/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
+ * 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 java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.Rectangle;
-
-import javax.swing.BoxLayout;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+import java.util.Vector;
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.getAlignment().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);
}
setDefaultMinMax();
-
+
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.predefinedColours);
- if (!acg.predefinedColours) {
+ currentColours.setState(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
+ {
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
+ // seqAssociated.setState(acg.isSeqAssociated());
}
- adjusting = true;
-
Vector list = new Vector();
int index = 1;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
{
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
+ {
list.addElement(label);
+ }
else
+ {
list.addElement(label + "_" + (index++));
+ }
}
for (int i = 0; i < list.size(); i++)
annotations.addItem(list.elementAt(i).toString());
}
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold"));
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
annotations.select(acg.getAnnotation());
- switch (acg.getAboveThreshold()) {
+ switch (acg.getAboveThreshold())
+ {
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.select("No Threshold");
+ threshold.select(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.select("Above Threshold");
+ threshold.select(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.select("Below Threshold");
+ threshold.select(1);
break;
- default:
- throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ default:
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
- thresholdValue.setText(""+acg.getAnnotationThreshold());
+ thresholdValue.setText("" + acg.getAnnotationThreshold());
}
adjusting = false;
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 560,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.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));
+ minColour.setBackground(av.applet.getDefaultColourParameter(
+ "ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(av.applet.getDefaultColourParameter(
+ "ANNOTATIONCOLOUR_MAX", Color.red));
}
+
public AnnotationColourChooser()
{
try
private void jbInit() throws Exception
{
minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setLabel("Min Colour");
+ minColour.setLabel(MessageManager.getString("label.min_colour"));
minColour.addActionListener(this);
maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setLabel("Max Colour");
+ maxColour.setLabel(MessageManager.getString("label.max_colour"));
maxColour.addActionListener(this);
thresholdIsMin.addItemListener(this);
- ok.setLabel("OK");
+ ok.setLabel(MessageManager.getString("action.ok"));
ok.addActionListener(this);
- cancel.setLabel("Cancel");
+ cancel.setLabel(MessageManager.getString("action.cancel"));
cancel.addActionListener(this);
- defColours.setLabel("Defaults");
+ defColours.setLabel(MessageManager.getString("action.set_defaults"));
defColours.addActionListener(this);
-
+
annotations.addItemListener(this);
thresholdValue.addActionListener(this);
slider.setBackground(Color.white);
- slider.setPreferredSize(new Dimension(193,21));
+ slider.setPreferredSize(new Dimension(193, 21));
slider.setEnabled(false);
- thresholdValue.setPreferredSize(new Dimension(79,22));
+ thresholdValue.setPreferredSize(new Dimension(79, 22));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel("Use Original Colours");
+ currentColours.setLabel(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel("Threshold is min/max");
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
-
+
jPanel1.setBackground(Color.white);
-
+
jPanel2.setLayout(new FlowLayout());
jPanel2.setBackground(Color.white);
threshold.addItemListener(this);
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);
-
-
+
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(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 ok = new Button();
Button cancel = new Button();
-
+
Button defColours = new Button();
Panel jPanel1 = new Panel();
}
else if (evt.getSource() == defColours)
{
- defColour_actionPerformed();
+ defColour_actionPerformed();
}
else if (evt.getSource() == ok)
{
- changeColour();
frame.setVisible(false);
}
else if (evt.getSource() == cancel)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
if (currentColours.getState()
&& !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
ap.paintAlignment(false);
}
}
new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
}
}
+
public void defColour_actionPerformed()
{
setDefaultMinMax();
maxColour.repaint();
changeColour();
}
+
void changeColour()
{
// Check if combobox is still adjusting
.getSelectedIndex()];
int aboveThreshold = -1;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.getState();
av.setGlobalColourScheme(acg);
+ // TODO: per group colour propagation not always desired
if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.getAlignment().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)
{
}
// update colours in linked windows
+ ap.alignmentChanged();
ap.paintAlignment(true);
}
av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.getAlignment().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