/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import net.miginfocom.swing.MigLayout;
-
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
-public class AnnotationColourChooser extends JPanel
-{
- JInternalFrame frame;
-
- AlignViewport av;
+import net.miginfocom.swing.MigLayout;
- AlignmentPanel ap;
+@SuppressWarnings("serial")
+public class AnnotationColourChooser extends AnnotationRowFilter
+{
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
-
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
- boolean adjusting = false;
/**
- * enabled if the user is dragging the slider - try to keep updates to a minimun
+ * enabled if the user is dragging the slider - try to keep updates to a
+ * minimun
*/
- boolean sliderDragging = false;
+
+ JComboBox<String> annotations;
+
+ JButton defColours = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JPanel jPanel2 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ private JComboBox<String> threshold = new JComboBox<String>();
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
+ super(av, ap);
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs != null)
}
}
}
- this.av = av;
- this.ap = ap;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
- slider.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
- valueChanged(!sliderDragging);
- }
- }
- });
- slider.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent e)
- {
- sliderDragging=true;
- super.mousePressed(e);
- }
-
- @Override
- public void mouseDragged(MouseEvent e)
- {
- sliderDragging=true;
- super.mouseDragged(e);
- }
- public void mouseReleased(MouseEvent evt)
- {
- if (sliderDragging)
- {
- sliderDragging=false;
- valueChanged(true);
- }
- ap.paintAlignment(true);
- }
- });
+ addSliderChangeListener();
+ addSliderMouseListeners();
if (av.getAlignment().getAlignmentAnnotation() == null)
{
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ currentColours.setSelected(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
seqAssociated.setSelected(acg.isSeqAssociated());
-
+
}
- annotations = new JComboBox(
+ annotations = new JComboBox<String>(
getAnnotationItems(seqAssociated.isSelected()));
- 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"));
+ populateThresholdComboBox(threshold);
if (oldcs instanceof AnnotationColourGradient)
{
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedIndex(0);
+ getThreshold().setSelectedIndex(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedIndex(1);
+ getThreshold().setSelectedIndex(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.setSelectedIndex(2);
+ getThreshold().setSelectedIndex(2);
break;
default:
throw new Error(
- "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ MessageManager
+ .getString("error.implementation_error_dont_know_about_thereshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
} catch (Exception ex)
{
}
-
adjusting = false;
- changeColour();
+ updateView();
frame.invalidate();
frame.pack();
-
- }
-
- private Vector<String> getAnnotationItems(boolean isSeqAssociated)
- {
- Vector<String> list = new Vector<String>();
- int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss = false;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
- {
- if (isSeqAssociated)
- {
- continue;
- }
- }
- else
- {
- enableSeqAss = true;
- }
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- {
- anmap[list.size()] = i;
- list.addElement(label);
-
- }
- else
- {
- if (!isSeqAssociated)
- {
- anmap[list.size()] = i;
- list.addElement(label + "_" + (index++));
- }
- }
- }
- seqAssociated.setEnabled(enableSeqAss);
- annmap = new int[list.size()];
- System.arraycopy(anmap, 0, annmap, 0, annmap.length);
- return list;
- }
- private void setDefaultMinMax()
- {
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
}
public AnnotationColourChooser()
minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (minColour.isEnabled())
maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (maxColour.isEnabled())
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
});
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
- defColours
- .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+ defColours.setToolTipText(MessageManager
+ .getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
}
});
- threshold.addActionListener(new ActionListener()
+ getThreshold().addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
threshold_actionPerformed(e);
});
thresholdValue.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
thresholdValue_actionPerformed(e);
thresholdValue.setColumns(7);
currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
- currentColours.setText(MessageManager.getString("label.use_original_colours"));
+ currentColours.setText(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
currentColours_actionPerformed(e);
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setText(MessageManager
+ .getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
thresholdIsMin_actionPerformed(actionEvent);
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
+ seqAssociated.setText(MessageManager
+ .getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- seqAssociated_actionPerformed(arg0);
+ seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
}
});
colpanel.add(minColour);
colpanel.add(maxColour);
jPanel2.add(colpanel, "wrap");
- jPanel2.add(threshold);
+ jPanel2.add(getThreshold());
jPanel2.add(defColours, "skip 1, wrap");
jPanel2.add(thresholdIsMin);
jPanel2.add(slider, "grow");
this.validate();
}
- protected void seqAssociated_actionPerformed(ActionEvent arg0)
- {
- adjusting = true;
- String cursel = (String) annotations.getSelectedItem();
- boolean isvalid = false, isseqs = seqAssociated.isSelected();
- this.annotations.removeAllItems();
- for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
- {
- if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
- {
- isvalid = true;
- cursel = anitem;
- }
- this.annotations.addItem(anitem);
- }
- adjusting = false;
- if (isvalid)
- {
- this.annotations.setSelectedItem(cursel);
- }
- else
- {
- if (annotations.getItemCount() > 0)
- {
- annotations.setSelectedIndex(0);
- }
- }
- }
-
protected void resetColours_actionPerformed(ActionEvent arg0)
{
setDefaultMinMax();
- changeColour();
+ updateView();
}
- JComboBox annotations;
-
- int[] annmap;
-
- JPanel minColour = new JPanel();
-
- JPanel maxColour = new JPanel();
-
- JButton defColours = new JButton();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- JComboBox threshold = new JComboBox();
-
- JSlider slider = new JSlider();
-
- JTextField thresholdValue = new JTextField(20);
-
- JCheckBox currentColours = new JCheckBox();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- JCheckBox seqAssociated = new JCheckBox();
+ private void setDefaultMinMax()
+ {
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
+ }
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
}
minColour.repaint();
- changeColour();
+ updateView();
}
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
}
maxColour.repaint();
- changeColour();
+ updateView();
}
- void changeColour()
+ public void reset()
{
- // Check if combobox is still adjusting
- if (adjusting)
- {
- return;
- }
-
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]];
-
- int aboveThreshold = -1;
- if (threshold.getSelectedIndex()==1)
- {
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
- }
- else if (threshold.getSelectedIndex()==2)
- {
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
- }
-
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
-
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
- {
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
- }
- 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;
- float range = currentAnnotation.graphMax * 1000
- - currentAnnotation.graphMin * 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.setMajorTickSpacing((int) (range / 10f));
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- adjusting = false;
- }
-
- AnnotationColourGradient acg = null;
- if (currentColours.isSelected())
- {
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
- }
- else
- {
- acg = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
- }
- acg.setSeqAssociated(seqAssociated.isSelected());
-
- if (currentAnnotation.graphMin == 0f
- && currentAnnotation.graphMax == 0f)
- {
- acg.setPredefinedColours(true);
- }
-
- acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
- av.setGlobalColourScheme(acg);
-
+ av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs == null)
- {
- continue;
- }
-
- if (currentColours.isSelected())
- {
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- aboveThreshold);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
-
- }
- else
- {
- sg.cs = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
- }
-
+ sg.cs = oldgroupColours.get(sg);
}
}
- ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
}
- public void ok_actionPerformed(ActionEvent e)
- {
- changeColour();
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
-
- public void cancel_actionPerformed(ActionEvent e)
- {
- reset();
- // ensure all original colouring is propagated to listeners.
- ap.paintAlignment(true);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
-
- void reset()
+ public void valueChanged(boolean updateAllAnnotation)
{
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
+ if (slider.isEnabled())
{
-
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ if (currentColours.isSelected()
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+ updateView();
}
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
}
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
+ public JComboBox<String> getThreshold()
{
- changeColour();
+ return threshold;
}
- public void threshold_actionPerformed(ActionEvent e)
+ public void setThreshold(JComboBox<String> threshold)
{
- changeColour();
+ this.threshold = threshold;
}
- public void thresholdValue_actionPerformed(ActionEvent e)
- {
- try
- {
- float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
- } catch (NumberFormatException ex)
- {
- }
- }
-
- public void valueChanged(boolean updateAllAnnotation)
+ public void currentColours_actionPerformed(ActionEvent e)
{
- if (currentColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (currentColours.isSelected())
{
- changeColour();
+ reset();
}
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
- propagateSeqAssociatedThreshold(updateAllAnnotation);
- ap.paintAlignment(false);
+ maxColour.setEnabled(!currentColours.isSelected());
+ minColour.setEnabled(!currentColours.isSelected());
+ updateView();
}
- private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+ @Override
+ public void updateView()
{
- if (currentAnnotation.sequenceRef == null
- || currentAnnotation.threshold == null)
+ // Check if combobox is still adjusting
+ if (adjusting)
{
return;
}
- // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
- float thr = currentAnnotation.threshold.value;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
- if (aa.label.equals(currentAnnotation.label))
- {
- aa.threshold.value = thr;
- }
- }
- }
+ setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
+ int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+ .getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
- reset();
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+ && getCurrentAnnotation().threshold == null)
+ {
+ getCurrentAnnotation()
+ .setThreshold(
+ new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
+ if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+ float range = getCurrentAnnotation().graphMax * 1000
+ - getCurrentAnnotation().graphMin * 1000;
- changeColour();
- }
+ slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
+ slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
+ slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+ colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
- {
- changeColour();
+ ap.alignmentChanged();
+ // ensure all associated views (overviews, structures, etc) are notified of
+ // updated colours.
+ ap.paintAlignment(true);
}
}
git://source.jalview.org / jalview.git / blobdiff