X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=f516bc96092356fd2bbd765add980f5060646948;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=25e08b046099ee9e09236a0163a9b08f398e9f35;hpb=aaf78c2f304b237a9c800137126967ace9437c99;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index 25e08b0..f516bc9
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,30 +1,54 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+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.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.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
 
 public class AnnotationColourChooser extends Panel implements
         ActionListener, AdjustmentListener, ItemListener, MouseListener
@@ -37,9 +61,15 @@ public class AnnotationColourChooser extends Panel implements
 
   ColourSchemeI oldcs;
 
-  Hashtable oldgroupColours;
+  Map<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  /*
+   * map from annotation to its menu item display label
+   * - so we know which item to pre-select on restore
+   */
+  private Map<AlignmentAnnotation, String> annotationLabels;
+
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 
@@ -53,22 +83,12 @@ public class AnnotationColourChooser extends Panel implements
     }
 
     oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.elementAt(g);
-        if (sg.cs != null)
-        {
-          oldgroupColours.put(sg, sg.cs);
-        }
-        else
-        {
-          oldgroupColours.put(sg, "null");
-        }
+        oldgroupColours.put(sg, sg.getColourScheme());
       }
     }
     this.av = av;
@@ -77,65 +97,65 @@ public class AnnotationColourChooser extends Panel implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.alignment.getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
 
-    minColour.setBackground(av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MIN",Color.orange));
-    maxColour.setBackground(av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MAX",Color.red));
+    setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setState(acg.predefinedColours);
-      if (!acg.predefinedColours) {
+      currentColours.setState(acg.isPredefinedColours()
+              || acg.getBaseColour() != null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
+      {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
+      // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    adjusting = true;
-
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label + "_" + (index++));
-    }
+    Vector<String> list = getAnnotationItems();
 
     for (int i = 0; i < list.size(); i++)
     {
       annotations.addItem(list.elementAt(i).toString());
     }
 
-    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"));
 
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.select(acg.getAnnotation());
-      switch (acg.getAboveThreshold()) {
+      String label = annotationLabels.get(acg.getAnnotation());
+      annotations.select(label);
+      switch (acg.getAboveThreshold())
+      {
       case AnnotationColourGradient.NO_THRESHOLD:
-          threshold.select("No Threshold");
+        threshold.select(0);
         break;
       case AnnotationColourGradient.ABOVE_THRESHOLD:
-          threshold.select("Above Threshold");
+        threshold.select(1);
         break;
       case AnnotationColourGradient.BELOW_THRESHOLD:
-        threshold.select("Below Threshold");
+        threshold.select(1);
         break;
-        default:
-          throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+      default:
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
       }
-      thresholdIsMin.setState(acg.thresholdIsMinMax);
-      thresholdValue.setText(""+acg.getAnnotationThreshold());
+      thresholdIsMin.setState(acg.isThresholdIsMinMax());
+      thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
     adjusting = false;
@@ -144,11 +164,66 @@ public class AnnotationColourChooser extends Panel implements
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480,
-            145);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.colour_by_annotation"), 560,
+            175);
     validate();
   }
 
+  /**
+   * Builds and returns a list of menu items (display text) for choice of
+   * annotation. Also builds a map between annotations and their display labels.
+   * 
+   * @return
+   */
+  protected Vector<String> getAnnotationItems()
+  {
+    // TODO remove duplication with gui.AnnotationRowFilter
+    // TODO add 'per sequence only' option / parameter
+
+    annotationLabels = new HashMap<AlignmentAnnotation, String>();
+    Vector<String> list = new Vector<String>();
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return list;
+    }
+    int index = 1;
+    for (int i = 0; i < anns.length; i++)
+    {
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        /*
+         * be helpful and include sequence id in label for
+         * sequence-associated annotation (JAL-2236)
+         */
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
+      if (!list.contains(label))
+      {
+        list.addElement(label);
+        annotationLabels.put(anns[i], label);
+      }
+      else
+      {
+        label = label + "_" + (index++);
+        list.addElement(label);
+        annotationLabels.put(anns[i], label);
+      }
+    }
+    return list;
+  }
+
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(av.applet.getDefaultColourParameter(
+            "ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(av.applet.getDefaultColourParameter(
+            "ANNOTATIONCOLOUR_MAX", Color.red));
+
+  }
+
   public AnnotationColourChooser()
   {
     try
@@ -163,58 +238,78 @@ public class AnnotationColourChooser extends Panel implements
   private void jbInit() throws Exception
   {
     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    minColour.setLabel("Min Colour");
+    minColour.setLabel(MessageManager.getString("label.min_colour"));
     minColour.addActionListener(this);
 
     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    maxColour.setLabel("Max Colour");
+    maxColour.setLabel(MessageManager.getString("label.max_colour"));
     maxColour.addActionListener(this);
 
     thresholdIsMin.addItemListener(this);
-    ok.setLabel("OK");
+    ok.setLabel(MessageManager.getString("action.ok"));
     ok.addActionListener(this);
 
-    cancel.setLabel("Cancel");
+    cancel.setLabel(MessageManager.getString("action.cancel"));
     cancel.addActionListener(this);
 
-    this.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
+    defColours.setLabel(MessageManager.getString("action.set_defaults"));
+    defColours.addActionListener(this);
+
     annotations.addItemListener(this);
 
-    jPanel1.setBackground(Color.white);
-    jPanel2.setBackground(Color.white);
-    threshold.addItemListener(this);
-    jPanel3.setLayout(null);
     thresholdValue.addActionListener(this);
-
     slider.setBackground(Color.white);
+    slider.setPreferredSize(new Dimension(193, 21));
     slider.setEnabled(false);
-    slider.setBounds(new Rectangle(153, 3, 93, 21));
+    thresholdValue.setPreferredSize(new Dimension(79, 22));
     thresholdValue.setEnabled(false);
-    thresholdValue.setBounds(new Rectangle(248, 2, 79, 22));
     thresholdValue.setColumns(5);
-    jPanel3.setBackground(Color.white);
     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    currentColours.setLabel("Use Original Colours");
+    currentColours.setLabel(MessageManager
+            .getString("label.use_original_colours"));
     currentColours.addItemListener(this);
 
-    threshold.setBounds(new Rectangle(11, 3, 139, 22));
     thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setLabel("Threshold is min/max");
-    thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
+    thresholdIsMin.setLabel(MessageManager
+            .getString("label.threshold_minmax"));
+
+    this.setLayout(borderLayout1);
+
+    jPanel1.setBackground(Color.white);
+
+    jPanel2.setLayout(new FlowLayout());
+    jPanel2.setBackground(Color.white);
+    threshold.addItemListener(this);
+    jPanel3.setLayout(new FlowLayout());
+    jPanel3.setBackground(Color.white);
+    Panel jPanel4 = new Panel();
+    jPanel4.setLayout(new BorderLayout());
+    jPanel4.setBackground(Color.white);
+
     jPanel1.add(ok);
     jPanel1.add(cancel);
+
     jPanel2.add(annotations);
     jPanel2.add(currentColours);
     jPanel2.add(minColour);
     jPanel2.add(maxColour);
-    jPanel3.add(threshold);
-    jPanel3.add(slider);
-    jPanel3.add(thresholdValue);
-    jPanel3.add(thresholdIsMin);
-    this.add(jPanel2, java.awt.BorderLayout.NORTH);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+
+    jPanel4.add(thresholdIsMin, BorderLayout.WEST);
+    jPanel4.add(slider, BorderLayout.CENTER);
+    jPanel4.add(thresholdValue, BorderLayout.EAST);
+
+    Panel jPanel34 = new Panel();
+    jPanel34.setLayout(new BorderLayout());
+    jPanel34.setBackground(Color.white);
+    jPanel34.add(jPanel2, BorderLayout.NORTH);
+    jPanel34.add(threshold, BorderLayout.WEST);
+    jPanel3.add(defColours);
+    jPanel34.add(jPanel3, BorderLayout.EAST);
+    jPanel34.add(jPanel4, BorderLayout.SOUTH);
+
+    this.add(jPanel34, java.awt.BorderLayout.CENTER);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+
   }
 
   Choice annotations = new Choice();
@@ -227,6 +322,8 @@ public class AnnotationColourChooser extends Panel implements
 
   Button cancel = new Button();
 
+  Button defColours = new Button();
+
   Panel jPanel1 = new Panel();
 
   Panel jPanel2 = new Panel();
@@ -247,6 +344,7 @@ public class AnnotationColourChooser extends Panel implements
 
   Checkbox thresholdIsMin = new Checkbox();
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)
@@ -268,10 +366,12 @@ public class AnnotationColourChooser extends Panel implements
     {
       maxColour_actionPerformed(null);
     }
-
+    else if (evt.getSource() == defColours)
+    {
+      defColour_actionPerformed();
+    }
     else if (evt.getSource() == ok)
     {
-      changeColour();
       frame.setVisible(false);
     }
     else if (evt.getSource() == cancel)
@@ -287,6 +387,7 @@ public class AnnotationColourChooser extends Panel implements
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == currentColours)
@@ -304,18 +405,19 @@ public class AnnotationColourChooser extends Panel implements
     changeColour();
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
     {
-      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
       if (currentColours.getState()
               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
         changeColour();
       }
 
-      currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+      currentAnnotation.threshold.value = slider.getValue() / 1000f;
       ap.paintAlignment(false);
     }
   }
@@ -349,6 +451,14 @@ public class AnnotationColourChooser extends Panel implements
     }
   }
 
+  public void defColour_actionPerformed()
+  {
+    setDefaultMinMax();
+    minColour.repaint();
+    maxColour.repaint();
+    changeColour();
+  }
+
   void changeColour()
   {
     // Check if combobox is still adjusting
@@ -357,26 +467,28 @@ public class AnnotationColourChooser extends Panel implements
       return;
     }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
             .getSelectedIndex()];
 
     int aboveThreshold = -1;
-    if (threshold.getSelectedItem().equals("Above Threshold"))
+    if (threshold.getSelectedIndex() == 1)
     {
       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
     }
-    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    else if (threshold.getSelectedIndex() == 2)
     {
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
     }
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
+    thresholdIsMin.setEnabled(true);
 
     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
+      thresholdIsMin.setEnabled(false);
       thresholdValue.setText("");
     }
     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
@@ -404,8 +516,6 @@ public class AnnotationColourChooser extends Panel implements
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), aboveThreshold);
     }
     else
     {
@@ -417,88 +527,77 @@ public class AnnotationColourChooser extends Panel implements
     if (currentAnnotation.graphMin == 0f
             && currentAnnotation.graphMax == 0f)
     {
-      acg.predefinedColours = true;
+      acg.setPredefinedColours(true);
     }
 
-    acg.thresholdIsMinMax = thresholdIsMin.getState();
+    acg.setThresholdIsMinMax(thresholdIsMin.getState());
 
     av.setGlobalColourScheme(acg);
 
-    if (av.alignment.getGroups() != null)
+    // TODO: per group colour propagation not always desired
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.elementAt(g);
-
-        if (sg.cs == null)
+        if (sg.getColourScheme() == null)
         {
           continue;
         }
 
         if (currentColours.getState())
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  aboveThreshold);
+          sg.setColourScheme(new AnnotationColourGradient(
+                  currentAnnotation, sg.getColourScheme(), aboveThreshold));
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  aboveThreshold);
+          sg.setColourScheme(new AnnotationColourGradient(
+                  currentAnnotation, minColour.getBackground(), maxColour
+                          .getBackground(), aboveThreshold));
         }
-
       }
     }
 
     // update colours in linked windows
+    ap.alignmentChanged();
     ap.paintAlignment(true);
   }
 
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.elementAt(g);
-        Object cs = oldgroupColours.get(sg);
-        if (cs instanceof ColourSchemeI)
-        {
-          sg.cs = (ColourSchemeI) cs;
-        }
-        else
-        {
-          // probably the "null" string we set it to if it was null originally.
-          sg.cs = null;
-        }
+        sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
     ap.paintAlignment(true);
-
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }