X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureColourChooser.java;h=30733efb404421b7780c936166a26422183fb216;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=4f673570d4a81a7c4a85b960b6477ac267171063;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 4f67357..30733ef 100644
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -1,98 +1,158 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.Rectangle;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.FeatureColour;
+import jalview.util.MessageManager;
+
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
 
 public class FeatureColourChooser extends Panel implements ActionListener,
         AdjustmentListener, ItemListener, MouseListener
 {
-  JVDialog frame;
+  /*
+   * the absolute min-max range of a feature score is scaled to 
+   * 1000 positions on the colour threshold slider
+   */
+  private static final int SCALE_FACTOR_1K = 1000;
 
-  Frame owner;
+  private static final String COLON = ":";
 
-  FeatureRenderer fr;
+  private JVDialog frame;
 
-  FeatureSettings fs = null;
+  private Frame owner;
 
-  // AlignmentPanel ap;
+  private FeatureRenderer fr;
 
-  GraduatedColor cs;
+  private FeatureSettings fs = null;
 
-  Object oldcs;
+  private FeatureColourI cs;
 
-  Hashtable oldgroupColours;
+  private FeatureColourI oldcs;
 
-  boolean adjusting = false;
+  private boolean adjusting = false;
 
   private float min, max;
 
-  String type = null;
+  private String type = null;
 
   private AlignFrame af = null;
 
-  public FeatureColourChooser(AlignFrame af, String type)
+  private Panel minColour = new Panel();
+
+  private Panel maxColour = new Panel();
+
+  private Choice threshold = new Choice();
+
+  private Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
+  private TextField thresholdValue = new TextField(20);
+
+  private Checkbox thresholdIsMin = new Checkbox();
+
+  private Checkbox colourFromLabel = new Checkbox();
+
+  private GraphLine threshline;
+
+  /**
+   * Constructor given a context AlignFrame and a feature type. This is used
+   * when opening the graduated colour dialog from the Amend Feature dialog.
+   * 
+   * @param alignFrame
+   * @param featureType
+   */
+  public FeatureColourChooser(AlignFrame alignFrame, String featureType)
   {
-    this.af = af;
-    init(af.getSeqcanvas().getFeatureRenderer(), type);
+    this.af = alignFrame;
+    init(alignFrame.getSeqcanvas().getFeatureRenderer(), featureType);
   }
 
-  public FeatureColourChooser(FeatureSettings fsettings, String type)
+  /**
+   * Constructor given a context FeatureSettings and a feature type. This is
+   * used when opening the graduated colour dialog from Feature Settings.
+   * 
+   * @param fsettings
+   * @param featureType
+   */
+  public FeatureColourChooser(FeatureSettings fsettings, String featureType)
   {
     this.fs = fsettings;
-    init(fsettings.fr, type);
-    // this.ap = fsettings.ap;
+    init(fsettings.fr, featureType);
   }
 
-  private void init(FeatureRenderer frenderer, String type)
+  private void init(FeatureRenderer frenderer, String featureType)
   {
-    this.type = type;
+    this.type = featureType;
     fr = frenderer;
-    float mm[] = ((float[][]) fr.minmax.get(type))[0];
+    float mm[] = fr.getMinMax().get(type)[0];
     min = mm[0];
     max = mm[1];
-    oldcs = fr.featureColours.get(type);
-    if (oldcs instanceof GraduatedColor)
+    threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
+    oldcs = fr.getFeatureColours().get(type);
+    if (oldcs.isGraduatedColour())
     {
-      cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+      threshline.value = oldcs.getThreshold();
+      cs = new FeatureColour(oldcs.getColour(), oldcs.getMinColour(),
+              oldcs.getMaxColour(), oldcs.getNoColour(), min, max);
     }
     else
     {
       // promote original color to a graduated color
       Color bl = Color.black;
-      if (oldcs instanceof Color)
+      if (oldcs.isSimpleColour())
       {
-        bl = (Color) oldcs;
+        bl = oldcs.getColour();
       }
       // original colour becomes the maximum colour
-      cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
+      cs = new FeatureColour(bl, Color.white, bl, Color.white, mm[0],
+              mm[1]);
     }
-    minColour.setBackground(cs.getMinColor());
-    maxColour.setBackground(cs.getMaxColor());
-    minColour.setForeground(cs.getMinColor());
-    maxColour.setForeground(cs.getMaxColor());
+    minColour.setBackground(cs.getMinColour());
+    maxColour.setBackground(cs.getMaxColour());
+    minColour.setForeground(cs.getMinColour());
+    maxColour.setForeground(cs.getMaxColour());
     colourFromLabel.setState(cs.isColourByLabel());
     adjusting = true;
 
@@ -102,31 +162,29 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     } catch (Exception ex)
     {
     }
-    threshold
-            .select(cs.getThreshType() == AnnotationColourGradient.NO_THRESHOLD ? 0
-                    : cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
-                            : 2);
+    threshold.select(
+            cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2 : 0));
 
     adjusting = false;
-    changeColour();
+    changeColour(true);
     colourFromLabel.addItemListener(this);
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
     owner = (af != null) ? af : fs.frame;
-    frame = new JVDialog(owner, "Graduated Feature Colour for " + type,
-            true, 480, 248);
+    frame = new JVDialog(owner, MessageManager
+            .formatMessage("label.variable_color_for", new String[]
+            { type }), true, 480, 248);
     frame.setMainPanel(this);
     validate();
     frame.setVisible(true);
     if (frame.accept)
     {
-      changeColour();
+      changeColour(true);
     }
     else
     {
       // cancel
       reset();
-      PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
       frame.setVisible(false);
     }
   }
@@ -144,7 +202,10 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
   private void jbInit() throws Exception
   {
-    Label minLabel = new Label("Min:"), maxLabel = new Label("Max:");
+    Label minLabel = new Label(
+            MessageManager.getString("label.min_value") + COLON);
+    Label maxLabel = new Label(
+            MessageManager.getString("label.max_value") + COLON);
     minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     // minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
@@ -160,18 +221,33 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     thresholdIsMin.addItemListener(this);
 
     this.setLayout(new GridLayout(4, 1));
+    Panel jPanel1 = new Panel();
     jPanel1.setLayout(new FlowLayout());
+    Panel jPanel2 = new Panel();
     jPanel2.setLayout(new FlowLayout());
+    Panel jPanel3 = new Panel();
     jPanel3.setLayout(new GridLayout(1, 1));
+    Panel jPanel4 = new Panel();
     jPanel4.setLayout(new FlowLayout());
     jPanel1.setBackground(Color.white);
     jPanel2.setBackground(Color.white);
     jPanel4.setBackground(Color.white);
     threshold.addItemListener(this);
-    threshold.addItem("No Threshold");
-    threshold.addItem("Above Threshold");
-    threshold.addItem("Below Threshold");
+    threshold.addItem(MessageManager
+            .getString("label.threshold_feature_no_threshold"));
+    threshold.addItem(MessageManager
+            .getString("label.threshold_feature_above_threshold"));
+    threshold.addItem(MessageManager
+            .getString("label.threshold_feature_below_threshold"));
     thresholdValue.addActionListener(this);
+    thresholdValue.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
     slider.setBackground(Color.white);
     slider.setEnabled(false);
     slider.setSize(new Dimension(93, 21));
@@ -183,11 +259,13 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     jPanel3.setBackground(Color.white);
 
     colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    colourFromLabel.setLabel("Colour by Label");
+    colourFromLabel
+            .setLabel(MessageManager.getString("label.colour_by_label"));
     colourFromLabel.setSize(new Dimension(139, 22));
     // threshold.setBounds(new Rectangle(11, 3, 139, 22));
     thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setLabel("Threshold is min/max");
+    thresholdIsMin
+            .setLabel(MessageManager.getString("label.threshold_minmax"));
     thresholdIsMin.setSize(new Dimension(135, 23));
     // thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
     jPanel1.add(minLabel);
@@ -205,44 +283,12 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     this.add(jPanel4);// , java.awt.BorderLayout.CENTER);
   }
 
-  Panel minColour = new Panel();
-
-  Panel maxColour = new Panel();
-
-  Panel jPanel1 = new Panel();
-
-  Panel jPanel2 = new Panel();
-
-  Choice threshold = new Choice();
-
-  Panel jPanel3 = new Panel();
-
-  Panel jPanel4 = new Panel();
-
-  Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
-
-  TextField thresholdValue = new TextField(20);
-
-  // BorderLayout borderLayout1 = new BorderLayout();
-
-  Checkbox thresholdIsMin = new Checkbox();
-
-  Checkbox colourFromLabel = new Checkbox();
-
-  private GraphLine threshline;
-
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)
     {
-      try
-      {
-        float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue((int) (f * 1000));
-        adjustmentValueChanged(null);
-      } catch (NumberFormatException ex)
-      {
-      }
+      thresholdValue_actionPerformed();
     }
     else if (evt.getSource() == minColour)
     {
@@ -254,49 +300,78 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     }
     else
     {
-      changeColour();
+      changeColour(true);
+    }
+  }
+
+  /**
+   * Action on input of a value for colour score threshold
+   */
+  protected void thresholdValue_actionPerformed()
+  {
+    try
+    {
+      float f = Float.valueOf(thresholdValue.getText()).floatValue();
+      slider.setValue((int) (f * SCALE_FACTOR_1K));
+      adjustmentValueChanged(null);
+
+      /*
+       * force repaint of any Overview window or structure
+       */
+      changeColour(true);
+    } catch (NumberFormatException ex)
+    {
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     maxColour.setEnabled(!colourFromLabel.getState());
     minColour.setEnabled(!colourFromLabel.getState());
-    changeColour();
+    changeColour(true);
   }
 
+  /**
+   * Handler called when the value of the threshold slider changes, either by
+   * user action or programmatically
+   */
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
     {
-      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
       valueChanged();
     }
   }
 
+  /**
+   * Responds to a change of colour threshold by computing the absolute value
+   * and refreshing the alignment.
+   */
   protected void valueChanged()
   {
-    threshline.value = (float) slider.getValue() / 1000f;
-    cs.setThresh(threshline.value);
-    changeColour();
-    PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
-    // ap.paintAlignment(false);
+    threshline.value = slider.getValue() / 1000f;
+    cs.setThreshold(threshline.value);
+    changeColour(false);
+    PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
   }
 
   public void minColour_actionPerformed(Color newCol)
   {
     if (newCol == null)
     {
-      UserDefinedColours udc = new UserDefinedColours(this,
-              minColour.getBackground(), owner,
-              "Select Colour for Minimum Value"); // frame.owner,
+      new UserDefinedColours(this, minColour.getBackground(), owner,
+              MessageManager
+                      .getString("label.select_colour_minimum_value"));
     }
     else
     {
       minColour.setBackground(newCol);
       minColour.setForeground(newCol);
       minColour.repaint();
-      changeColour();
+      changeColour(true);
     }
 
   }
@@ -305,23 +380,20 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     if (newCol == null)
     {
-
-      // UserDefinedColours udc = new UserDefinedColours(this,
-      // "Select Colour for Maximum Value",maxColour.getBackground(),true);
-      UserDefinedColours udc = new UserDefinedColours(this,
-              maxColour.getBackground(), owner,
-              "Select Colour for Maximum Value");
+      new UserDefinedColours(this, maxColour.getBackground(), owner,
+              MessageManager
+                      .getString("label.select_colour_maximum_value"));
     }
     else
     {
       maxColour.setBackground(newCol);
       maxColour.setForeground(newCol);
       maxColour.repaint();
-      changeColour();
+      changeColour(true);
     }
   }
 
-  void changeColour()
+  void changeColour(boolean updateOverview)
   {
     // Check if combobox is still adjusting
     if (adjusting)
@@ -329,109 +401,113 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       return;
     }
 
-    int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
-    if (threshold.getSelectedItem().equals("Above Threshold"))
+    int thresholdOption = AnnotationColourGradient.NO_THRESHOLD;
+    if (threshold.getSelectedIndex() == 1)
     {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+      thresholdOption = AnnotationColourGradient.ABOVE_THRESHOLD;
     }
-    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    else if (threshold.getSelectedIndex() == 2)
     {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+      thresholdOption = AnnotationColourGradient.BELOW_THRESHOLD;
     }
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
-    GraduatedColor acg = new GraduatedColor(minColour.getBackground(),
-            maxColour.getBackground(), min, max);
+    Color minc = minColour.getBackground();
+    Color maxc = maxColour.getBackground();
+    FeatureColour acg = new FeatureColour(maxc, minc, maxc, minc, min, max);
 
     acg.setColourByLabel(colourFromLabel.getState());
     maxColour.setEnabled(!colourFromLabel.getState());
     minColour.setEnabled(!colourFromLabel.getState());
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    if (thresholdOption == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
     }
 
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
-            && threshline == null)
-    {
-      // todo visual indication of feature threshold
-      threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
-              "Threshold", Color.black);
-    }
-
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    if (thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      acg.setThresh(threshline.value);
-
-      float range = max * 1000f - min * 1000f;
+      acg.setThreshold(threshline.value);
 
-      slider.setMinimum((int) (min * 1000));
-      slider.setMaximum((int) (max * 1000));
-      slider.setValue((int) (threshline.value * 1000));
+      slider.setMinimum((int) (min * SCALE_FACTOR_1K));
+      slider.setMaximum((int) (max * SCALE_FACTOR_1K));
+      slider.setValue((int) (threshline.value * SCALE_FACTOR_1K));
       thresholdValue.setText(threshline.value + "");
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
 
-    acg.setThreshType(aboveThreshold);
+    acg.setAboveThreshold(
+            thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
+    acg.setBelowThreshold(
+            thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
+
     if (thresholdIsMin.getState()
-            && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+            && thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
     {
-      if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+      if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
       {
-        acg = new GraduatedColor(acg, threshline.value, max);
+        acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+                acg.getMaxColour(), acg.getNoColour(), threshline.value,
+                max);
       }
       else
       {
-        acg = new GraduatedColor(acg, min, threshline.value);
+        acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+                acg.getMaxColour(), acg.getNoColour(), min,
+                threshline.value);
       }
     }
 
-    fr.featureColours.put(type, acg);
+    fr.setColour(type, acg);
     cs = acg;
-    PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
-    // ap.paintAlignment(false);
+    fs.selectionChanged(updateOverview);
   }
 
   void reset()
   {
-    fr.featureColours.put(type, oldcs);
-    PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
-    // ap.paintAlignment(true);
-
+    fr.setColour(type, oldcs);
+    fs.selectionChanged(true);
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
-    if (evt.getSource() == minColour || evt.getSource() == maxColour)
+    if (evt.getSource() == minColour)
+    {
+      minColour_actionPerformed(null);
+    }
+    else if (evt.getSource() == maxColour)
     {
-      // relay the event
-      actionPerformed(new ActionEvent(evt.getSource(), 1, "Clicked"));
+      maxColour_actionPerformed(null);
     }
     else
     {
-      PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+      changeColour(true);
+      // PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     }
-    // ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }