/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.datamodel.*;
import jalview.schemes.*;
-import java.awt.Rectangle;
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
}
oldcs = av.getGlobalColourScheme();
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.elementAt(g);
if (sg.cs != null)
{
oldgroupColours.put(sg, sg.cs);
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- if (av.alignment.getAlignmentAnnotation() == null)
+ if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
+ setDefaultMinMax();
+
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;
Vector list = new Vector();
int index = 1;
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
{
- String label = av.alignment.getAlignmentAnnotation()[i].label;
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
list.addElement(label);
else
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", 560,
+ 175);
validate();
}
+ private void setDefaultMinMax()
+ {
+ minColour.setBackground(av.applet.getDefaultColourParameter(
+ "ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(av.applet.getDefaultColourParameter(
+ "ANNOTATIONCOLOUR_MAX", Color.red));
+
+ }
+
public AnnotationColourChooser()
{
try
cancel.setLabel("Cancel");
cancel.addActionListener(this);
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ defColours.setLabel("Defaults");
+ defColours.addActionListener(this);
+
annotations.addItemListener(this);
- jPanel1.setBackground(Color.white);
- jPanel2.setBackground(Color.white);
- threshold.addItemListener(this);
- jPanel3.setLayout(null);
thresholdValue.addActionListener(this);
-
slider.setBackground(Color.white);
+ slider.setPreferredSize(new Dimension(193, 21));
slider.setEnabled(false);
- slider.setBounds(new Rectangle(153, 3, 93, 21));
+ thresholdValue.setPreferredSize(new Dimension(79, 22));
thresholdValue.setEnabled(false);
- thresholdValue.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));
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setLabel("Threshold is min/max");
- thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
+
+ this.setLayout(borderLayout1);
+
+ jPanel1.setBackground(Color.white);
+
+ jPanel2.setLayout(new FlowLayout());
+ jPanel2.setBackground(Color.white);
+ threshold.addItemListener(this);
+ jPanel3.setLayout(new FlowLayout());
+ jPanel3.setBackground(Color.white);
+ Panel jPanel4 = new Panel();
+ jPanel4.setLayout(new BorderLayout());
+ jPanel4.setBackground(Color.white);
+
jPanel1.add(ok);
jPanel1.add(cancel);
+
jPanel2.add(annotations);
jPanel2.add(currentColours);
jPanel2.add(minColour);
jPanel2.add(maxColour);
- jPanel3.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);
+
+ jPanel4.add(thresholdIsMin, BorderLayout.WEST);
+ jPanel4.add(slider, BorderLayout.CENTER);
+ jPanel4.add(thresholdValue, BorderLayout.EAST);
+
+ Panel jPanel34 = new Panel();
+ jPanel34.setLayout(new BorderLayout());
+ jPanel34.setBackground(Color.white);
+ jPanel34.add(jPanel2, BorderLayout.NORTH);
+ jPanel34.add(threshold, BorderLayout.WEST);
+ jPanel3.add(defColours);
+ jPanel34.add(jPanel3, BorderLayout.EAST);
+ jPanel34.add(jPanel4, BorderLayout.SOUTH);
+
+ this.add(jPanel34, java.awt.BorderLayout.CENTER);
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+
}
Choice annotations = new Choice();
Button cancel = new Button();
+ Button defColours = new Button();
+
Panel jPanel1 = new Panel();
Panel jPanel2 = new Panel();
{
maxColour_actionPerformed(null);
}
-
+ else if (evt.getSource() == defColours)
+ {
+ defColour_actionPerformed();
+ }
else if (evt.getSource() == ok)
{
changeColour();
}
}
+ public void defColour_actionPerformed()
+ {
+ setDefaultMinMax();
+ minColour.repaint();
+ maxColour.repaint();
+ changeColour();
+ }
+
void changeColour()
{
// Check if combobox is still adjusting
return;
}
- currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
.getSelectedIndex()];
int aboveThreshold = -1;
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
+ thresholdIsMin.setEnabled(false);
thresholdValue.setText("");
}
else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
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(), aboveThreshold);
+ acg = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold);
}
if (currentAnnotation.graphMin == 0f
av.setGlobalColourScheme(acg);
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.elementAt(g);
if (sg.cs == null)
{
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, minColour
- .getBackground(), maxColour.getBackground(),
+ sg.cs = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
}
}
}
- ap.paintAlignment(false);
+ // update colours in linked windows
+ ap.paintAlignment(true);
}
void reset()
{
av.setGlobalColourScheme(oldcs);
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.elementAt(g);
Object cs = oldgroupColours.get(sg);
if (cs instanceof ColourSchemeI)
{
git://source.jalview.org / jalview.git / blobdiff