/*
- * 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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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.appletgui;
import jalview.schemes.*;
import java.awt.Rectangle;
-public class FeatureColourChooser extends Panel implements
- ActionListener, AdjustmentListener, ItemListener, MouseListener
+public class FeatureColourChooser extends Panel implements ActionListener,
+ AdjustmentListener, ItemListener, MouseListener
{
- Frame frame;
+ JVDialog frame;
+
+ Frame owner;
FeatureRenderer fr;
- FeatureSettings fs;
- AlignmentPanel ap;
+
+ FeatureSettings fs = null;
+
+ // AlignmentPanel ap;
GraduatedColor cs;
+
Object oldcs;
Hashtable oldgroupColours;
-
boolean adjusting = false;
- private float min,max;
- String type=null;
-
+
+ private float min, max;
+
+ String type = null;
+
+ private AlignFrame af = null;
+
+ public FeatureColourChooser(AlignFrame af, String type)
+ {
+ this.af = af;
+ init(af.getSeqcanvas().getFeatureRenderer(), type);
+ }
+
public FeatureColourChooser(FeatureSettings fsettings, String type)
{
this.fs = fsettings;
+ init(fsettings.fr, type);
+ // this.ap = fsettings.ap;
+ }
+
+ private void init(FeatureRenderer frenderer, String type)
+ {
this.type = type;
- fr = fsettings.fr;
- ap = fsettings.ap;
+ fr = frenderer;
float mm[] = ((float[][]) fr.minmax.get(type))[0];
min = mm[0];
max = mm[1];
if (oldcs instanceof GraduatedColor)
{
cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
- } 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]);
}
minColour.setBackground(cs.getMinColor());
maxColour.setBackground(cs.getMaxColor());
+ minColour.setForeground(cs.getMinColor());
+ maxColour.setForeground(cs.getMaxColor());
+ colourFromLabel.setState(cs.isColourByLabel());
adjusting = true;
try
} catch (Exception ex)
{
}
- // To HERE!
+ threshold
+ .select(cs.getThreshType() == AnnotationColourGradient.NO_THRESHOLD ? 0
+ : cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
+ : 2);
+
adjusting = false;
changeColour();
+ colourFromLabel.addItemListener(this);
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- frame = new Frame();
- frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Graduated Feature Colour for "+type, 480,
- 145);
+ owner = (af != null) ? af : fs.frame;
+ frame = new JVDialog(owner, "Graduated Feature Colour for " + type,
+ true, 480, 248);
+ frame.setMainPanel(this);
validate();
+ frame.setVisible(true);
+ if (frame.accept)
+ {
+ changeColour();
+ }
+ else
+ {
+ // cancel
+ reset();
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ frame.setVisible(false);
+ }
}
public FeatureColourChooser()
private void jbInit() throws Exception
{
- minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setLabel("Min Colour");
- minColour.addActionListener(this);
+ Label minLabel = new Label("Min:"), maxLabel = new Label("Max:");
+ minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ // minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ // minColour.setLabel("Min Colour");
+
+ minColour.setBounds(0, 0, 40, 27);
+ maxColour.setBounds(0, 0, 40, 27);
+ minColour.addMouseListener(this);
maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setLabel("Max Colour");
- maxColour.addActionListener(this);
+ maxColour.addMouseListener(this);
thresholdIsMin.addItemListener(this);
- ok.setLabel("OK");
- ok.addActionListener(this);
-
- cancel.setLabel("Cancel");
- cancel.addActionListener(this);
-
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ this.setLayout(new GridLayout(4, 1));
+ jPanel1.setLayout(new FlowLayout());
+ jPanel2.setLayout(new FlowLayout());
+ jPanel3.setLayout(new GridLayout(1, 1));
+ jPanel4.setLayout(new FlowLayout());
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
+ jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
threshold.addItem("No Threshold");
threshold.addItem("Above Threshold");
threshold.addItem("Below Threshold");
- jPanel3.setLayout(null);
thresholdValue.addActionListener(this);
-
slider.setBackground(Color.white);
slider.setEnabled(false);
- slider.setBounds(new Rectangle(153, 3, 93, 21));
+ slider.setSize(new Dimension(93, 21));
thresholdValue.setEnabled(false);
- thresholdValue.setBounds(new Rectangle(248, 2, 79, 22));
+ thresholdValue.setSize(new Dimension(79, 22)); // 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.addItemListener(this);
- threshold.setBounds(new Rectangle(11, 3, 139, 22));
+ colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ colourFromLabel.setLabel("Colour by Label");
+ colourFromLabel.setSize(new Dimension(139, 22));
+ // 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));
- jPanel1.add(ok);
- jPanel1.add(cancel);
- //jPanel2.add(currentColours);
- jPanel2.add(minColour);
- jPanel2.add(maxColour);
- jPanel3.add(threshold);
+ thresholdIsMin.setSize(new Dimension(135, 23));
+ // thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
+ jPanel1.add(minLabel);
+ jPanel1.add(minColour);
+ jPanel1.add(maxLabel);
+ jPanel1.add(maxColour);
+ jPanel1.add(colourFromLabel);
+ jPanel2.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);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ jPanel4.add(thresholdValue);
+ jPanel4.add(thresholdIsMin);
+ this.add(jPanel1);// , java.awt.BorderLayout.NORTH);
+ this.add(jPanel2);// , java.awt.BorderLayout.NORTH);
+ this.add(jPanel3);// , java.awt.BorderLayout.CENTER);
+ this.add(jPanel4);// , java.awt.BorderLayout.CENTER);
}
- Button minColour = new Button();
-
- Button maxColour = new Button();
+ Panel minColour = new Panel();
- Button ok = new Button();
-
- Button cancel = new Button();
+ Panel maxColour = new Panel();
Panel jPanel1 = new Panel();
Choice threshold = new Choice();
- FlowLayout flowLayout1 = new FlowLayout();
-
Panel jPanel3 = new Panel();
+ Panel jPanel4 = new Panel();
+
Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
TextField thresholdValue = new TextField(20);
-
- BorderLayout borderLayout1 = new BorderLayout();
+ // BorderLayout borderLayout1 = new BorderLayout();
Checkbox thresholdIsMin = new Checkbox();
+ Checkbox colourFromLabel = new Checkbox();
+
private GraphLine threshline;
public void actionPerformed(ActionEvent evt)
{
maxColour_actionPerformed(null);
}
-
- else if (evt.getSource() == ok)
- {
- changeColour();
- frame.setVisible(false);
- }
- else if (evt.getSource() == cancel)
- {
- reset();
- ap.paintAlignment(true);
- frame.setVisible(false);
- }
-
else
{
changeColour();
public void itemStateChanged(ItemEvent evt)
{
-
+ maxColour.setEnabled(!colourFromLabel.getState());
+ minColour.setEnabled(!colourFromLabel.getState());
changeColour();
}
valueChanged();
}
}
- protected void valueChanged() {
- changeColour();
+
+ protected void valueChanged()
+ {
threshline.value = (float) slider.getValue() / 1000f;
- ap.paintAlignment(false);
+ cs.setThresh(threshline.value);
+ changeColour();
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(false);
}
+
public void minColour_actionPerformed(Color newCol)
{
- if (newCol != null)
+ if (newCol == null)
{
- minColour.setBackground(newCol);
- minColour.repaint();
- changeColour();
+ UserDefinedColours udc = new UserDefinedColours(this,
+ minColour.getBackground(), owner,
+ "Select Colour for Minimum Value"); // frame.owner,
}
else
{
- new UserDefinedColours(this, "Select Colour for Minimum Value", minColour.getBackground());
+ minColour.setBackground(newCol);
+ minColour.setForeground(newCol);
+ minColour.repaint();
+ changeColour();
}
}
public void maxColour_actionPerformed(Color newCol)
{
- if (newCol != null)
+ if (newCol == null)
{
- maxColour.setBackground(newCol);
- maxColour.repaint();
- changeColour();
+
+ // UserDefinedColours udc = new UserDefinedColours(this,
+ // "Select Colour for Maximum Value",maxColour.getBackground(),true);
+ UserDefinedColours udc = new UserDefinedColours(this,
+ maxColour.getBackground(), owner,
+ "Select Colour for Maximum Value");
}
else
{
- new UserDefinedColours(this, "Select Colour for Maximum Value", maxColour.getBackground());
+ maxColour.setBackground(newCol);
+ maxColour.setForeground(newCol);
+ maxColour.repaint();
+ changeColour();
}
}
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max);
+ GraduatedColor acg = new GraduatedColor(minColour.getBackground(),
+ maxColour.getBackground(), min, max);
+ acg.setColourByLabel(colourFromLabel.getState());
+ maxColour.setEnabled(!colourFromLabel.getState());
+ minColour.setEnabled(!colourFromLabel.getState());
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);
+ 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.getState() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (thresholdIsMin.getState()
+ && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
{
- 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
+ {
+ acg = new GraduatedColor(acg, min, threshline.value);
}
}
-
- fr.featureColours.put(type,acg);
+
+ fr.featureColours.put(type, acg);
cs = acg;
- ap.paintAlignment(false);
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(false);
}
void reset()
{
fr.featureColours.put(type, oldcs);
- ap.paintAlignment(true);
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(true);
}
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ if (evt.getSource() == minColour || evt.getSource() == maxColour)
+ {
+ // relay the event
+ actionPerformed(new ActionEvent(evt.getSource(), 1, "Clicked"));
+ }
+ else
+ {
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ }
+ // ap.paintAlignment(true);
}
public void mouseEntered(MouseEvent evt)
git://source.jalview.org / jalview.git / blobdiff