/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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 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.gui;
import jalview.schemes.*;
import java.awt.Dimension;
-public class FeatureColourChooser extends JPanel
+public class FeatureColourChooser extends JalviewDialog
{
- JDialog frame;
-
-
-// FeatureSettings fs;
+ // 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
+ * @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)
+ public Object getLastColour()
+ {
+ if (cs == null)
{
return oldcs;
}
return cs;
}
+
Hashtable oldgroupColours;
-
+
AlignmentPanel ap;
-
boolean adjusting = false;
private float min;
private float max;
+
String type = null;
+
public FeatureColourChooser(FeatureRenderer frender, String type)
{
- this(frender,false,type);
+ this(frender, false, type);
}
- public FeatureColourChooser(FeatureRenderer frender, boolean block, String type)
- {
+
+ public FeatureColourChooser(FeatureRenderer frender, boolean block,
+ String type)
+ {
this.fr = frender;
this.type = type;
ap = fr.ap;
- 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);
+ initDialogFrame(this,true, block,"Graduated Feature Colour for " + type, 480, 185);
+ // 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 (ap!=null) { ap.paintAlignment(true); };
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+ ;
}
});
oldcs = fr.featureColours.get(type);
if (oldcs instanceof GraduatedColor)
{
- if (((GraduatedColor)oldcs).isAutoScale())
+ if (((GraduatedColor) oldcs).isAutoScale())
{
// update the scale
cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
- } else {
+ }
+ else
+ {
cs = new GraduatedColor((GraduatedColor) oldcs);
}
- } else {
+ }
+ 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]);
+ cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
cs.setColourByLabel(false);
}
- minColour.setBackground(oldminColour=cs.getMinColor());
- maxColour.setBackground(oldmaxColour=cs.getMaxColor());
+ minColour.setBackground(oldminColour = cs.getMinColor());
+ maxColour.setBackground(oldmaxColour = cs.getMaxColor());
adjusting = true;
-
+
try
{
jbInit();
// update the gui from threshold state
thresholdIsMin.setSelected(!cs.isAutoScale());
colourByLabel.setSelected(cs.isColourByLabel());
- if (cs.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
{
// initialise threshold slider and selector
- threshold.setSelectedIndex(cs.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD ? 1 : 2);
- slider.setEnabled(true);
+ 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);
-
- }
+ 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();
- }
+ waitForInput();
}
public FeatureColourChooser()
private void jbInit() throws Exception
{
-
- minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+
+ minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createLineBorder(Color.black));
minColour.setPreferredSize(new Dimension(40, 20));
minColour.setToolTipText("Minimum Colour");
}
}
});
- maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ maxColour.setFont(JvSwingUtils.getLabelFont());
maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
maxColour.setPreferredSize(new Dimension(40, 20));
maxColour.setToolTipText("Maximum Colour");
});
maxColour.setBorder(new LineBorder(Color.black));
minText.setText("Min:");
- minText.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ minText.setFont(JvSwingUtils.getLabelFont());
maxText.setText("Max:");
- maxText.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- 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);
- }
- });
+ maxText.setFont(JvSwingUtils.getLabelFont());
this.setLayout(borderLayout1);
jPanel2.setLayout(flowLayout1);
jPanel1.setBackground(Color.white);
jPanel3.setBackground(Color.white);
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setText("Threshold is Min/Max");
- thresholdIsMin.setToolTipText("Toggle between absolute and relative display threshold.");
+ thresholdIsMin
+ .setToolTipText("Toggle between absolute and relative display threshold.");
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent 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
+ .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)
colourPanel.setBackground(Color.white);
jPanel1.add(ok);
jPanel1.add(cancel);
- jPanel2.add(colourByLabel,java.awt.BorderLayout.WEST);
- jPanel2.add(colourPanel,java.awt.BorderLayout.EAST);
+ jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
+ jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
colourPanel.add(minText);
colourPanel.add(minColour);
colourPanel.add(maxText);
this.add(jPanel2, java.awt.BorderLayout.NORTH);
}
-
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 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()
if (col != null)
{
minColour.setBackground(col);
+ minColour.setForeground(col);
}
minColour.repaint();
changeColour();
if (col != null)
{
maxColour.setBackground(col);
+ maxColour.setForeground(col);
}
maxColour.repaint();
changeColour();
return;
}
-
int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
if (threshold.getSelectedItem().equals("Above Threshold"))
{
else if (threshold.getSelectedItem().equals("Below Threshold"))
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
- }
+ }
slider.setEnabled(true);
thresholdValue.setEnabled(true);
-
+
GraduatedColor acg;
if (cs.isColourByLabel())
- {
- acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
- } else {
- acg = new GraduatedColor(oldminColour=minColour.getBackground(), oldmaxColour=maxColour.getBackground(), min, max);
-
- }
+ {
+ acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
+ }
+ else
+ {
+ acg = new GraduatedColor(oldminColour = minColour.getBackground(),
+ oldmaxColour = maxColour.getBackground(), min, max);
+
+ }
if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
{
&& threshline == null)
{
// todo visual indication of feature threshold
- threshline = new jalview.datamodel.GraphLine(
- (max - min) / 2f,
- "Threshold", Color.black);
+ 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;
+ float range = max * 1000f - min * 1000f;
slider.setMinimum((int) (min * 1000));
slider.setMaximum((int) (max * 1000));
}
acg.setThreshType(aboveThreshold);
- if (thresholdIsMin.isSelected() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (thresholdIsMin.isSelected()
+ && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
{
acg.setAutoScaled(false);
- if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD)
- {
+ if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
acg = new GraduatedColor(acg, threshline.value, max);
- } else {
- acg = new GraduatedColor(acg, min,threshline.value);
}
- } else {
+ else
+ {
+ acg = new GraduatedColor(acg, min, threshline.value);
+ }
+ }
+ else
+ {
acg.setAutoScaled(true);
}
acg.setColourByLabel(colourByLabel.isSelected());
maxColour.setEnabled(false);
minColour.setEnabled(false);
maxColour.setBackground(this.getBackground());
+ maxColour.setForeground(this.getBackground());
minColour.setBackground(this.getBackground());
- } else {
+ minColour.setForeground(this.getBackground());
+
+ }
+ else
+ {
maxColour.setEnabled(true);
minColour.setEnabled(true);
maxColour.setBackground(oldmaxColour);
minColour.setBackground(oldminColour);
+ maxColour.setForeground(oldmaxColour);
+ minColour.setForeground(oldminColour);
}
- fr.featureColours.put(type,acg);
+ fr.featureColours.put(type, acg);
cs = acg;
ap.paintAlignment(false);
}
- private void raiseClosed() {
- if (this.colourEditor!=null)
+
+ protected void raiseClosed()
+ {
+ if (this.colourEditor != null)
{
colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
}
}
- public void ok_actionPerformed(ActionEvent e)
+
+ public void okPressed()
{
changeColour();
- try
- {
- frame.dispose();
- raiseClosed();
- } catch (Exception ex)
- {
- }
}
- public void cancel_actionPerformed(ActionEvent e)
+
+ public void cancelPressed()
{
reset();
- try
- {
- frame.dispose();
-// frame.setClosed(true);
- raiseClosed();
- } catch (Exception ex)
- {
- }
}
void reset()
{
changeColour();
}
+
public void colourByLabel_actionPerformed(ActionEvent actionEvent)
{
changeColour();
}
- ActionListener colourEditor=null;
+
+ ActionListener colourEditor = null;
+
public void addActionListener(ActionListener graduatedColorEditor)
{
- if (colourEditor!=null)
+ if (colourEditor != null)
{
- System.err.println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
+ System.err
+ .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
}
colourEditor = graduatedColorEditor;
}
git://source.jalview.org / jalview.git / blobdiff