X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;fp=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=850088844206e586aa4b34ef118f909ad37a908b;hb=71b7dc2dbc920391e3209bde9e915dd3436871f3;hp=f6352d7be728d628c9c636f1a5b6790a0fea7432;hpb=2d5838594f5ac09384c684209c16961f47b42af5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index f6352d7..8500888 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -21,6 +21,8 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -35,9 +37,11 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Hashtable;
+import java.util.Vector;
 
 import javax.swing.BorderFactory;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JColorChooser;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
@@ -49,27 +53,21 @@ import net.miginfocom.swing.MigLayout;
 @SuppressWarnings("serial")
 public class AnnotationColourChooser extends AnnotationRowFilter
 {
+  private static final int ONETHOUSAND = 1000;
 
-  ColourSchemeI oldcs;
+  private ColourSchemeI oldcs;
 
-  Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
+  private JButton defColours;
 
-  /**
-   * enabled if the user is dragging the slider - try to keep updates to a
-   * minimun
-   */
+  private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  JComboBox<String> annotations;
+  private JCheckBox useOriginalColours = new JCheckBox();
 
-  JButton defColours = new JButton();
+  private JPanel minColour = new JPanel();
 
-  JPanel jPanel1 = new JPanel();
+  private JPanel maxColour = new JPanel();
 
-  JPanel jPanel2 = new JPanel();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  private JComboBox<String> threshold = new JComboBox<String>();
+  private JCheckBox thresholdIsMin = new JCheckBox();
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
@@ -108,7 +106,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.isPredefinedColours()
+      useOriginalColours.setSelected(acg.isPredefinedColours()
               || acg.getBaseColour() != null);
       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
       {
@@ -118,15 +116,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       seqAssociated.setSelected(acg.isSeqAssociated());
 
     }
-    annotations = new JComboBox<String>(
-            getAnnotationItems(seqAssociated.isSelected()));
+    Vector<String> annotItems = getAnnotationItems(seqAssociated
+            .isSelected());
+    annotations = new JComboBox<String>(annotItems);
 
     populateThresholdComboBox(threshold);
 
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.setSelectedItem(acg.getAnnotation());
+      String label = getAnnotationMenuLabel(acg.getAnnotation());
+      annotations.setSelectedItem(label);
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
@@ -143,16 +143,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 MessageManager
                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
       }
-      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
       thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-    }
+    jbInit();
     adjusting = false;
 
     updateView();
@@ -160,19 +155,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     frame.pack();
   }
 
-  public AnnotationColourChooser()
+  @Override
+  protected void jbInit()
   {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
+    super.jbInit();
 
-  private void jbInit() throws Exception
-  {
     minColour.setFont(JvSwingUtils.getLabelFont());
     minColour.setBorder(BorderFactory.createEtchedBorder());
     minColour.setPreferredSize(new Dimension(40, 20));
@@ -203,26 +190,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         }
       }
     });
-    ok.setOpaque(false);
-    ok.setText(MessageManager.getString("action.ok"));
-    ok.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed();
-      }
-    });
-    cancel.setOpaque(false);
-    cancel.setText(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed();
-      }
-    });
+
+    defColours = new JButton();
     defColours.setOpaque(false);
     defColours.setText(MessageManager.getString("action.set_defaults"));
     defColours.setToolTipText(MessageManager
@@ -237,48 +206,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       }
     });
 
-    annotations.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed();
-      }
-    });
-    getThreshold().addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed();
-      }
-    });
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed();
-      }
-    });
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    currentColours.setFont(JvSwingUtils.getLabelFont());
-    currentColours.setOpaque(false);
-    currentColours.setText(MessageManager
+    useOriginalColours.setFont(JvSwingUtils.getLabelFont());
+    useOriginalColours.setOpaque(false);
+    useOriginalColours.setText(MessageManager
             .getString("label.use_original_colours"));
-    currentColours.addActionListener(new ActionListener()
+    useOriginalColours.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        currentColours_actionPerformed();
+        originalColours_actionPerformed();
       }
     });
     thresholdIsMin.setBackground(Color.white);
@@ -307,7 +244,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       }
     });
 
-    this.setLayout(borderLayout1);
+    this.setLayout(new BorderLayout());
+    JPanel jPanel1 = new JPanel();
+    JPanel jPanel2 = new JPanel();
     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
     jPanel1.setBackground(Color.white);
     jPanel2.setBackground(Color.white);
@@ -316,7 +255,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     jPanel1.add(cancel);
     jPanel2.add(annotations, "grow, wrap");
     jPanel2.add(seqAssociated);
-    jPanel2.add(currentColours);
+    jPanel2.add(useOriginalColours);
     JPanel colpanel = new JPanel(new FlowLayout());
     colpanel.setBackground(Color.white);
     colpanel.add(minColour);
@@ -391,7 +330,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   {
     if (slider.isEnabled())
     {
-      if (currentColours.isSelected()
+      if (useOriginalColours.isSelected()
               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
         updateView();
@@ -403,24 +342,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     }
   }
 
-  public JComboBox<String> getThreshold()
+  public void originalColours_actionPerformed()
   {
-    return threshold;
-  }
-
-  public void setThreshold(JComboBox<String> threshold)
-  {
-    this.threshold = threshold;
-  }
-
-  public void currentColours_actionPerformed()
-  {
-    if (currentColours.isSelected())
+    boolean selected = useOriginalColours.isSelected();
+    if (selected)
     {
       reset();
     }
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
+    maxColour.setEnabled(!selected);
+    minColour.setEnabled(!selected);
+    thresholdIsMin.setEnabled(!selected);
     updateView();
   }
 
@@ -441,7 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
-    thresholdIsMin.setEnabled(true);
+    thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
@@ -455,7 +386,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     {
       getCurrentAnnotation()
               .setThreshold(
-                      new jalview.datamodel.GraphLine(
+                      new GraphLine(
                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
                               "Threshold", Color.black));
     }
@@ -463,19 +394,19 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      float range = getCurrentAnnotation().graphMax * ONETHOUSAND
+              - getCurrentAnnotation().graphMin * ONETHOUSAND;
 
-      slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
-      slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
-      slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+      slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
+      slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
+      slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
       slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 
     ap.alignmentChanged();
     // ensure all associated views (overviews, structures, etc) are notified of
@@ -483,4 +414,60 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     ap.paintAlignment(true);
   }
 
+  protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
+  {
+  
+    AnnotationColourGradient acg = null;
+    if (useOriginalColours.isSelected())
+    {
+      acg = new AnnotationColourGradient(currentAnn,
+              av.getGlobalColourScheme(), selectedThresholdOption);
+    }
+    else
+    {
+      acg = new AnnotationColourGradient(currentAnn,
+              minColour.getBackground(), maxColour.getBackground(),
+              selectedThresholdOption);
+    }
+    acg.setSeqAssociated(seqAssociated.isSelected());
+  
+    if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+    {
+      acg.setPredefinedColours(true);
+    }
+  
+    acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+  
+    av.setGlobalColourScheme(acg);
+  
+    if (av.getAlignment().getGroups() != null)
+    {
+  
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        if (sg.cs == null)
+        {
+          continue;
+        }
+  
+        if (useOriginalColours.isSelected())
+        {
+          sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
+                  .getColourScheme(), selectedThresholdOption));
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+        }
+        else
+        {
+          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
+                  minColour.getBackground(), maxColour.getBackground(),
+                  selectedThresholdOption));
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+        }
+      }
+    }
+    return false;
+  }
+
 }