/*
- * 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
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
+import javax.swing.border.LineBorder;
import javax.swing.event.*;
import jalview.datamodel.*;
import jalview.schemes.*;
import java.awt.Dimension;
-public class FeatureColourChooser extends JPanel
+public class FeatureColourChooser extends JPanel
{
- JInternalFrame frame;
+ JDialog frame;
- FeatureRenderer fr;
-
- FeatureSettings fs;
-
- GraduatedColor cs;
- Object oldcs;
+// FeatureSettings fs;
+ FeatureRenderer fr;
+
+
+ private GraduatedColor cs;
+ private Object oldcs;
+ /**
+ *
+ * @return the last colour setting selected by user - either oldcs (which may be a java.awt.Color) or the new GraduatedColor
+ */
+ public Object getLastColour() {
+ if (cs==null)
+ {
+ return oldcs;
+ }
+ return cs;
+ }
Hashtable oldgroupColours;
AlignmentPanel ap;
private float max;
String type = null;
- public FeatureColourChooser(FeatureSettings fsettings, String type)
+ public FeatureColourChooser(FeatureRenderer frender, String type)
{
- this.fs = fsettings;
+ this(frender,false,type);
+ }
+ public FeatureColourChooser(FeatureRenderer frender, boolean block, String type)
+ {
+ this.fr = frender;
this.type = type;
- fr = fsettings.fr;
ap = fr.ap;
- frame = new JInternalFrame();
+ frame = new JDialog(Desktop.instance,true);
+ frame.setTitle("Graduated Feature Colour for "+type);
+ Rectangle deskr = Desktop.instance.getBounds();
+ frame.setBounds(new Rectangle((int) (deskr.getCenterX()-240),(int) (deskr.getCenterY()-92),480,185));
frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, 480, 145);
+ //frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ //Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, 480, 145);
slider.addChangeListener(new ChangeListener()
{
{
public void mouseReleased(MouseEvent evt)
{
- if (fr.ap!=null) { fr.ap.paintAlignment(true); };
+ if (ap!=null) { ap.paintAlignment(true); };
}
});
oldcs = fr.featureColours.get(type);
if (oldcs instanceof GraduatedColor)
{
- cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+ if (((GraduatedColor)oldcs).isAutoScale())
+ {
+ // update the scale
+ cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+ } else {
+ cs = new GraduatedColor((GraduatedColor) oldcs);
+ }
} else {
// promote original color to a graduated color
Color bl = Color.black;
}
// original colour becomes the maximum colour
cs = new GraduatedColor(Color.white,bl,mm[0],mm[1]);
+ cs.setColourByLabel(false);
}
- minColour.setBackground(cs.getMinColor());
- maxColour.setBackground(cs.getMaxColor());
+ minColour.setBackground(oldminColour=cs.getMinColor());
+ maxColour.setBackground(oldmaxColour=cs.getMaxColor());
adjusting = true;
try
} catch (Exception ex)
{
}
+ // update the gui from threshold state
+ thresholdIsMin.setSelected(!cs.isAutoScale());
+ colourByLabel.setSelected(cs.isColourByLabel());
+ if (cs.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ {
+ // initialise threshold slider and selector
+ threshold.setSelectedIndex(cs.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD ? 1 : 2);
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ threshline = new jalview.datamodel.GraphLine(
+ (max - min) / 2f,
+ "Threshold", Color.black);
+
+ }
adjusting = false;
changeColour();
+ if (!block)
+ {
+ new Thread(new Runnable() {
+ public void run()
+ {
+ frame.show();
+ }
+
+ }).start();
+ } else {
+ frame.show();
+ }
}
public FeatureColourChooser()
private void jbInit() throws Exception
{
+
minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setBorder(BorderFactory.createEtchedBorder());
+ minColour.setBorder(BorderFactory.createLineBorder(Color.black));
minColour.setPreferredSize(new Dimension(40, 20));
minColour.setToolTipText("Minimum Colour");
minColour.addMouseListener(new MouseAdapter()
}
});
maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setBorder(BorderFactory.createEtchedBorder());
+ maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
maxColour.setPreferredSize(new Dimension(40, 20));
maxColour.setToolTipText("Maximum Colour");
maxColour.addMouseListener(new MouseAdapter()
}
}
});
+ maxColour.setBorder(new LineBorder(Color.black));
+ minText.setText("Min:");
+ minText.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ maxText.setText("Max:");
+ maxText.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
ok.setOpaque(false);
ok.setText("OK");
ok.addActionListener(new ActionListener()
threshold_actionPerformed(e);
}
});
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ threshold.setToolTipText("Threshold the feature display by score.");
+ threshold.addItem("No Threshold"); // index 0
+ threshold.addItem("Above Threshold"); // index 1
+ threshold.addItem("Below Threshold"); // index 2
jPanel3.setLayout(flowLayout2);
thresholdValue.addActionListener(new ActionListener()
{
slider.setEnabled(false);
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
+ slider.setToolTipText("Adjust threshold");
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.setToolTipText("Toggle between absolute and relative display threshold.");
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
thresholdIsMin_actionPerformed(actionEvent);
}
});
+ colourByLabel.setBackground(Color.white);
+ colourByLabel.setText("Colour by Label");
+ colourByLabel.setToolTipText("Display features of the same type with a different label using a different colour. (e.g. domain features)");
+ colourByLabel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ colourByLabel_actionPerformed(actionEvent);
+ }
+ });
+ colourPanel.setBackground(Color.white);
jPanel1.add(ok);
jPanel1.add(cancel);
- // jPanel2.add(currentColours);
- jPanel2.add(minColour);
- jPanel2.add(maxColour);
+ jPanel2.add(colourByLabel,java.awt.BorderLayout.WEST);
+ jPanel2.add(colourPanel,java.awt.BorderLayout.EAST);
+ colourPanel.add(minText);
+ colourPanel.add(minColour);
+ colourPanel.add(maxText);
+ colourPanel.add(maxColour);
this.add(jPanel3, java.awt.BorderLayout.CENTER);
jPanel3.add(threshold);
jPanel3.add(slider);
}
+ JLabel minText = new JLabel();
+ JLabel maxText = new JLabel();
JPanel minColour = new JPanel();
JPanel maxColour = new JPanel();
JButton ok = new JButton();
JButton cancel = new JButton();
-
+ JPanel colourPanel = new JPanel();
JPanel jPanel1 = new JPanel();
JPanel jPanel2 = new JPanel();
JSlider slider = new JSlider();
JTextField thresholdValue = new JTextField(20);
- // TODO refactor to tolower flag
- JCheckBox currentColours = new JCheckBox();
+ // TODO implement GUI for tolower flag
+ // JCheckBox toLower = new JCheckBox();
JCheckBox thresholdIsMin = new JCheckBox();
+ JCheckBox colourByLabel = new JCheckBox();
private GraphLine threshline;
+
+ private Color oldmaxColour;
+
+
+ private Color oldminColour;
+
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max);
+
+ GraduatedColor acg;
+ if (cs.isColourByLabel())
+ {
+ acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
+ } else {
+ acg = new GraduatedColor(oldminColour=minColour.getBackground(), oldmaxColour=maxColour.getBackground(), min, max);
+
+ }
if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
}
else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
&& threshline == null)
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(!colourByLabel.isSelected());
adjusting = false;
}
acg.setThreshType(aboveThreshold);
if (thresholdIsMin.isSelected() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
{
+ acg.setAutoScaled(false);
if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD)
{
acg = new GraduatedColor(acg, threshline.value, max);
} else {
acg = new GraduatedColor(acg, min,threshline.value);
}
+ } else {
+ acg.setAutoScaled(true);
+ }
+ acg.setColourByLabel(colourByLabel.isSelected());
+ if (acg.isColourByLabel())
+ {
+ maxColour.setEnabled(false);
+ minColour.setEnabled(false);
+ maxColour.setBackground(this.getBackground());
+ minColour.setBackground(this.getBackground());
+ } else {
+ maxColour.setEnabled(true);
+ minColour.setEnabled(true);
+ maxColour.setBackground(oldmaxColour);
+ minColour.setBackground(oldminColour);
}
-
fr.featureColours.put(type,acg);
cs = acg;
ap.paintAlignment(false);
}
-
+ private void raiseClosed() {
+ if (this.colourEditor!=null)
+ {
+ colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
+ }
+ }
public void ok_actionPerformed(ActionEvent e)
{
changeColour();
try
{
- frame.setClosed(true);
+ frame.dispose();
+ raiseClosed();
} catch (Exception ex)
{
}
reset();
try
{
- frame.setClosed(true);
+ frame.dispose();
+// frame.setClosed(true);
+ raiseClosed();
} catch (Exception ex)
{
}
void reset()
{
fr.featureColours.put(type, oldcs);
+ ap.paintAlignment(false);
+ cs = null;
}
public void thresholdCheck_actionPerformed(ActionEvent e)
ap.paintAlignment(false);
}
- public void currentColours_actionPerformed(ActionEvent e)
+ public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
{
- if (currentColours.isSelected())
- {
- reset();
- }
-
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
-
changeColour();
}
-
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ public void colourByLabel_actionPerformed(ActionEvent actionEvent)
{
changeColour();
}
+ ActionListener colourEditor=null;
+ public void addActionListener(ActionListener graduatedColorEditor)
+ {
+ if (colourEditor!=null)
+ {
+ System.err.println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
+ }
+ colourEditor = graduatedColorEditor;
+ }
}
git://source.jalview.org / jalview.git / blobdiff