].getType()))
         {
             allFeatures.addElement(tmpfeatures[index].getType());
         }
-
-
-        index ++;
+         index ++;
       }
     }
 
-    resetTable();
-    featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5));
-    featurePanel.validate();
+    resetTable(false);
   }
 
-  void resetTable()
+ //This routine adds and removes checkboxes depending on
+ //Group selection states
+  void resetTable(boolean groupsChanged)
   {
-    featurePanel.removeAll();
-    Enumeration groups = fr.featureGroups.keys();
     SequenceFeature [] tmpfeatures;
-    String group, type;
-    Vector checksAdded = new Vector();
-
-    while(groups.hasMoreElements())
-    {
-     group = groups.nextElement().toString();
-     if ( !( (Boolean) fr.featureGroups.get(group)).booleanValue())
-       continue;
+    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;
 
@@ -138,28 +208,120 @@ public class FeatureSettings extends Panel implements ItemListener,
          int index = 0;
          while (index < tmpfeatures.length)
          {
-           if (tmpfeatures[index].getFeatureGroup() != null &&
-               tmpfeatures[index].getFeatureGroup().equals(group))
+           group = tmpfeatures[index].featureGroup;
+
+           if (group==null || fr.featureGroups.get(group)==null ||
+               ((Boolean) fr.featureGroups.get(group)).booleanValue())
            {
              type = tmpfeatures[index].getType();
-             if(!checksAdded.contains(type))
+             if(!visibleChecks.contains(type) )
              {
-               checksAdded.addElement(type);
-               Checkbox check = new Checkbox(type, true);
-               check.addMouseListener(this);
-               check.addMouseMotionListener(this);
-               check.setBackground(fr.getColour(type));
-               check.addItemListener(this);
-               featurePanel.add(check);
+               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))
+                continue;
+
+              visibleChecks.removeElement(item);
+
+              addCheck(false, item);
+         }
+       }
+
+       // 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)
@@ -175,11 +337,15 @@ public class FeatureSettings extends Panel implements ItemListener,
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        resetTable();
+        resetTable(true);
         return;
       }
     }
+    selectionChanged();
+  }
 
+  void selectionChanged()
+  {
       Component[] comps = featurePanel.getComponents();
       int cSize = comps.length;
 
@@ -188,9 +354,6 @@ public class FeatureSettings extends Panel implements ItemListener,
       for (int i = 0; i < cSize; i++)
       {
         Checkbox check = (Checkbox) comps[i];
-        if(!check.getState())
-          continue;
-
         tmp[tmpSize][0] = check.getLabel();
         tmp[tmpSize][1] = fr.getColour(check.getLabel());
         tmp[tmpSize][2] = new Boolean(check.getState());
@@ -206,29 +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)
@@ -245,7 +425,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     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++)
@@ -254,7 +436,6 @@ public class FeatureSettings extends Panel implements ItemListener,
           { targetIndex = i; break; }
       }
 
-
       featurePanel.remove(selectedCheck);
       featurePanel.add(selectedCheck, targetIndex);
       featurePanel.validate();
@@ -262,9 +443,71 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  public void setUserColour(String feature, Color col)
+  {
+    fr.setColour(feature, col);
+    featurePanel.removeAll();
+    resetTable(false);
+    ap.repaint();
+  }
 
   public void mouseEntered(MouseEvent evt){}
   public void mouseExited(MouseEvent evt){}
-  public void mouseClicked(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();
+
+  }
+
+  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);
+    }
+  }
 }
+
+