graduated feature schemes (with visual indication of thresholding)
[jalview.git] / src / jalview / gui / FeatureRenderer.java
index 8d09d10..6abe899 100755 (executable)
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
@@ -818,18 +818,34 @@ public class FeatureRenderer
     sortOrder = null;
     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
   }
-
-  public Color getColour(String featureType)
-  {
+  /**
+   * get a feature style object for the given type string.
+   * Creates a java.awt.Color for a featureType with no existing
+   * colourscheme.
+   * TODO: replace return type with object implementing standard abstract colour/style interface
+   * @param featureType
+   * @return java.awt.Color or GraduatedColor
+   */
+  public Object getFeatureStyle(String featureType) {
     Object fc = featureColours.get(featureType);
     if (fc == null)
     {
       jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
       Color col = ucs.createColourFromName(featureType);
-      featureColours.put(featureType, col);
-      return col;
+      featureColours.put(featureType, fc = col);
     }
-    else if (fc instanceof Color)
+    return fc;
+  }
+  /**
+   * return a nominal colour for this feature
+   * @param featureType
+   * @return standard color, or maximum colour for graduated colourscheme
+   */
+  public Color getColour(String featureType)
+  {
+    Object fc = getFeatureStyle(featureType);
+    
+    if (fc instanceof Color)
     {
       return (Color) fc;
     }
@@ -839,28 +855,20 @@ public class FeatureRenderer
       {
         return ((GraduatedColor) fc).getMaxColor();
       }
-      // TODO: raise an implementation error here.
-      return null; // Color.white;
     }
+    throw new Error("Implementation Error: Unrecognised render object "+fc.getClass()+" for features of type "+featureType);
   }
 
   /**
-   * implement graduated colouring for features with scores
+   * calculate the render colour for a specific feature using current feature settings.
    * 
    * @param feature
    * @return render colour for the given feature
    */
   public Color getColour(SequenceFeature feature)
   {
-    Object fc = featureColours.get(feature.type);
-    if (fc == null)
-    {
-      jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
-      Color col = ucs.createColourFromName(feature.type);
-      featureColours.put(feature.type, col);
-      return col;
-    }
-    else if (fc instanceof Color)
+    Object fc = getFeatureStyle(feature.getType());
+    if (fc instanceof Color)
     {
       return (Color) fc;
     }
@@ -870,26 +878,28 @@ public class FeatureRenderer
       {
         return ((GraduatedColor) fc).findColor(feature);
       }
-      // TODO: raise an implementation error here.
-      return null; // Color.white;
     }
+    throw new Error("Implementation Error: Unrecognised render object "+fc.getClass()+" for features of type "+feature.getType());
   }
   private boolean showFeature(SequenceFeature sequenceFeature)
   {
-    Object fc = featureColours.get(sequenceFeature.type);
+    Object fc = getFeatureStyle(sequenceFeature.type);
     if (fc instanceof GraduatedColor)
     {
       return ((GraduatedColor) fc).isColored(sequenceFeature);
     } else { return true; }
   }
 
-
+  //// /////////////
+  //// Feature Editing Dialog
+  //// Will be refactored in next release.
+  
   static String lastFeatureAdded;
 
   static String lastFeatureGroupAdded;
 
   static String lastDescriptionAdded;
-
+  Object oldcol,fcol;
   int featureIndex = 0;
 
   boolean amendFeatures(final SequenceI[] sequences,
@@ -899,7 +909,7 @@ public class FeatureRenderer
 
     featureIndex = 0;
 
-    JPanel bigPanel = new JPanel(new BorderLayout());
+    final JPanel bigPanel = new JPanel(new BorderLayout());
     final JComboBox overlaps;
     final JTextField name = new JTextField(25);
     final JTextField source = new JTextField(25);
@@ -908,23 +918,49 @@ public class FeatureRenderer
     final JSpinner end = new JSpinner();
     start.setPreferredSize(new Dimension(80, 20));
     end.setPreferredSize(new Dimension(80, 20));
-
-    final JPanel colour = new JPanel();
-    colour.setBorder(BorderFactory.createEtchedBorder());
-    colour.setMaximumSize(new Dimension(40, 10));
+    final FeatureRenderer me = this;
+    final JLabel colour = new JLabel();
+    colour.setOpaque(true);
+    //colour.setBorder(BorderFactory.createEtchedBorder());
+    colour.setMaximumSize(new Dimension(30, 16));
     colour.addMouseListener(new MouseAdapter()
     {
+      FeatureColourChooser fcc =null;
       public void mousePressed(MouseEvent evt)
       {
-        // TODO: use featurecolourchooser here
+        if (fcol instanceof Color)
+        {
         Color col = JColorChooser.showDialog(Desktop.desktop,
-                "Select Feature Colour", colour.getBackground());
+                "Select Feature Colour", ((Color)fcol));
         if (col != null)
-          colour.setBackground(col);
+        {
+          fcol = col;
+          updateColourButton(bigPanel,colour,col);
+        }
+        } else {
+          
+          if (fcc==null) {
+            final String type =  features[featureIndex].getType();
+            fcc = new FeatureColourChooser(me, type);
+            fcc.setRequestFocusEnabled(true);
+            fcc.requestFocus();
+
+            fcc.addActionListener(new ActionListener() {
 
+              public void actionPerformed(ActionEvent e)
+              {
+                fcol = fcc.getLastColour();
+                fcc = null;
+                setColour(type, fcol);
+                updateColourButton(bigPanel,colour,fcol);
+              }
+            }
+            );
+            
+          }
+        }
       }
     });
-
     JPanel tmp = new JPanel();
     JPanel panel = new JPanel(new GridLayout(3, 1));
 
@@ -966,14 +1002,14 @@ public class FeatureRenderer
             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 
           }
-          Color col = getColour(name.getText());
+          Object col = getFeatureStyle(name.getText());
           if (col == null)
           {
             col = new jalview.schemes.UserColourScheme()
                     .createColourFromName(name.getText());
           }
-
-          colour.setBackground(col);
+          oldcol = fcol = col;
+          updateColourButton(bigPanel, colour,col);
         }
       });
 
@@ -997,7 +1033,12 @@ public class FeatureRenderer
     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
     tmp.add(colour);
     colour.setPreferredSize(new Dimension(150, 15));
-
+    colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
+    colour.setForeground(Color.black);
+    colour.setHorizontalAlignment(SwingConstants.CENTER);
+    colour.setVerticalAlignment(SwingConstants.CENTER);
+    colour.setHorizontalTextPosition(SwingConstants.CENTER);
+    colour.setVerticalTextPosition(SwingConstants.CENTER);
     bigPanel.add(panel, BorderLayout.NORTH);
 
     panel = new JPanel();
@@ -1060,8 +1101,7 @@ public class FeatureRenderer
     start.setValue(new Integer(features[0].getBegin()));
     end.setValue(new Integer(features[0].getEnd()));
     description.setText(features[0].getDescription());
-    colour.setBackground(getColour(name.getText()));
-
+    updateColourButton(bigPanel, colour, (oldcol = fcol = getFeatureStyle(name.getText())));
     Object[] options;
     if (!newFeatures)
     {
@@ -1091,7 +1131,7 @@ public class FeatureRenderer
       lastFeatureAdded = name.getText().trim();
       lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
-
+      // TODO: determine if the null feature group is valid
       if (lastFeatureGroupAdded.length() < 1)
         lastFeatureGroupAdded = null;
     }
@@ -1110,9 +1150,8 @@ public class FeatureRenderer
         sf.featureGroup = lastFeatureGroupAdded;
         sf.description = lastDescriptionAdded;
 
-        setColour(sf.type, colour.getBackground());
-        av.featuresDisplayed.put(sf.type, new Integer(colour
-                .getBackground().getRGB()));
+        setColour(sf.type, fcol);
+        av.featuresDisplayed.put(sf.type, getColour(sf.type));
 
         try
         {
@@ -1151,11 +1190,8 @@ public class FeatureRenderer
             featureGroups = new Hashtable();
           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
         }
-
-        Color col = colour.getBackground();
-        setColour(lastFeatureAdded, colour.getBackground());
-        av.featuresDisplayed.put(lastFeatureAdded,
-                new Integer(col.getRGB()));
+        setColour(lastFeatureAdded, fcol);
+        av.featuresDisplayed.put(lastFeatureAdded, getColour(lastFeatureAdded));
 
         findAllFeatures(false);
 
@@ -1174,10 +1210,35 @@ public class FeatureRenderer
     return true;
   }
 
-  public void setColour(String featureType, Color col)
+  /**
+   * update the amend feature button dependent on the given style
+   * @param bigPanel 
+   * @param col
+   * @param col2 
+   */
+  protected void updateColourButton(JPanel bigPanel, JLabel colour, Object col2)
+  {
+    colour.removeAll();
+    colour.setIcon(null);
+    colour.setToolTipText(null);
+    colour.setText("");
+    
+    if (col2 instanceof Color) {
+      colour.setBackground((Color)col2);
+    } else {
+      colour.setBackground(bigPanel.getBackground());
+      colour.setForeground(Color.black);
+      FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
+      //colour.setForeground(colour.getBackground());
+    }
+  }
+
+  public void setColour(String featureType, Object col)
   {
-    Object c = featureColours.get(featureType);
-    if (c == null || c instanceof Color || (c instanceof GraduatedColor && !((GraduatedColor)c).getMaxColor().equals(col)))
+    // overwrite
+//    Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; 
+//    Object c = featureColours.get(featureType);
+//    if (c == null || c instanceof Color || (c instanceof GraduatedColor && !((GraduatedColor)c).getMaxColor().equals(_col)))
     {
       featureColours.put(featureType, col);
     }
@@ -1239,7 +1300,7 @@ public class FeatureRenderer
       for (int i = 0; i < data.length; i++)
       {
         String type = data[i][0].toString();
-        setColour(type, (Color) data[i][1]);
+        setColour(type, data[i][1]); // todo : typesafety - feature color interface object
         if (((Boolean) data[i][2]).booleanValue())
         {
           av.featuresDisplayed.put(type, new Integer(getColour(type)