X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=5f61eadc20ad374e07011d85b225f6db2feee45f;hb=452e24303ecf7861ff827c19fcd0fdaa1d288ea1;hp=c932962e14b849ce3e95074bcc8b60e3f8aa5762;hpb=f8534ee55f528a291d8802b1b4461296bf9ff460;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index c932962..5f61ead
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
  */
 package jalview.appletgui;
 
@@ -25,18 +24,23 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.awt.Rectangle;
+import jalview.util.MessageManager;
 
-public class AnnotationColourChooser
-    extends Panel implements ActionListener,
-    AdjustmentListener, ItemListener, MouseListener
+public class AnnotationColourChooser extends Panel implements
+        ActionListener, AdjustmentListener, ItemListener, MouseListener
 {
   Frame frame;
+
   AlignViewport av;
+
   AlignmentPanel ap;
+
   ColourSchemeI oldcs;
+
   Hashtable oldgroupColours;
+
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
   boolean adjusting = false;
 
   public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
@@ -44,23 +48,22 @@ public class AnnotationColourChooser
     try
     {
       jbInit();
+    } catch (Exception ex)
+    {
     }
-    catch (Exception ex)
-    {}
 
     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.elementAt(g);
-        if (sg.cs!=null)
+        if (sg.cs != null)
+        {
+          oldgroupColours.put(sg, sg.cs);
+        }
+        else
         {
-            oldgroupColours.put(sg, sg.cs);
-        } else {
           oldgroupColours.put(sg, "null");
         }
       }
@@ -71,139 +74,205 @@ public class AnnotationColourChooser
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.alignment.getAlignmentAnnotation() == null)
+    if (av.getAlignment().getAlignmentAnnotation() == null)
     {
       return;
     }
 
+    setDefaultMinMax();
+
     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.setState(acg.predefinedColours);
+      if (!acg.predefinedColours)
+      {
+        minColour.setBackground(acg.getMinColour());
+        maxColour.setBackground(acg.getMaxColour());
+      }
     }
 
     adjusting = true;
 
     Vector list = new Vector();
     int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
     {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
       if (!list.contains(label))
         list.addElement(label);
       else
-        list.addElement(label+"_"+(index++));
+        list.addElement(label + "_" + (index++));
     }
 
     for (int i = 0; i < list.size(); i++)
     {
-        annotations.addItem(list.elementAt(i).toString());
+      annotations.addItem(list.elementAt(i).toString());
     }
 
     threshold.addItem("No Threshold");
     threshold.addItem("Above Threshold");
     threshold.addItem("Below Threshold");
 
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.select(acg.getAnnotation());
+      switch (acg.getAboveThreshold())
+      {
+      case AnnotationColourGradient.NO_THRESHOLD:
+        threshold.select("No Threshold");
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+        threshold.select("Above Threshold");
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        threshold.select("Below Threshold");
+        break;
+      default:
+        throw new Error(
+                "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+      }
+      thresholdIsMin.setState(acg.thresholdIsMinMax);
+      thresholdValue.setText("" + acg.getAnnotationThreshold());
+    }
+
     adjusting = false;
 
     changeColour();
 
     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();
   }
 
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(av.applet.getDefaultColourParameter(
+            "ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(av.applet.getDefaultColourParameter(
+            "ANNOTATIONCOLOUR_MAX", Color.red));
+
+  }
+
   public AnnotationColourChooser()
   {
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  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();
+
   Button minColour = new Button();
+
   Button maxColour = new Button();
+
   Button ok = new Button();
+
   Button cancel = new Button();
+
+  Button defColours = new Button();
+
   Panel jPanel1 = new Panel();
+
   Panel jPanel2 = new Panel();
+
   Choice threshold = new Choice();
+
   FlowLayout flowLayout1 = new FlowLayout();
+
   Panel jPanel3 = new Panel();
+
   Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
   TextField thresholdValue = new TextField(20);
+
   Checkbox currentColours = new Checkbox();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   Checkbox thresholdIsMin = new Checkbox();
 
   public void actionPerformed(ActionEvent evt)
@@ -213,11 +282,11 @@ public class AnnotationColourChooser
       try
       {
         float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue( (int) (f * 1000));
+        slider.setValue((int) (f * 1000));
         adjustmentValueChanged(null);
+      } catch (NumberFormatException ex)
+      {
       }
-      catch (NumberFormatException ex)
-      {}
     }
     else if (evt.getSource() == minColour)
     {
@@ -227,7 +296,10 @@ public class AnnotationColourChooser
     {
       maxColour_actionPerformed(null);
     }
-
+    else if (evt.getSource() == defColours)
+    {
+      defColour_actionPerformed();
+    }
     else if (evt.getSource() == ok)
     {
       changeColour();
@@ -267,9 +339,9 @@ public class AnnotationColourChooser
   {
     if (!adjusting)
     {
-      thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
       if (currentColours.getState()
-          && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+              && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
         changeColour();
       }
@@ -289,8 +361,7 @@ public class AnnotationColourChooser
     }
     else
     {
-      new UserDefinedColours(this, "Min Colour",
-                             minColour.getBackground());
+      new UserDefinedColours(this, "Min Colour", minColour.getBackground());
     }
 
   }
@@ -305,11 +376,18 @@ public class AnnotationColourChooser
     }
     else
     {
-      new UserDefinedColours(this, "Max Colour",
-                             maxColour.getBackground());
+      new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
     }
   }
 
+  public void defColour_actionPerformed()
+  {
+    setDefaultMinMax();
+    minColour.repaint();
+    maxColour.repaint();
+    changeColour();
+  }
+
   void changeColour()
   {
     // Check if combobox is still adjusting
@@ -318,9 +396,8 @@ public class AnnotationColourChooser
       return;
     }
 
-
-    currentAnnotation = av.alignment.getAlignmentAnnotation()
-        [annotations.getSelectedIndex()];
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
+            .getSelectedIndex()];
 
     int aboveThreshold = -1;
     if (threshold.getSelectedItem().equals("Above Threshold"))
@@ -334,30 +411,31 @@ public class AnnotationColourChooser
 
     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 &&
-             currentAnnotation.threshold == null)
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+            && currentAnnotation.threshold == null)
     {
-      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
-                                     ( (currentAnnotation.graphMax -
-                                        currentAnnotation.graphMin) / 2f,
-                                      "Threshold",
-                                      Color.black));
+      currentAnnotation
+              .setThreshold(new jalview.datamodel.GraphLine(
+                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+                      "Threshold", Color.black));
     }
 
     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
 
-      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
-      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
-      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
+      slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+      slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+      slider.setValue((int) (currentAnnotation.threshold.value * 1000));
       thresholdValue.setText(currentAnnotation.threshold.value + "");
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
@@ -367,21 +445,18 @@ public class AnnotationColourChooser
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
     {
-      acg = new AnnotationColourGradient(
-          currentAnnotation,
-          av.getGlobalColourScheme(), aboveThreshold);
+      acg = new AnnotationColourGradient(currentAnnotation,
+              av.getGlobalColourScheme(), aboveThreshold);
     }
     else
     {
-      acg =
-          new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
+      acg = new AnnotationColourGradient(currentAnnotation,
+              minColour.getBackground(), maxColour.getBackground(),
               aboveThreshold);
     }
 
-    if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)
+    if (currentAnnotation.graphMin == 0f
+            && currentAnnotation.graphMax == 0f)
     {
       acg.predefinedColours = true;
     }
@@ -390,13 +465,10 @@ public class AnnotationColourChooser
 
     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++)
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.elementAt(g);
 
         if (sg.cs == null)
         {
@@ -405,40 +477,37 @@ public class AnnotationColourChooser
 
         if (currentColours.getState())
         {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              sg.cs, aboveThreshold);
+          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+                  aboveThreshold);
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
+          sg.cs = new AnnotationColourGradient(currentAnnotation,
+                  minColour.getBackground(), maxColour.getBackground(),
+                  aboveThreshold);
         }
 
       }
     }
 
-    ap.paintAlignment(false);
+    // update colours in linked windows
+    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 {
+          sg.cs = (ColourSchemeI) cs;
+        }
+        else
+        {
           // probably the "null" string we set it to if it was null originally.
           sg.cs = null;
         }
@@ -448,11 +517,25 @@ public class AnnotationColourChooser
 
   }
 
-  public void mouseClicked(MouseEvent evt){}
-  public void mousePressed(MouseEvent evt){}
-  public void mouseReleased(MouseEvent evt){ ap.paintAlignment(true);}
-  public void mouseEntered(MouseEvent evt){}
-  public void mouseExited(MouseEvent evt){}
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
 
+  public void mousePressed(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    ap.paintAlignment(true);
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
 
 }