From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Feb 2006 15:50:44 +0000 (+0000)
Subject: Incorporated threshold slider
X-Git-Tag: Root_VamJalview_2_07b+~116
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=09003bd97d75ad14cd000fc581d6ec93b7a08bcb;p=jalview.git

Incorporated threshold slider
---

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 25eee10..49e835d 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -19,12 +19,13 @@
 package jalview.gui;
 
 import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-import java.awt.BorderLayout;
+import java.awt.event.*;
 import java.awt.*;
 
 import jalview.schemes.*;
+import javax.swing.event.*;
+import java.util.*;
+import jalview.datamodel.SequenceGroup;
 
 public class AnnotationColourChooser
     extends JPanel
@@ -33,29 +34,54 @@ public class AnnotationColourChooser
   AlignViewport av;
   AlignmentPanel ap;
   ColourSchemeI oldcs;
+  Hashtable oldgroupColours;
+  jalview.datamodel.AlignmentAnnotation currentAnnotation;
 
   public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
+    if (av.alignment.getGroups() != null)
+    {
+      oldgroupColours = new Hashtable();
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+        oldgroupColours.put(sg, sg.cs);
+      }
+    }
     this.av = av;
     this.ap = ap;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 110, false);
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145, false);
 
-    try{
+    try
+    {
       jbInit();
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {}
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+        valueChanged();
+      }
+    });
 
-    if(av.alignment.getAlignmentAnnotation()==null)
+    if (av.alignment.getAlignmentAnnotation() == null)
       return;
 
-    if(oldcs instanceof AnnotationColourGradient)
+    if (oldcs instanceof AnnotationColourGradient)
     {
-      AnnotationColourGradient acg = (AnnotationColourGradient)oldcs;
-      minColour.setBackground( acg.getMinColour() );
-      maxColour.setBackground( acg.getMaxColour() );
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      minColour.setBackground(acg.getMinColour());
+      maxColour.setBackground(acg.getMaxColour());
     }
     else
     {
@@ -65,7 +91,7 @@ public class AnnotationColourChooser
 
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
-      if(av.alignment.getAlignmentAnnotation()[i].graph>0)
+      if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
         annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
     }
 
@@ -90,7 +116,7 @@ public class AnnotationColourChooser
   private void jbInit()
       throws Exception
   {
-    minColour.setBounds(new Rectangle(145, 5, 85, 25));
+    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     minColour.setToolTipText("");
     minColour.setMargin(new Insets(2, 2, 2, 2));
     minColour.setText("Min Colour");
@@ -101,7 +127,7 @@ public class AnnotationColourChooser
         minColour_actionPerformed(e);
       }
     });
-    maxColour.setBounds(new Rectangle(235, 5, 89, 25));
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     maxColour.setMargin(new Insets(2, 2, 2, 2));
     maxColour.setText("Max Colour");
     maxColour.addActionListener(new ActionListener()
@@ -130,8 +156,7 @@ public class AnnotationColourChooser
       }
     });
     this.setLayout(borderLayout1);
-    jPanel2.setLayout(null);
-    annotations.setBounds(new Rectangle(5, 7, 135, 21));
+    jPanel2.setLayout(flowLayout1);
     annotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -141,7 +166,6 @@ public class AnnotationColourChooser
     });
     jPanel1.setBackground(Color.white);
     jPanel2.setBackground(Color.white);
-    threshold.setBounds(new Rectangle(328, 6, 125, 22));
     threshold.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -149,14 +173,43 @@ public class AnnotationColourChooser
         threshold_actionPerformed(e);
       }
     });
+    jPanel3.setLayout(flowLayout2);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed(e);
+      }
+    });
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(10);
+    jPanel3.setBackground(Color.white);
+    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    currentColours.setOpaque(false);
+    currentColours.setText("Use Original Colours");
+    currentColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        currentColours_actionPerformed(e);
+      }
+    });
     jPanel1.add(ok);
     jPanel1.add(cancel);
     jPanel2.add(annotations);
+    jPanel2.add(currentColours);
     jPanel2.add(minColour);
     jPanel2.add(maxColour);
-    jPanel2.add(threshold);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    jPanel3.add(threshold);
+    jPanel3.add(slider);
+    jPanel3.add(thresholdValue);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.CENTER);
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);
   }
 
   JComboBox annotations = new JComboBox();
@@ -168,6 +221,12 @@ public class AnnotationColourChooser
   JPanel jPanel2 = new JPanel();
   BorderLayout borderLayout1 = new BorderLayout();
   JComboBox threshold = new JComboBox();
+  FlowLayout flowLayout1 = new FlowLayout();
+  JPanel jPanel3 = new JPanel();
+  FlowLayout flowLayout2 = new FlowLayout();
+  JSlider slider = new JSlider();
+  JTextField thresholdValue = new JTextField(20);
+  JCheckBox currentColours = new JCheckBox();
 
   public void minColour_actionPerformed(ActionEvent e)
   {
@@ -194,8 +253,8 @@ public class AnnotationColourChooser
   void changeColour()
   {
     // Check if combobox is still adjusting
-    if(threshold.getSelectedIndex()==-1)
-          return;
+    if (threshold.getSelectedIndex() == -1)
+      return;
 
     // We removed the non-graph annotations when filling the combobox
     // so allow for them again here
@@ -203,56 +262,131 @@ public class AnnotationColourChooser
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
-        nograph ++;
+        nograph++;
       else
-        graph ++;
+        graph++;
 
-      if(graph==annotations.getSelectedIndex())
+      if (graph == annotations.getSelectedIndex())
         break;
     }
 
-    jalview.datamodel.AlignmentAnnotation aa
-        = av.alignment.getAlignmentAnnotation()[graph+nograph];
-
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
 
     int aboveThreshold = -1;
-    if(threshold.getSelectedItem().equals("Above Threshold"))
+    if (threshold.getSelectedItem().equals("Above Threshold"))
       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
-    else if(threshold.getSelectedItem().equals("Below Threshold"))
+    else if (threshold.getSelectedItem().equals("Below Threshold"))
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 
-    if(aboveThreshold!=AnnotationColourGradient.NO_THRESHOLD && aa.threshold==null)
-   {
-     aa.setThreshold(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));
-   }
-
-    AnnotationColourGradient acg = new AnnotationColourGradient(aa,
-     minColour.getBackground(),
-     maxColour.getBackground(),
-     aboveThreshold );
+    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    {
+      currentAnnotation.threshold = null;
+      slider.setEnabled(false);
+      thresholdValue.setEnabled(false);
+      thresholdValue.setText("");
+    }
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
+             currentAnnotation.threshold == null)
+    {
+      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
+                                     ( (currentAnnotation.graphMax -
+                                        currentAnnotation.graphMin) / 2f,
+                                      "Threshold",
+                                      Color.black));
+      float range = currentAnnotation.graphMax * 1000 -
+          currentAnnotation.graphMin * 1000;
+
+      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
+      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
+      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
+      thresholdValue.setText(currentAnnotation.threshold.value + "");
+      slider.setMajorTickSpacing( (int) (range / 10f));
+      slider.setMinorTickSpacing( (int) (range / 100f));
+      slider.setEnabled(true);
+      thresholdValue.setEnabled(true);
+    }
 
+    AnnotationColourGradient acg = null;
+    if (currentColours.isSelected())
+      acg = new AnnotationColourGradient(
+          currentAnnotation,
+          av.getGlobalColourScheme(), aboveThreshold);
+    else
+      acg =
+          new AnnotationColourGradient(
+              currentAnnotation,
+              minColour.getBackground(),
+              maxColour.getBackground(),
+              aboveThreshold);
 
+    av.setGlobalColourScheme(acg);
 
+    if (av.alignment.getGroups() != null)
+    {
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+
+        if (sg.cs == null)
+        {
+          continue;
+        }
+
+        if (currentColours.isSelected())
+          sg.cs = new AnnotationColourGradient(
+              currentAnnotation,
+              sg.cs, aboveThreshold);
+        else
+          sg.cs = new AnnotationColourGradient(
+              currentAnnotation,
+              minColour.getBackground(),
+              maxColour.getBackground(),
+              aboveThreshold);
 
-   av.setGlobalColourScheme(acg);
-   ap.repaint();
+      }
+    }
 
+    ap.repaint();
   }
 
   public void ok_actionPerformed(ActionEvent e)
   {
     changeColour();
-    try{
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {}
   }
 
   public void cancel_actionPerformed(ActionEvent e)
   {
-    av.setGlobalColourScheme(oldcs);
-    try{
+    reset();
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {}
+  }
+
+
+  void reset()
+  {
+    av.setGlobalColourScheme(oldcs);
+    if (av.alignment.getGroups() != null)
+    {
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+        sg.cs = (ColourSchemeI)oldgroupColours.get(sg);
+      }
+    }
   }
 
   public void thresholdCheck_actionPerformed(ActionEvent e)
@@ -262,6 +396,8 @@ public class AnnotationColourChooser
 
   public void annotations_actionPerformed(ActionEvent e)
   {
+    if(currentAnnotation!=null)
+      currentAnnotation.threshold = null;
     changeColour();
   }
 
@@ -270,4 +406,34 @@ public class AnnotationColourChooser
     changeColour();
   }
 
+  public void thresholdValue_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      float f = Float.parseFloat(thresholdValue.getText());
+      slider.setValue( (int) (f * 1000));
+    }
+    catch (NumberFormatException ex)
+    {}
+  }
+
+  public void valueChanged()
+  {
+    currentAnnotation.threshold.value = (float)slider.getValue()/1000f;
+    ap.repaint();
+  }
+
+  public void currentColours_actionPerformed(ActionEvent e)
+  {
+    if(currentColours.isSelected())
+    {
+      reset();
+    }
+
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+
+    changeColour();
+  }
+
 }