prototype dialog for setting feature display shading and threshold

diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
new file mode 100644 (file)
index 0000000..993cd2e
--- /dev/null
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -0,0 +1,450 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.Dimension;
+
+public class FeatureColourChooser extends JPanel
+{
+  JInternalFrame frame;
+  
+  FeatureRenderer fr;
+
+  FeatureSettings fs;
+
+  GraduatedColor cs;
+  Object oldcs;
+
+  Hashtable oldgroupColours;
+  
+  AlignmentPanel ap;
+  
+
+  boolean adjusting = false;
+
+  private float min;
+
+  private float max;
+  String type = null;
+  public FeatureColourChooser(FeatureSettings fsettings, String type)
+  {
+    this.fs = fsettings;
+    this.type = type;
+    fr = fsettings.fr;
+    ap = fr.ap;
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, 480, 145);
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        if (!adjusting)
+        {
+          thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+          valueChanged();
+        }
+      }
+    });
+    slider.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent evt)
+      {
+        if (fr.ap!=null) { fr.ap.paintAlignment(true); };
+      }
+    });
+
+    float mm[] = ((float[][]) fr.minmax.get(type))[0];
+    min = mm[0];
+    max = mm[1];
+    oldcs = fr.featureColours.get(type);
+    if (oldcs instanceof GraduatedColor)
+    {
+      cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+    } else {
+      // promote original color to a graduated color
+      Color bl = Color.black;
+      if (oldcs instanceof Color)
+      {
+        bl = (Color) oldcs;
+      }
+      // original colour becomes the maximum colour
+      cs = new GraduatedColor(Color.white,bl,mm[0],mm[1]);
+    }
+    minColour.setBackground(cs.getMinColor());
+    maxColour.setBackground(cs.getMaxColor());
+    adjusting = true;
+    
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+    }
+
+    adjusting = false;
+
+    changeColour();
+
+  }
+
+  public FeatureColourChooser()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    minColour.setBorder(BorderFactory.createEtchedBorder());
+    minColour.setPreferredSize(new Dimension(40, 20));
+    minColour.setToolTipText("Minimum Colour");
+    minColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (minColour.isEnabled())
+        {
+          minColour_actionPerformed();
+        }
+      }
+    });
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    maxColour.setBorder(BorderFactory.createEtchedBorder());
+    maxColour.setPreferredSize(new Dimension(40, 20));
+    maxColour.setToolTipText("Maximum Colour");
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    ok.setOpaque(false);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setOpaque(false);
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+    threshold.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed(e);
+      }
+    });
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+    jPanel3.setLayout(flowLayout2);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed(e);
+      }
+    });
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    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.setOpaque(false);
+    currentColours.setText("Use Original Colours");
+    currentColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        currentColours_actionPerformed(e);
+      }
+    });
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        thresholdIsMin_actionPerformed(actionEvent);
+      }
+    });
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    // 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);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);
+  }
+
+
+  JPanel minColour = new JPanel();
+
+  JPanel maxColour = new JPanel();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JPanel jPanel2 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  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);
+  // TODO refactor to tolower flag
+  JCheckBox currentColours = new JCheckBox();
+
+  JCheckBox thresholdIsMin = new JCheckBox();
+
+  private GraphLine threshline;
+
+  public void minColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Minimum Value", minColour.getBackground());
+    if (col != null)
+    {
+      minColour.setBackground(col);
+    }
+    minColour.repaint();
+    changeColour();
+  }
+
+  public void maxColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Maximum Value", maxColour.getBackground());
+    if (col != null)
+    {
+      maxColour.setBackground(col);
+    }
+    maxColour.repaint();
+    changeColour();
+  }
+
+  void changeColour()
+  {
+    // Check if combobox is still adjusting
+    if (adjusting)
+    {
+      return;
+    }
+
+
+    int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
+    if (threshold.getSelectedItem().equals("Above Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    }
+    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+    } 
+
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+    GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max);
+
+    if (aboveThreshold == 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)
+    {
+      adjusting = true;
+      acg.setThresh(threshline.value);
+
+      float range = max * 1000f
+              - min * 1000f;
+
+      slider.setMinimum((int) (min * 1000));
+      slider.setMaximum((int) (max * 1000));
+      slider.setValue((int) (threshline.value * 1000));
+      thresholdValue.setText(threshline.value + "");
+      slider.setMajorTickSpacing((int) (range / 10f));
+      slider.setEnabled(true);
+      thresholdValue.setEnabled(true);
+      adjusting = false;
+    }
+
+    acg.setThreshType(aboveThreshold);
+    if (thresholdIsMin.isSelected() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD)
+      { 
+        acg = new GraduatedColor(acg, threshline.value, max);
+      } else { 
+        acg = new GraduatedColor(acg, min,threshline.value);
+      }
+    }
+    
+    fr.featureColours.put(type,acg);
+    cs = acg;
+    ap.paintAlignment(false);
+  }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    reset();
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  void reset()
+  {
+    fr.featureColours.put(type, oldcs);
+  }
+
+  public void thresholdCheck_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void threshold_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void thresholdValue_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      float f = Float.parseFloat(thresholdValue.getText());
+      slider.setValue((int) (f * 1000));
+      threshline.value = f;
+    } catch (NumberFormatException ex)
+    {
+    }
+  }
+
+  public void valueChanged()
+  {
+    threshline.value = (float) slider.getValue() / 1000f;
+    cs.setThresh(threshline.value);
+    changeColour();
+    ap.paintAlignment(false);
+  }
+
+  public void currentColours_actionPerformed(ActionEvent e)
+  {
+    if (currentColours.isSelected())
+    {
+      reset();
+    }
+
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+
+    changeColour();
+  }
+
+  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  {
+    changeColour();
+  }
+
+}