Incorporated threshold slider

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