X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=7dc11c1d6bac662f25fa0e77db2e8cc8079c4a7c;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=b58d3456e3533e85d338994c56f17fe77bb66320;hpb=b96e3c46826eb2f6809e2a5579b6407daa5fb0c4;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index b58d345..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
@@ -18,13 +18,15 @@
  */
 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,
+public class FeatureSettings
+    extends Panel implements ItemListener,
     MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
 {
   FeatureRenderer fr;
@@ -36,23 +38,25 @@ public class FeatureSettings extends Panel implements ItemListener,
   ScrollPane scrollPane;
   boolean alignmentHasFeatures = false;
   Image linkImage;
-  Scrollbar transparency ;
+  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);
+                                 100 - (int) (fr.transparency * 100), 1, 1, 100);
 
-    if(fr.transparencySetter!=null)
+    if (fr.transparencySetter != null)
     {
       transparency.addAdjustmentListener(this);
     }
     else
+    {
       transparency.setEnabled(false);
+    }
 
     java.net.URL url = getClass().getResource("/images/link.gif");
     if (url != null)
@@ -60,9 +64,10 @@ public class FeatureSettings extends Panel implements ItemListener,
       linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
     }
 
-
-    if(av.featuresDisplayed==null)
+    if (av.featuresDisplayed == null)
+    {
       fr.findAllFeatures();
+    }
 
     setTableData();
 
@@ -70,42 +75,44 @@ public class FeatureSettings extends Panel implements ItemListener,
     scrollPane = new ScrollPane();
     scrollPane.add(featurePanel);
     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));
+    Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
     lowerPanel.add(invert);
 
     Panel tPanel = new Panel(new BorderLayout());
 
-    if(fr.transparencySetter!=null)
+    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);
+    {
+      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)
+    if (groupPanel != null)
     {
       groupPanel.setLayout(
-          new GridLayout( fr.featureGroups.size() / 4 + 1, 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 +60;
-
+    int height = featurePanel.getComponentCount() * 50 + 60;
 
     height = Math.max(200, height);
     height = Math.min(400, height);
@@ -126,19 +133,22 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     alignmentHasFeatures = false;
 
-    if(fr.featureGroups==null)
+    if (fr.featureGroups == null)
+    {
       fr.featureGroups = new Hashtable();
+    }
 
     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;
 
@@ -146,141 +156,145 @@ public class FeatureSettings extends Panel implements ItemListener,
       int index = 0;
       while (index < tmpfeatures.length)
       {
-        if(tmpfeatures[index].getFeatureGroup()!=null)
+        if (tmpfeatures[index].getFeatureGroup() != null)
         {
           group = tmpfeatures[index].featureGroup;
-          if(!allGroups.contains(group))
-           {
-             allGroups.addElement(group);
+          if (!allGroups.contains(group))
+          {
+            allGroups.addElement(group);
 
-             boolean visible = true;
-             if (fr.featureGroups.containsKey(group))
-             {
-               visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-             }
+            boolean visible = true;
+            if (fr.featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+            }
 
-             fr.featureGroups.put(group, new Boolean(visible));
+            fr.featureGroups.put(group, new Boolean(visible));
 
-             if (groupPanel == null)
-             {
-               groupPanel = new Panel();
-             }
+            if (groupPanel == null)
+            {
+              groupPanel = new Panel();
+            }
 
-             Checkbox check =  new MyCheckbox(
+            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);
-           }
+                (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());
+          allFeatures.addElement(tmpfeatures[index].getType());
         }
-         index ++;
+        index++;
       }
     }
 
     resetTable(false);
   }
 
- //This routine adds and removes checkboxes depending on
- //Group selection states
+  //This routine adds and removes checkboxes depending on
+  //Group selection states
   void resetTable(boolean groupsChanged)
   {
-    SequenceFeature [] tmpfeatures;
-    String group=null, type;
+    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))
-                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);
+    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))
+        {
+          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();
+    Component[] comps = featurePanel.getComponents();
     Checkbox check;
     addCheck = true;
     for (int i = 0; i < featurePanel.getComponentCount(); i++)
@@ -303,8 +317,9 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       check = new MyCheckbox(type,
                              selected,
-          (fr.featureLinks!=null && fr.featureLinks.containsKey(type))
-           );
+                             (fr.featureLinks != null &&
+                              fr.featureLinks.containsKey(type))
+          );
 
       check.addMouseListener(this);
       check.addMouseMotionListener(this);
@@ -316,9 +331,9 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   public void actionPerformed(ActionEvent evt)
   {
-    for(int i=0; i<featurePanel.getComponentCount(); i++)
+    for (int i = 0; i < featurePanel.getComponentCount(); i++)
     {
-      Checkbox check = (Checkbox)featurePanel.getComponent(i);
+      Checkbox check = (Checkbox) featurePanel.getComponent(i);
       check.setState(!check.getState());
     }
     selectionChanged();
@@ -335,7 +350,9 @@ 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;
@@ -346,27 +363,26 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   void selectionChanged()
   {
-      Component[] comps = featurePanel.getComponents();
-      int cSize = comps.length;
+    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[][] 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[tmpSize][3];
+    System.arraycopy(tmp, 0, data, 0, tmpSize);
 
-      Object[][]data = new Object[tmpSize][3];
-      System.arraycopy(tmp, 0, data,0, tmpSize);
+    fr.setFeaturePriority(data);
 
-      fr.setFeaturePriority(data);
-      ap.seqPanel.seqCanvas.repaint();
-      if (ap.overviewPanel != null)
-        ap.overviewPanel.updateOverviewImage();
+    ap.paintAlignment(true);
   }
 
   MyCheckbox selectedCheck;
@@ -375,65 +391,74 @@ public class FeatureSettings extends Panel implements ItemListener,
   public void mousePressed(MouseEvent evt)
   {
 
-    selectedCheck = (MyCheckbox)evt.getSource();
+    selectedCheck = (MyCheckbox) evt.getSource();
 
-    if(fr.featureLinks!=null
-       && fr.featureLinks.containsKey(selectedCheck.getLabel() )
+    if (fr.featureLinks != null
+        && fr.featureLinks.containsKey(selectedCheck.getLabel())
         )
+    {
+      if (evt.getX() > selectedCheck.stringWidth + 20)
       {
-        if(evt.getX()>selectedCheck.stringWidth+20)
-        {
-          evt.consume();
-        }
+        evt.consume();
       }
+    }
 
   }
 
   public void mouseDragged(MouseEvent evt)
   {
-    if(((Component)evt.getSource()).getParent()!=featurePanel)
+    if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+    {
       return;
-      dragging = true;
+    }
+    dragging = true;
   }
 
   public void mouseReleased(MouseEvent evt)
   {
-    if(((Component)evt.getSource()).getParent()!=featurePanel)
+    if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+    {
       return;
+    }
 
     Component comp = null;
-    Checkbox  target = null;
-
-    int height = evt.getY()+evt.getComponent().getLocation().y;
-
-    if(height > featurePanel.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);
-     }
-
-    if(comp!=null && comp instanceof Checkbox)
-      target = (Checkbox)comp;
-
-    if (   selectedCheck != null
+    Checkbox target = null;
+
+    int height = evt.getY() + evt.getComponent().getLocation().y;
+
+    if (height > featurePanel.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);
+    }
+
+    if (comp != null && comp instanceof Checkbox)
+    {
+      target = (Checkbox) comp;
+    }
+
+    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);
@@ -448,16 +473,20 @@ public class FeatureSettings extends Panel implements ItemListener,
     fr.setColour(feature, col);
     featurePanel.removeAll();
     resetTable(false);
-    ap.repaint();
+    ap.paintAlignment(true);
   }
 
-  public void mouseEntered(MouseEvent evt){}
-  public void mouseExited(MouseEvent evt){}
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
   public void mouseClicked(MouseEvent evt)
   {
     MyCheckbox check = (MyCheckbox) evt.getSource();
 
-    if (fr.featureLinks!=null
+    if (fr.featureLinks != null
         && fr.featureLinks.containsKey(check.getLabel()))
     {
       if (evt.getX() > check.stringWidth + 20)
@@ -469,16 +498,20 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
     }
 
-    if(check.getParent()!=featurePanel)
+    if (check.getParent() != featurePanel)
+    {
       return;
+    }
 
-    if(evt.getClickCount()>1)
+    if (evt.getClickCount() > 1)
     {
-       new UserDefinedColours(this, check.getLabel(),
-                              fr.getColour(check.getLabel()));
+      new UserDefinedColours(this, check.getLabel(),
+                             fr.getColour(check.getLabel()));
     }
   }
-  public void mouseMoved(MouseEvent evt){}
+
+  public void mouseMoved(MouseEvent evt)
+  {}
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
@@ -487,7 +520,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   }
 
-  class MyCheckbox extends Checkbox
+  class MyCheckbox
+      extends Checkbox
   {
     public int stringWidth;
     boolean hasLink;
@@ -503,11 +537,11 @@ public class FeatureSettings extends Panel implements ItemListener,
     public void paint(Graphics g)
     {
       if (hasLink)
-        g.drawImage(linkImage, stringWidth + 25,(
-        getSize().height-linkImage.getHeight(this))/2,
+      {
+        g.drawImage(linkImage, stringWidth + 25, (
+            getSize().height - linkImage.getHeight(this)) / 2,
                     this);
+      }
     }
   }
 }
-
-