X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=60ad75d4f78f5904cb4745fe285e605c676ef8d0;hb=16d109024847af92482237e43f99b82fd997451a;hp=69b54eac5a044f09e95628624b43edc49b9567f3;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 69b54ea..60ad75d 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,117 +1,102 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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.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 net.miginfocom.swing.MigLayout;
-public class AnnotationColourChooser extends JPanel
+@SuppressWarnings("serial")
+public class AnnotationColourChooser extends AnnotationRowFilter
{
- JInternalFrame frame;
+ private static final int ONETHOUSAND = 1000;
+
+ private ColourSchemeI oldcs;
- AlignViewport av;
+ private JButton defColours;
- AlignmentPanel ap;
+ private Hashtable oldgroupColours;
- ColourSchemeI oldcs;
+ private JCheckBox useOriginalColours = new JCheckBox();
- Hashtable oldgroupColours;
+ private JPanel minColour = new JPanel();
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ private JPanel maxColour = new JPanel();
- boolean adjusting = false;
- /**
- * enabled if the user is dragging the slider - try to keep updates to a minimun
- */
- boolean sliderDragging = false;
+ private JCheckBox thresholdIsMin = new JCheckBox();
+
+ protected static final int MIN_WIDTH = 500;
+
+ protected static final int MIN_HEIGHT = 240;
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
+ super(av, ap);
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new Hashtable<>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
+ if (sg.getColourScheme() != null)
{
- oldgroupColours.put(sg, sg.cs);
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
}
- this.av = av;
- this.ap = ap;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "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);
- }
- });
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ addSliderChangeListener();
+ addSliderMouseListeners();
if (av.getAlignment().getAlignmentAnnotation() == null)
{
@@ -125,127 +110,66 @@ public class AnnotationColourChooser extends JPanel
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ useOriginalColours.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(
- getAnnotationItems(seqAssociated.isSelected()));
+ Vector annotItems = getAnnotationItems(
+ seqAssociated.isSelected());
+ annotations = new JComboBox<>(annotItems);
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ populateThresholdComboBox(threshold);
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- annotations.setSelectedItem(acg.getAnnotation());
+ String label = getAnnotationMenuLabel(acg.getAnnotation());
+ annotations.setSelectedItem(label);
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedItem("No Threshold");
+ getThreshold().setSelectedIndex(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedItem("Above Threshold");
+ getThreshold().setSelectedIndex(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.setSelectedItem("Below Threshold");
+ getThreshold().setSelectedIndex(2);
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_about_threshold_setting"));
}
- thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+ thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
}
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- }
-
+ jbInit();
adjusting = false;
- changeColour();
+ updateView();
frame.invalidate();
frame.pack();
-
}
- private Vector getAnnotationItems(boolean isSeqAssociated)
+ @Override
+ protected void jbInit()
{
- Vector list = new Vector();
- 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));
- }
+ super.jbInit();
- public AnnotationColourChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
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())
@@ -257,9 +181,10 @@ public class AnnotationColourChooser extends JPanel
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())
@@ -268,101 +193,63 @@ public class AnnotationColourChooser extends JPanel
}
}
});
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
+
+ defColours = new JButton();
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
- defColours
- .setToolTipText("Reset min and max colours to defaults from user preferences.");
+ defColours.setToolTipText(MessageManager
+ .getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- resetColours_actionPerformed(arg0);
+ resetColours_actionPerformed();
}
});
- annotations.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- threshold.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed(e);
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- currentColours.setFont(JvSwingUtils.getLabelFont());
- currentColours.setOpaque(false);
- currentColours.setText(MessageManager.getString("label.use_original_colours"));
- currentColours.addActionListener(new ActionListener()
+ useOriginalColours.setFont(JvSwingUtils.getLabelFont());
+ useOriginalColours.setOpaque(false);
+ useOriginalColours.setText(
+ MessageManager.getString("label.use_original_colours"));
+ useOriginalColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- currentColours_actionPerformed(e);
+ originalColours_actionPerformed();
}
});
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);
+ thresholdIsMin_actionPerformed();
}
});
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(annotations);
}
});
- this.setLayout(borderLayout1);
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
+ JPanel jPanel2 = new JPanel();
jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
@@ -371,13 +258,13 @@ public class AnnotationColourChooser extends JPanel
jPanel1.add(cancel);
jPanel2.add(annotations, "grow, wrap");
jPanel2.add(seqAssociated);
- jPanel2.add(currentColours);
+ jPanel2.add(useOriginalColours);
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(getThreshold());
jPanel2.add(defColours, "skip 1, wrap");
jPanel2.add(thresholdIsMin);
jPanel2.add(slider, "grow");
@@ -387,177 +274,175 @@ public class AnnotationColourChooser extends JPanel
this.validate();
}
- protected void seqAssociated_actionPerformed(ActionEvent arg0)
+ protected void resetColours_actionPerformed()
{
- 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);
- }
- }
+ setDefaultMinMax();
+ updateView();
}
- protected void resetColours_actionPerformed(ActionEvent arg0)
+ private void setDefaultMinMax()
{
- setDefaultMinMax();
- changeColour();
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
}
- 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();
-
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()
+ @Override
+ public void reset()
{
- // Check if combobox is still adjusting
- if (adjusting)
+ this.ap.alignFrame.changeColour(oldcs);
+ if (av.getAlignment().getGroups() != null)
{
- return;
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ sg.setColourScheme(oldgroupColours.get(sg));
+ }
}
+ }
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]];
+ @Override
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ if (slider.isEnabled())
+ {
+ if (useOriginalColours.isSelected() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
+ {
+ updateView();
+ }
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false, false);
+ }
+ }
- int aboveThreshold = -1;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ public void originalColours_actionPerformed()
+ {
+ boolean selected = useOriginalColours.isSelected();
+ if (selected)
{
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ reset();
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ maxColour.setEnabled(!selected);
+ minColour.setEnabled(!selected);
+ thresholdIsMin.setEnabled(!selected);
+ updateView();
+ }
+
+ @Override
+ public void updateView()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
{
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ return;
}
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
+
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
+
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
+ thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
thresholdIsMin.setEnabled(false);
}
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && currentAnnotation.threshold == null)
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+ && getCurrentAnnotation().threshold == null)
{
- currentAnnotation
- .setThreshold(new jalview.datamodel.GraphLine(
- (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
- "Threshold", Color.black));
+ getCurrentAnnotation().setThreshold(new GraphLine(
+ (getCurrentAnnotation().graphMax
+ - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (selectedThresholdItem != 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 + "");
+ float range = getCurrentAnnotation().graphMax * ONETHOUSAND
+ - getCurrentAnnotation().graphMin * ONETHOUSAND;
+
+ slider.setMinimum(
+ (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
+ slider.setMaximum(
+ (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
+ slider.setValue(
+ (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
}
+ colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
+
+ ap.alignmentChanged();
+ }
+
+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
+ {
AnnotationColourGradient acg = null;
- if (currentColours.isSelected())
+ if (useOriginalColours.isSelected())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
}
else
{
- acg = new AnnotationColourGradient(currentAnnotation,
+ acg = new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
+ selectedThresholdOption);
}
acg.setSeqAssociated(seqAssociated.isSelected());
- if (currentAnnotation.graphMin == 0f
- && currentAnnotation.graphMax == 0f)
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
{
acg.setPredefinedColours(true);
}
- acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+ acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
- av.setGlobalColourScheme(acg);
+ this.ap.alignFrame.changeColour(acg);
if (av.getAlignment().getGroups() != null)
{
@@ -568,143 +453,16 @@ public class AnnotationColourChooser extends JPanel
{
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());
- }
-
- }
- }
- 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()
- {
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
- {
-
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
- {
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+ sg.setColourScheme(
+ acg.getInstance(av, sg));
}
}
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
+ @Override
+ protected void sliderDragReleased()
{
- changeColour();
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
}
-
- 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)
- {
- if (currentColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
- {
- changeColour();
- }
- currentAnnotation.threshold.value = (float) 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))
- {
- aa.threshold.value = thr;
- }
- }
- }
-
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
- {
- reset();
- }
-
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
-
- changeColour();
- }
-
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
- {
- changeColour();
- }
-
}