X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=9afe54fdc0531ce963bb2757a5ec12069f440bdc;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=a05ccf134d5943704c4b10c52a8b368a40849bae;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index a05ccf1..9afe54f
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -21,11 +22,17 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
+import net.miginfocom.swing.MigLayout;
+
+import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.util.MessageManager;
+
 import java.awt.Dimension;
 
 public class AnnotationColourChooser extends JPanel
@@ -43,18 +50,19 @@ public class AnnotationColourChooser extends JPanel
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
+  /**
+   * enabled if the user is dragging the slider - try to keep updates to a minimun
+   */
+  boolean sliderDragging = false;
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
     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++)
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         if (sg.cs != null)
         {
           oldgroupColours.put(sg, sg.cs);
@@ -66,7 +74,7 @@ public class AnnotationColourChooser extends JPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
 
     slider.addChangeListener(new ChangeListener()
     {
@@ -75,53 +83,87 @@ public class AnnotationColourChooser extends JPanel
         if (!adjusting)
         {
           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
-          valueChanged();
+          valueChanged(!sliderDragging);
         }
       }
     });
     slider.addMouseListener(new MouseAdapter()
     {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mousePressed(e);
+      }
+
+      @Override
+      public void mouseDragged(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mouseDragged(e);
+      }
       public void mouseReleased(MouseEvent evt)
       {
+        if (sliderDragging)
+        {
+          sliderDragging=false;
+          valueChanged(true);
+        }
         ap.paintAlignment(true);
       }
     });
 
-    if (av.alignment.getAlignmentAnnotation() == null)
+    if (av.getAlignment().getAlignmentAnnotation() == null)
     {
       return;
     }
 
+    // Always get default shading from preferences.
+    setDefaultMinMax();
+
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      minColour.setBackground(acg.getMinColour());
-      maxColour.setBackground(acg.getMaxColour());
-    }
-    else
-    {
-      minColour.setBackground(Color.orange);
-      maxColour.setBackground(Color.red);
+      currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+      {
+        minColour.setBackground(acg.getMinColour());
+        maxColour.setBackground(acg.getMaxColour());
+      }
+      seqAssociated.setSelected(acg.isSeqAssociated());
+      
     }
+    annotations = new JComboBox(
+            getAnnotationItems(seqAssociated.isSelected()));
 
-    adjusting = true;
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
+    threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
+    threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+
+    if (oldcs instanceof AnnotationColourGradient)
     {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label + "_" + (index++));
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.setSelectedItem(acg.getAnnotation());
+      switch (acg.getAboveThreshold())
+      {
+      case AnnotationColourGradient.NO_THRESHOLD:
+        threshold.setSelectedIndex(0);
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+        threshold.setSelectedIndex(1);
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        threshold.setSelectedIndex(2);
+        break;
+      default:
+        throw new Error(
+                "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+      }
+      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
-    annotations = new JComboBox(list);
-
-    threshold.addItem("No Threshold");
-    threshold.addItem("Above Threshold");
-    threshold.addItem("Below Threshold");
-
     try
     {
       jbInit();
@@ -132,7 +174,57 @@ public class AnnotationColourChooser extends JPanel
     adjusting = false;
 
     changeColour();
+    frame.invalidate();
+    frame.pack();
+
+  }
+
+  private Vector<String> getAnnotationItems(boolean isSeqAssociated)
+  {
+    Vector<String> list = new Vector<String>();
+    int index = 1;
+    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+    boolean enableSeqAss = false;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
+      {
+        if (isSeqAssociated)
+        {
+          continue;
+        }
+      }
+      else
+      {
+        enableSeqAss = true;
+      }
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+      {
+        anmap[list.size()] = i;
+        list.addElement(label);
 
+      }
+      else
+      {
+        if (!isSeqAssociated)
+        {
+          anmap[list.size()] = i;
+          list.addElement(label + "_" + (index++));
+        }
+      }
+    }
+    seqAssociated.setEnabled(enableSeqAss);
+    annmap = new int[list.size()];
+    System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+    return list;
+  }
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+            Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+            Color.red));
   }
 
   public AnnotationColourChooser()
@@ -148,10 +240,10 @@ public class AnnotationColourChooser extends JPanel
 
   private void jbInit() throws Exception
   {
-    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    minColour.setFont(JvSwingUtils.getLabelFont());
     minColour.setBorder(BorderFactory.createEtchedBorder());
     minColour.setPreferredSize(new Dimension(40, 20));
-    minColour.setToolTipText("Minimum Colour");
+    minColour.setToolTipText(MessageManager.getString("label.min_colour"));
     minColour.addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent e)
@@ -162,10 +254,10 @@ public class AnnotationColourChooser extends JPanel
         }
       }
     });
-    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    maxColour.setFont(JvSwingUtils.getLabelFont());
     maxColour.setBorder(BorderFactory.createEtchedBorder());
     maxColour.setPreferredSize(new Dimension(40, 20));
-    maxColour.setToolTipText("Maximum Colour");
+    maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
     maxColour.addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent e)
@@ -177,7 +269,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     ok.setOpaque(false);
-    ok.setText("OK");
+    ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -186,7 +278,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     cancel.setOpaque(false);
-    cancel.setText("Cancel");
+    cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -194,8 +286,20 @@ public class AnnotationColourChooser extends JPanel
         cancel_actionPerformed(e);
       }
     });
-    this.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
+    defColours.setOpaque(false);
+    defColours.setText(MessageManager.getString("action.set_defaults"));
+    defColours
+            .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+    defColours.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        resetColours_actionPerformed(arg0);
+      }
+    });
+
     annotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -203,8 +307,6 @@ public class AnnotationColourChooser extends JPanel
         annotations_actionPerformed(e);
       }
     });
-    jPanel1.setBackground(Color.white);
-    jPanel2.setBackground(Color.white);
     threshold.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -212,7 +314,6 @@ public class AnnotationColourChooser extends JPanel
         threshold_actionPerformed(e);
       }
     });
-    jPanel3.setLayout(flowLayout2);
     thresholdValue.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -228,10 +329,9 @@ public class AnnotationColourChooser extends JPanel
     slider.setPreferredSize(new Dimension(100, 32));
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(7);
-    jPanel3.setBackground(Color.white);
-    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    currentColours.setFont(JvSwingUtils.getLabelFont());
     currentColours.setOpaque(false);
-    currentColours.setText("Use Original Colours");
+    currentColours.setText(MessageManager.getString("label.use_original_colours"));
     currentColours.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -240,7 +340,8 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+    thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
     thresholdIsMin.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -248,27 +349,89 @@ public class AnnotationColourChooser extends JPanel
         thresholdIsMin_actionPerformed(actionEvent);
       }
     });
+    seqAssociated.setBackground(Color.white);
+    seqAssociated.setFont(JvSwingUtils.getLabelFont());
+    seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
+    seqAssociated.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        seqAssociated_actionPerformed(arg0);
+      }
+    });
+
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+
     jPanel1.add(ok);
     jPanel1.add(cancel);
-    jPanel2.add(annotations);
+    jPanel2.add(annotations, "grow, wrap");
+    jPanel2.add(seqAssociated);
     jPanel2.add(currentColours);
-    jPanel2.add(minColour);
-    jPanel2.add(maxColour);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
-    jPanel3.add(threshold);
-    jPanel3.add(slider);
-    jPanel3.add(thresholdValue);
-    jPanel3.add(thresholdIsMin);
+    JPanel colpanel = new JPanel(new FlowLayout());
+    colpanel.setBackground(Color.white);
+    colpanel.add(minColour);
+    colpanel.add(maxColour);
+    jPanel2.add(colpanel, "wrap");
+    jPanel2.add(threshold);
+    jPanel2.add(defColours, "skip 1, wrap");
+    jPanel2.add(thresholdIsMin);
+    jPanel2.add(slider, "grow");
+    jPanel2.add(thresholdValue, "grow");
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.NORTH);
+    this.add(jPanel2, java.awt.BorderLayout.CENTER);
+    this.validate();
+  }
+
+  protected void seqAssociated_actionPerformed(ActionEvent arg0)
+  {
+    adjusting = true;
+    String cursel = (String) annotations.getSelectedItem();
+    boolean isvalid = false, isseqs = seqAssociated.isSelected();
+    this.annotations.removeAllItems();
+    for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
+    {
+      if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
+      {
+        isvalid = true;
+        cursel = anitem;
+      }
+      this.annotations.addItem(anitem);
+    }
+    adjusting = false;
+    if (isvalid)
+    {
+      this.annotations.setSelectedItem(cursel);
+    }
+    else
+    {
+      if (annotations.getItemCount() > 0)
+      {
+        annotations.setSelectedIndex(0);
+      }
+    }
+  }
+
+  protected void resetColours_actionPerformed(ActionEvent arg0)
+  {
+    setDefaultMinMax();
+    changeColour();
   }
 
   JComboBox annotations;
 
+  int[] annmap;
+
   JPanel minColour = new JPanel();
 
   JPanel maxColour = new JPanel();
 
+  JButton defColours = new JButton();
+
   JButton ok = new JButton();
 
   JButton cancel = new JButton();
@@ -281,12 +444,6 @@ public class AnnotationColourChooser extends JPanel
 
   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);
@@ -295,6 +452,8 @@ public class AnnotationColourChooser extends JPanel
 
   JCheckBox thresholdIsMin = new JCheckBox();
 
+  JCheckBox seqAssociated = new JCheckBox();
+
   public void minColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
@@ -327,27 +486,29 @@ public class AnnotationColourChooser extends JPanel
       return;
     }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
-            .getSelectedIndex()];
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[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);
       thresholdValue.setText("");
+      thresholdIsMin.setEnabled(false);
     }
     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
             && currentAnnotation.threshold == null)
@@ -386,25 +547,23 @@ public class AnnotationColourChooser extends JPanel
               minColour.getBackground(), maxColour.getBackground(),
               aboveThreshold);
     }
+    acg.setSeqAssociated(seqAssociated.isSelected());
 
     if (currentAnnotation.graphMin == 0f
             && currentAnnotation.graphMax == 0f)
     {
-      acg.predefinedColours = true;
+      acg.setPredefinedColours(true);
     }
 
     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 
     av.setGlobalColourScheme(acg);
 
-    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++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
 
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
         if (sg.cs == null)
         {
           continue;
@@ -414,18 +573,25 @@ public class AnnotationColourChooser extends JPanel
         {
           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
                   aboveThreshold);
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+
         }
         else
         {
           sg.cs = new AnnotationColourGradient(currentAnnotation,
                   minColour.getBackground(), maxColour.getBackground(),
                   aboveThreshold);
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
         }
 
       }
     }
-
-    ap.paintAlignment(false);
+    ap.alignmentChanged();
+    // ensure all associated views (overviews, structures, etc) are notified of
+    // updated colours.
+    ap.paintAlignment(true);
   }
 
   public void ok_actionPerformed(ActionEvent e)
@@ -442,6 +608,8 @@ public class AnnotationColourChooser extends JPanel
   public void cancel_actionPerformed(ActionEvent e)
   {
     reset();
+    // ensure all original colouring is propagated to listeners.
+    ap.paintAlignment(true);
     try
     {
       frame.setClosed(true);
@@ -453,13 +621,11 @@ public class AnnotationColourChooser extends JPanel
   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.get(g);
         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }
@@ -491,18 +657,38 @@ public class AnnotationColourChooser extends JPanel
     }
   }
 
-  public void valueChanged()
+  public void valueChanged(boolean updateAllAnnotation)
   {
     if (currentColours.isSelected()
             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
     {
       changeColour();
     }
-
     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    propagateSeqAssociatedThreshold(updateAllAnnotation);
     ap.paintAlignment(false);
   }
 
+  private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+  {
+    if (currentAnnotation.sequenceRef == null
+            || currentAnnotation.threshold == null)
+    {
+      return;
+    }
+    // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+
+    float thr = currentAnnotation.threshold.value;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+      if (aa.label.equals(currentAnnotation.label))
+      {
+        aa.threshold.value = thr;
+      }
+    }
+  }
+
   public void currentColours_actionPerformed(ActionEvent e)
   {
     if (currentColours.isSelected())