/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 AnnotationColourChooser
- extends Panel implements ActionListener,
- AdjustmentListener, ItemListener, MouseListener
+public class AnnotationColourChooser extends Panel implements
+ ActionListener, AdjustmentListener, ItemListener, MouseListener
{
Frame frame;
+
AlignViewport av;
+
AlignmentPanel ap;
+
ColourSchemeI oldcs;
+
Hashtable oldgroupColours;
+
jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
boolean adjusting = false;
public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
try
{
jbInit();
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
oldcs = av.getGlobalColourScheme();
if (av.alignment.getGroups() != null)
for (int g = 0; g < allGroups.size(); g++)
{
sg = (SequenceGroup) allGroups.elementAt(g);
- if (sg.cs!=null)
+ if (sg.cs != null)
+ {
+ oldgroupColours.put(sg, sg.cs);
+ }
+ else
{
- oldgroupColours.put(sg, sg.cs);
- } else {
oldgroupColours.put(sg, "null");
}
}
return;
}
+ minColour.setBackground(av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MIN",Color.orange));
+ maxColour.setBackground(av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MAX",Color.red));
+
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- minColour.setBackground(acg.getMinColour());
- maxColour.setBackground(acg.getMaxColour());
- }
- else
- {
- minColour.setBackground(Color.orange);
- maxColour.setBackground(Color.red);
+ currentColours.setState(acg.predefinedColours);
+ if (!acg.predefinedColours) {
+ minColour.setBackground(acg.getMinColour());
+ maxColour.setBackground(acg.getMaxColour());
+ }
}
adjusting = true;
if (!list.contains(label))
list.addElement(label);
else
- list.addElement(label+"_"+(index++));
+ list.addElement(label + "_" + (index++));
}
for (int i = 0; i < list.size(); i++)
{
- annotations.addItem(list.elementAt(i).toString());
+ annotations.addItem(list.elementAt(i).toString());
}
threshold.addItem("No Threshold");
threshold.addItem("Above Threshold");
threshold.addItem("Below Threshold");
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ annotations.select(acg.getAnnotation());
+ switch (acg.getAboveThreshold()) {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ threshold.select("No Threshold");
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ threshold.select("Above Threshold");
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ threshold.select("Below Threshold");
+ break;
+ default:
+ throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ }
+ thresholdIsMin.setState(acg.thresholdIsMinMax);
+ thresholdValue.setText(""+acg.getAnnotationThreshold());
+ }
+
adjusting = false;
changeColour();
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145);
+ jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480,
+ 145);
validate();
}
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
minColour.setLabel("Min Colour");
}
Choice annotations = new Choice();
+
Button minColour = new Button();
+
Button maxColour = new Button();
+
Button ok = new Button();
+
Button cancel = new Button();
+
Panel jPanel1 = new Panel();
+
Panel jPanel2 = new Panel();
+
Choice threshold = new Choice();
+
FlowLayout flowLayout1 = new FlowLayout();
+
Panel jPanel3 = new Panel();
+
Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
TextField thresholdValue = new TextField(20);
+
Checkbox currentColours = new Checkbox();
+
BorderLayout borderLayout1 = new BorderLayout();
+
Checkbox thresholdIsMin = new Checkbox();
public void actionPerformed(ActionEvent evt)
try
{
float f = new Float(thresholdValue.getText()).floatValue();
- slider.setValue( (int) (f * 1000));
+ slider.setValue((int) (f * 1000));
adjustmentValueChanged(null);
+ } catch (NumberFormatException ex)
+ {
}
- catch (NumberFormatException ex)
- {}
}
else if (evt.getSource() == minColour)
{
{
if (!adjusting)
{
- thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
if (currentColours.getState()
- && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
}
else
{
- new UserDefinedColours(this, "Min Colour",
- minColour.getBackground());
+ new UserDefinedColours(this, "Min Colour", minColour.getBackground());
}
}
}
else
{
- new UserDefinedColours(this, "Max Colour",
- maxColour.getBackground());
+ new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
}
}
return;
}
-
- currentAnnotation = av.alignment.getAlignmentAnnotation()
- [annotations.getSelectedIndex()];
+ currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+ .getSelectedIndex()];
int aboveThreshold = -1;
if (threshold.getSelectedItem().equals("Above Threshold"))
thresholdValue.setEnabled(false);
thresholdValue.setText("");
}
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
- currentAnnotation.threshold == null)
- {
- currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
- ( (currentAnnotation.graphMax -
- currentAnnotation.graphMin) / 2f,
- "Threshold",
- Color.black));
+ else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+ && currentAnnotation.threshold == null)
+ {
+ currentAnnotation
+ .setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+ "Threshold", Color.black));
}
if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
- slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
- slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
+ slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+ slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+ slider.setValue((int) (currentAnnotation.threshold.value * 1000));
thresholdValue.setText(currentAnnotation.threshold.value + "");
slider.setEnabled(true);
thresholdValue.setEnabled(true);
AnnotationColourGradient acg = null;
if (currentColours.getState())
{
- acg = new AnnotationColourGradient(
- currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
+ acg = new AnnotationColourGradient(currentAnnotation,
+ av.getGlobalColourScheme(), aboveThreshold);
}
else
{
- acg =
- new AnnotationColourGradient(
- currentAnnotation,
- minColour.getBackground(),
- maxColour.getBackground(),
+ acg = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
}
- if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)
+ if (currentAnnotation.graphMin == 0f
+ && currentAnnotation.graphMax == 0f)
{
acg.predefinedColours = true;
}
if (currentColours.getState())
{
- sg.cs = new AnnotationColourGradient(
- currentAnnotation,
- sg.cs, aboveThreshold);
+ sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+ aboveThreshold);
}
else
{
- sg.cs = new AnnotationColourGradient(
- currentAnnotation,
- minColour.getBackground(),
- maxColour.getBackground(),
- aboveThreshold);
+ sg.cs = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold);
}
}
}
- ap.paintAlignment(false);
+ // update colours in linked windows
+ ap.paintAlignment(true);
}
void reset()
Object cs = oldgroupColours.get(sg);
if (cs instanceof ColourSchemeI)
{
- sg.cs = (ColourSchemeI) cs;
- } else {
+ sg.cs = (ColourSchemeI) cs;
+ }
+ else
+ {
// probably the "null" string we set it to if it was null originally.
sg.cs = null;
}
}
- public void mouseClicked(MouseEvent evt){}
- public void mousePressed(MouseEvent evt){}
- public void mouseReleased(MouseEvent evt){ ap.paintAlignment(true);}
- public void mouseEntered(MouseEvent evt){}
- public void mouseExited(MouseEvent evt){}
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ ap.paintAlignment(true);
+ }
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff