/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.datamodel.AlignmentAnnotation;
+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.HashMap;
+import java.util.Map;
+import java.util.Vector;
+
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
+ Map<SequenceGroup, ColourSchemeI> oldgroupColours;
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ /*
+ * map from annotation to its menu item display label
+ * - so we know which item to pre-select on restore
+ */
+ private Map<AlignmentAnnotation, String> annotationLabels;
+
+ AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
- {
- oldgroupColours.put(sg, sg.cs);
- }
- else
- {
- oldgroupColours.put(sg, "null");
- }
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
this.av = av;
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- if (av.getAlignment().getAlignmentAnnotation() == null)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
{
return;
}
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ 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());
}
-
- 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++));
- }
+ Vector<String> list = getAnnotationItems();
for (int i = 0; i < list.size(); i++)
{
annotations.addItem(list.elementAt(i).toString());
}
- 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"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_threshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_threshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_threshold"));
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- annotations.select(acg.getAnnotation());
+ String label = annotationLabels.get(acg.getAnnotation());
+ annotations.select(label);
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
threshold.select(1);
break;
default:
- throw new Error(
- "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_threshold_annotationcolourgradient"));
}
- thresholdIsMin.setState(acg.thresholdIsMinMax);
+ thresholdIsMin.setState(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
}
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 560,
175);
validate();
}
+ /**
+ * Builds and returns a list of menu items (display text) for choice of
+ * annotation. Also builds a map between annotations and their display labels.
+ *
+ * @return
+ */
+ protected Vector<String> getAnnotationItems()
+ {
+ // TODO remove duplication with gui.AnnotationRowFilter
+ // TODO add 'per sequence only' option / parameter
+
+ annotationLabels = new HashMap<AlignmentAnnotation, String>();
+ Vector<String> list = new Vector<String>();
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
+ {
+ return list;
+ }
+ int index = 1;
+ for (int i = 0; i < anns.length; i++)
+ {
+ String label = anns[i].label;
+ if (anns[i].sequenceRef != null)
+ {
+ /*
+ * be helpful and include sequence id in label for
+ * sequence-associated annotation (JAL-2236)
+ */
+ label = label + "_" + anns[i].sequenceRef.getName();
+ }
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ annotationLabels.put(anns[i], label);
+ }
+ else
+ {
+ label = label + "_" + (index++);
+ list.addElement(label);
+ annotationLabels.put(anns[i], label);
+ }
+ }
+ return list;
+ }
+
private void setDefaultMinMax()
{
minColour.setBackground(av.applet.getDefaultColourParameter(
"ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(av.applet.getDefaultColourParameter(
- "ANNOTATIONCOLOUR_MAX", Color.red));
+ maxColour.setBackground(av.applet
+ .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
}
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel(MessageManager.getString("label.use_original_colours"));
+ currentColours.setLabel(
+ MessageManager.getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setLabel(MessageManager.getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
Checkbox thresholdIsMin = new Checkbox();
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
}
else if (evt.getSource() == ok)
{
- changeColour();
frame.setVisible(false);
}
else if (evt.getSource() == cancel)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == currentColours)
changeColour();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
- if (currentColours.getState()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ 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);
}
}
return;
}
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
- .getSelectedIndex()];
+ currentAnnotation = av.getAlignment()
+ .getAlignmentAnnotation()[annotations.getSelectedIndex()];
int aboveThreshold = -1;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
&& currentAnnotation.threshold == null)
{
- currentAnnotation
- .setThreshold(new jalview.datamodel.GraphLine(
- (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
- "Threshold", Color.black));
+ currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
+ "Threshold", Color.black));
}
if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
AnnotationColourGradient acg = null;
if (currentColours.getState())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
}
else
{
acg.setPredefinedColours(true);
}
- acg.thresholdIsMinMax = thresholdIsMin.getState();
+ acg.setThresholdIsMinMax(thresholdIsMin.getState());
av.setGlobalColourScheme(acg);
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
-
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
continue;
}
if (currentColours.getState())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
+ sg.getColourScheme(), aboveThreshold));
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
+ sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
+ aboveThreshold));
}
-
}
}
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- Object cs = oldgroupColours.get(sg);
- if (cs instanceof ColourSchemeI)
- {
- sg.cs = (ColourSchemeI) cs;
- }
- else
- {
- // probably the "null" string we set it to if it was null originally.
- sg.cs = null;
- }
+ sg.setColourScheme(oldgroupColours.get(sg));
}
}
ap.paintAlignment(true);
-
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
git://source.jalview.org / jalview.git / blobdiff