/*
- * 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 2.8.2b1)
+ * 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.
- *
+ * 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 jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+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 java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import net.miginfocom.swing.MigLayout;
public class AnnotationColourChooser extends JPanel
{
boolean adjusting = false;
+ /**
+ * enabled if the user is dragging the slider - try to keep updates to a
+ * minimun
+ */
+ boolean sliderDragging = false;
+
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
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.get(g);
if (sg.cs != null)
{
oldgroupColours.put(sg, sg.cs);
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
- valueChanged();
+ thresholdValue.setText((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);
+ }
+
+ @Override
public void mouseReleased(MouseEvent evt)
{
+ if (sliderDragging)
+ {
+ sliderDragging = false;
+ valueChanged(true);
+ }
ap.paintAlignment(true);
}
});
- if (av.alignment.getAlignmentAnnotation() == null)
+ if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
// Always get default shading from preferences.
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ setDefaultMinMax();
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.predefinedColours);
- if (acg.predefinedColours)
+ currentColours.setSelected(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
-
- } else {
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
- }
+ seqAssociated.setSelected(acg.isSeqAssociated());
- adjusting = true;
- Vector list = new Vector();
- int index = 1;
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
- {
- String label = av.alignment.getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- list.addElement(label);
- else
- list.addElement(label + "_" + (index++));
}
+ annotations = new JComboBox(
+ getAnnotationItems(seqAssociated.isSelected()));
- annotations = new JComboBox(list);
-
- 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.setSelectedItem(acg.getAnnotation());
- switch (acg.getAboveThreshold()) {
+ switch (acg.getAboveThreshold())
+ {
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedItem("No Threshold");
+ threshold.setSelectedIndex(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedItem("Above Threshold");
+ threshold.setSelectedIndex(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.setSelectedItem("Below Threshold");
+ threshold.setSelectedIndex(2);
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_about_thereshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
- thresholdValue.setText(""+acg.getAnnotationThreshold());
+ thresholdValue.setText("" + acg.getAnnotationThreshold());
}
try
adjusting = false;
changeColour();
- validate();
+ 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.add(label);
+ }
+ else
+ {
+ if (!isSeqAssociated)
+ {
+ anmap[list.size()] = i;
+ list.add(label + "_" + (index++));
+ }
+ }
+ }
+ seqAssociated.setEnabled(enableSeqAss);
+ this.annmap = new int[list.size()];
+ System.arraycopy(anmap, 0, this.annmap, 0, this.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()
private void jbInit() throws Exception
{
- minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
- minColour.setToolTipText("Minimum Colour");
+ minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (minColour.isEnabled())
}
}
});
- maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ maxColour.setFont(JvSwingUtils.getLabelFont());
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.setToolTipText("Maximum Colour");
+ maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (maxColour.isEnabled())
}
});
ok.setOpaque(false);
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
}
});
cancel.setOpaque(false);
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
}
});
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ defColours.setOpaque(false);
+ defColours.setText(MessageManager.getString("action.set_defaults"));
+ defColours.setToolTipText(MessageManager
+ .getString("label.reset_min_max_colours_to_defaults"));
+ defColours.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ resetColours_actionPerformed(arg0);
+ }
+ });
+
annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
}
});
- jPanel1.setBackground(Color.white);
- jPanel2.setBackground(Color.white);
threshold.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
threshold_actionPerformed(e);
}
});
- jPanel3.setLayout(flowLayout2);
thresholdValue.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
thresholdValue_actionPerformed(e);
slider.setPreferredSize(new Dimension(100, 32));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
- jPanel3.setBackground(Color.white);
- currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
- currentColours.setText("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.setText("Threshold is Min/Max");
+ thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+ 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.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ seqAssociated_actionPerformed(arg0);
+ }
+ });
+
+ this.setLayout(borderLayout1);
+ jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
+ jPanel1.setBackground(Color.white);
+ jPanel2.setBackground(Color.white);
+
jPanel1.add(ok);
jPanel1.add(cancel);
- jPanel2.add(annotations);
+ jPanel2.add(annotations, "grow, wrap");
+ jPanel2.add(seqAssociated);
jPanel2.add(currentColours);
- jPanel2.add(minColour);
- jPanel2.add(maxColour);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- jPanel3.add(threshold);
- jPanel3.add(slider);
- jPanel3.add(thresholdValue);
- jPanel3.add(thresholdIsMin);
+ JPanel colpanel = new JPanel(new FlowLayout());
+ colpanel.setBackground(Color.white);
+ colpanel.add(minColour);
+ colpanel.add(maxColour);
+ jPanel2.add(colpanel, "wrap");
+ jPanel2.add(threshold);
+ jPanel2.add(defColours, "skip 1, wrap");
+ jPanel2.add(thresholdIsMin);
+ jPanel2.add(slider, "grow");
+ jPanel2.add(thresholdValue, "grow");
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ 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();
}
JComboBox annotations;
+ int[] annmap;
+
JPanel minColour = new JPanel();
JPanel maxColour = new JPanel();
+ JButton defColours = new JButton();
+
JButton ok = new JButton();
JButton cancel = new JButton();
JComboBox threshold = new JComboBox();
- FlowLayout flowLayout1 = new FlowLayout();
-
- JPanel jPanel3 = new JPanel();
-
- FlowLayout flowLayout2 = new FlowLayout();
-
JSlider slider = new JSlider();
JTextField thresholdValue = new JTextField(20);
JCheckBox thresholdIsMin = new JCheckBox();
+ JCheckBox seqAssociated = new JCheckBox();
+
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);
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);
return;
}
- currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
- .getSelectedIndex()];
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .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;
}
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)
minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
}
+ acg.setSeqAssociated(seqAssociated.isSelected());
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
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++)
- {
- sg = (SequenceGroup) allGroups.get(g);
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
if (sg.cs == null)
{
continue;
{
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());
}
}
}
- // ensure all associated views (overviews, structures, etc) are notified of updated colours.
+ ap.alignmentChanged();
+ // ensure all associated views (overviews, structures, etc) are notified of
+ // updated colours.
ap.paintAlignment(true);
}
public void cancel_actionPerformed(ActionEvent e)
{
reset();
+ // ensure all original colouring is propagated to listeners.
+ ap.paintAlignment(true);
try
{
frame.setClosed(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.get(g);
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
}
}
}
- public void valueChanged()
+ public void valueChanged(boolean updateAllAnnotation)
{
if (currentColours.isSelected()
&& !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
-
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation);
ap.paintAlignment(false);
}
+ private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+ {
+ if (currentAnnotation.sequenceRef == null
+ || currentAnnotation.threshold == null)
+ {
+ 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)
+ && (currentAnnotation.getCalcId() == null ? aa.getCalcId() == null
+ : currentAnnotation.getCalcId()
+ .equals(aa.getCalcId())))
+ {
+ if (aa.threshold == null)
+ {
+ aa.threshold = new GraphLine(currentAnnotation.threshold);
+ }
+ else
+ {
+ aa.threshold.value = thr;
+ }
+ }
+ }
+ }
+
public void currentColours_actionPerformed(ActionEvent e)
{
if (currentColours.isSelected())
git://source.jalview.org / jalview.git / blobdiff