/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 jalview.api.FeatureColourI;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.FeatureColour;
+import jalview.util.MessageManager;
+
+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.GridLayout;
+import java.awt.Label;
+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.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+public class FeatureColourChooser extends Panel implements ActionListener,
+ AdjustmentListener, ItemListener, MouseListener
+{
+ /*
+ * the absolute min-max range of a feature score is scaled to
+ * 1000 positions on the colour threshold slider
+ */
+ private static final int SCALE_FACTOR_1K = 1000;
-import java.awt.*;
-import java.awt.event.*;
+ private static final String COLON = ":";
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.Rectangle;
+ private JVDialog frame;
-public class FeatureColourChooser extends Panel implements
- ActionListener, AdjustmentListener, ItemListener, MouseListener
-{
- Frame frame;
+ private Frame owner;
+
+ private FeatureRenderer fr;
+
+ private FeatureSettings fs = null;
+
+ private FeatureColourI cs;
+
+ private FeatureColourI oldcs;
+
+ private boolean adjusting = false;
+
+ private float min, max;
+
+ private String type = null;
+
+ private AlignFrame af = null;
+
+ private Panel minColour = new Panel();
- FeatureRenderer fr;
- FeatureSettings fs;
- AlignmentPanel ap;
+ private Panel maxColour = new Panel();
- GraduatedColor cs;
- Object oldcs;
+ private Choice threshold = new Choice();
- Hashtable oldgroupColours;
+ private Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+ private TextField thresholdValue = new TextField(20);
- boolean adjusting = false;
- private float min,max;
- String type=null;
-
- public FeatureColourChooser(FeatureSettings fsettings, String type)
+ private Checkbox thresholdIsMin = new Checkbox();
+
+ private Checkbox colourFromLabel = new Checkbox();
+
+ private GraphLine threshline;
+
+ /**
+ * Constructor given a context AlignFrame and a feature type. This is used
+ * when opening the graduated colour dialog from the Amend Feature dialog.
+ *
+ * @param alignFrame
+ * @param featureType
+ */
+ public FeatureColourChooser(AlignFrame alignFrame, String featureType)
+ {
+ this.af = alignFrame;
+ init(alignFrame.getSeqcanvas().getFeatureRenderer(), featureType);
+ }
+
+ /**
+ * Constructor given a context FeatureSettings and a feature type. This is
+ * used when opening the graduated colour dialog from Feature Settings.
+ *
+ * @param fsettings
+ * @param featureType
+ */
+ public FeatureColourChooser(FeatureSettings fsettings, String featureType)
{
this.fs = fsettings;
- this.type = type;
- fr = fsettings.fr;
- ap = fsettings.ap;
- float mm[] = ((float[][]) fr.minmax.get(type))[0];
+ init(fsettings.fr, featureType);
+ }
+
+ private void init(FeatureRenderer frenderer, String featureType)
+ {
+ this.type = featureType;
+ fr = frenderer;
+ float mm[] = fr.getMinMax().get(type)[0];
min = mm[0];
max = mm[1];
- oldcs = fr.featureColours.get(type);
- if (oldcs instanceof GraduatedColor)
+ threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
+ oldcs = fr.getFeatureColours().get(type);
+ if (oldcs.isGraduatedColour())
+ {
+ threshline.value = oldcs.getThreshold();
+ cs = new FeatureColour(oldcs.getColour(), oldcs.getMinColour(),
+ oldcs.getMaxColour(), oldcs.getNoColour(), min, max);
+ }
+ else
{
- cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
- } else {
// promote original color to a graduated color
Color bl = Color.black;
- if (oldcs instanceof Color)
+ if (oldcs.isSimpleColour())
{
- bl = (Color) oldcs;
+ bl = oldcs.getColour();
}
// original colour becomes the maximum colour
- cs = new GraduatedColor(Color.white,bl,mm[0],mm[1]);
+ cs = new FeatureColour(bl, Color.white, bl, Color.white, mm[0],
+ mm[1]);
}
- minColour.setBackground(cs.getMinColor());
- maxColour.setBackground(cs.getMaxColor());
+ minColour.setBackground(cs.getMinColour());
+ maxColour.setBackground(cs.getMaxColour());
+ minColour.setForeground(cs.getMinColour());
+ maxColour.setForeground(cs.getMaxColour());
+ colourFromLabel.setState(cs.isColourByLabel());
adjusting = true;
try
} catch (Exception ex)
{
}
- // To HERE!
+ threshold.select(
+ cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2 : 0));
+
adjusting = false;
- changeColour();
+ changeColour(true);
+ colourFromLabel.addItemListener(this);
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- frame = new Frame();
- frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Graduated Feature Colour for "+type, 480,
- 145);
+ owner = (af != null) ? af : fs.frame;
+ frame = new JVDialog(owner, MessageManager.formatMessage(
+ "label.variable_color_for", new String[] { type }), true, 480,
+ 248);
+ frame.setMainPanel(this);
validate();
+ frame.setVisible(true);
+ if (frame.accept)
+ {
+ changeColour(true);
+ }
+ else
+ {
+ // cancel
+ reset();
+ frame.setVisible(false);
+ }
}
public FeatureColourChooser()
private void jbInit() throws Exception
{
- minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setLabel("Min Colour");
- minColour.addActionListener(this);
+ Label minLabel = new Label(
+ MessageManager.getString("label.min_value") + COLON);
+ Label maxLabel = new Label(
+ MessageManager.getString("label.max_value") + COLON);
+ minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ // minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ // minColour.setLabel("Min Colour");
+
+ minColour.setBounds(0, 0, 40, 27);
+ maxColour.setBounds(0, 0, 40, 27);
+ minColour.addMouseListener(this);
maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setLabel("Max Colour");
- maxColour.addActionListener(this);
+ maxColour.addMouseListener(this);
thresholdIsMin.addItemListener(this);
- ok.setLabel("OK");
- ok.addActionListener(this);
-
- cancel.setLabel("Cancel");
- cancel.addActionListener(this);
-
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ this.setLayout(new GridLayout(4, 1));
+ Panel jPanel1 = new Panel();
+ jPanel1.setLayout(new FlowLayout());
+ Panel jPanel2 = new Panel();
+ jPanel2.setLayout(new FlowLayout());
+ Panel jPanel3 = new Panel();
+ jPanel3.setLayout(new GridLayout(1, 1));
+ Panel jPanel4 = new Panel();
+ jPanel4.setLayout(new FlowLayout());
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
+ jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
- jPanel3.setLayout(null);
+ 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"));
thresholdValue.addActionListener(this);
-
+ thresholdValue.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ thresholdValue_actionPerformed();
+ }
+ });
slider.setBackground(Color.white);
slider.setEnabled(false);
- slider.setBounds(new Rectangle(153, 3, 93, 21));
+ slider.setSize(new Dimension(93, 21));
thresholdValue.setEnabled(false);
- thresholdValue.setBounds(new Rectangle(248, 2, 79, 22));
+ thresholdValue.setSize(new Dimension(79, 22)); // setBounds(new
+ // Rectangle(248, 2, 79,
+ // 22));
thresholdValue.setColumns(5);
jPanel3.setBackground(Color.white);
- //currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- //currentColours.setLabel("Use Original Colours");
- //currentColours.addItemListener(this);
- threshold.setBounds(new Rectangle(11, 3, 139, 22));
+ colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ colourFromLabel
+ .setLabel(MessageManager.getString("label.colour_by_label"));
+ colourFromLabel.setSize(new Dimension(139, 22));
+ // threshold.setBounds(new Rectangle(11, 3, 139, 22));
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel("Threshold is min/max");
- thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
- jPanel1.add(ok);
- jPanel1.add(cancel);
- //jPanel2.add(currentColours);
- jPanel2.add(minColour);
- jPanel2.add(maxColour);
- jPanel3.add(threshold);
+ thresholdIsMin
+ .setLabel(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setSize(new Dimension(135, 23));
+ // thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
+ jPanel1.add(minLabel);
+ jPanel1.add(minColour);
+ jPanel1.add(maxLabel);
+ jPanel1.add(maxColour);
+ jPanel1.add(colourFromLabel);
+ jPanel2.add(threshold);
jPanel3.add(slider);
- jPanel3.add(thresholdValue);
- jPanel3.add(thresholdIsMin);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ jPanel4.add(thresholdValue);
+ jPanel4.add(thresholdIsMin);
+ this.add(jPanel1);// , java.awt.BorderLayout.NORTH);
+ this.add(jPanel2);// , java.awt.BorderLayout.NORTH);
+ this.add(jPanel3);// , java.awt.BorderLayout.CENTER);
+ this.add(jPanel4);// , java.awt.BorderLayout.CENTER);
}
- Button minColour = new Button();
-
- Button maxColour = new Button();
-
- Button ok = new Button();
-
- Button cancel = new Button();
-
- Panel jPanel1 = new Panel();
-
- Panel jPanel2 = new Panel();
-
- Choice threshold = new Choice();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- Panel jPanel3 = new Panel();
-
- Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
-
- TextField thresholdValue = new TextField(20);
-
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- Checkbox thresholdIsMin = new Checkbox();
-
- private GraphLine threshline;
-
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
{
- try
- {
- float f = new Float(thresholdValue.getText()).floatValue();
- slider.setValue((int) (f * 1000));
- adjustmentValueChanged(null);
- } catch (NumberFormatException ex)
- {
- }
+ thresholdValue_actionPerformed();
}
else if (evt.getSource() == minColour)
{
{
maxColour_actionPerformed(null);
}
-
- else if (evt.getSource() == ok)
- {
- changeColour();
- frame.setVisible(false);
- }
- else if (evt.getSource() == cancel)
+ else
{
- reset();
- ap.paintAlignment(true);
- frame.setVisible(false);
+ changeColour(true);
}
+ }
- else
+ /**
+ * Action on input of a value for colour score threshold
+ */
+ protected void thresholdValue_actionPerformed()
+ {
+ try
+ {
+ float f = new Float(thresholdValue.getText()).floatValue();
+ slider.setValue((int) (f * SCALE_FACTOR_1K));
+ adjustmentValueChanged(null);
+
+ /*
+ * force repaint of any Overview window or structure
+ */
+ changeColour(true);
+ } catch (NumberFormatException ex)
{
- changeColour();
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
-
- changeColour();
+ maxColour.setEnabled(!colourFromLabel.getState());
+ minColour.setEnabled(!colourFromLabel.getState());
+ changeColour(true);
}
+ /**
+ * Handler called when the value of the threshold slider changes, either by
+ * user action or programmatically
+ */
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
valueChanged();
}
}
- protected void valueChanged() {
- changeColour();
- threshline.value = (float) slider.getValue() / 1000f;
- ap.paintAlignment(false);
+
+ /**
+ * Responds to a change of colour threshold by computing the absolute value
+ * and refreshing the alignment.
+ */
+ protected void valueChanged()
+ {
+ threshline.value = slider.getValue() / 1000f;
+ cs.setThreshold(threshline.value);
+ changeColour(false);
+ PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
}
+
public void minColour_actionPerformed(Color newCol)
{
- if (newCol != null)
+ if (newCol == null)
{
- minColour.setBackground(newCol);
- minColour.repaint();
- changeColour();
+ new UserDefinedColours(this, minColour.getBackground(), owner,
+ MessageManager
+ .getString("label.select_colour_minimum_value"));
}
else
{
- new UserDefinedColours(this, "Select Colour for Minimum Value", minColour.getBackground());
+ minColour.setBackground(newCol);
+ minColour.setForeground(newCol);
+ minColour.repaint();
+ changeColour(true);
}
}
public void maxColour_actionPerformed(Color newCol)
{
- if (newCol != null)
+ if (newCol == null)
{
- maxColour.setBackground(newCol);
- maxColour.repaint();
- changeColour();
+ new UserDefinedColours(this, maxColour.getBackground(), owner,
+ MessageManager
+ .getString("label.select_colour_maximum_value"));
}
else
{
- new UserDefinedColours(this, "Select Colour for Maximum Value", maxColour.getBackground());
+ maxColour.setBackground(newCol);
+ maxColour.setForeground(newCol);
+ maxColour.repaint();
+ changeColour(true);
}
}
- void changeColour()
+ void changeColour(boolean updateOverview)
{
// Check if combobox is still adjusting
if (adjusting)
return;
}
- int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ int thresholdOption = AnnotationColourGradient.NO_THRESHOLD;
+ if (threshold.getSelectedIndex() == 1)
{
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ thresholdOption = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex() == 2)
{
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ thresholdOption = AnnotationColourGradient.BELOW_THRESHOLD;
}
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max);
-
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ Color minc = minColour.getBackground();
+ Color maxc = maxColour.getBackground();
+ FeatureColour acg = new FeatureColour(maxc, minc, maxc, minc, min, max);
+
+ acg.setColourByLabel(colourFromLabel.getState());
+ maxColour.setEnabled(!colourFromLabel.getState());
+ minColour.setEnabled(!colourFromLabel.getState());
+ if (thresholdOption == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
}
-
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && threshline == null)
- {
- // todo visual indication of feature threshold
- threshline = new jalview.datamodel.GraphLine(
- (max - min) / 2f,
- "Threshold", Color.black);
- }
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- acg.setThresh(threshline.value);
-
- float range = max * 1000f
- - min * 1000f;
+ acg.setThreshold(threshline.value);
- slider.setMinimum((int) (min * 1000));
- slider.setMaximum((int) (max * 1000));
- slider.setValue((int) (threshline.value * 1000));
+ slider.setMinimum((int) (min * SCALE_FACTOR_1K));
+ slider.setMaximum((int) (max * SCALE_FACTOR_1K));
+ slider.setValue((int) (threshline.value * SCALE_FACTOR_1K));
thresholdValue.setText(threshline.value + "");
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
}
- acg.setThreshType(aboveThreshold);
- if (thresholdIsMin.getState() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ acg.setAboveThreshold(
+ thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
+ acg.setBelowThreshold(
+ thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
+
+ if (thresholdIsMin.getState()
+ && thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
{
- if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- acg = new GraduatedColor(acg, threshline.value, max);
- } else {
- acg = new GraduatedColor(acg, min,threshline.value);
+ if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+ acg.getMaxColour(), acg.getNoColour(), threshline.value,
+ max);
+ }
+ else
+ {
+ acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+ acg.getMaxColour(), acg.getNoColour(), min,
+ threshline.value);
}
}
-
- fr.featureColours.put(type,acg);
+
+ fr.setColour(type, acg);
cs = acg;
- ap.paintAlignment(false);
+ fs.selectionChanged(updateOverview);
}
void reset()
{
- fr.featureColours.put(type, oldcs);
- ap.paintAlignment(true);
-
+ fr.setColour(type, oldcs);
+ fs.selectionChanged(true);
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ if (evt.getSource() == minColour)
+ {
+ minColour_actionPerformed(null);
+ }
+ else if (evt.getSource() == maxColour)
+ {
+ maxColour_actionPerformed(null);
+ }
+ else
+ {
+ changeColour(true);
+ // PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
+ }
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
git://source.jalview.org / jalview.git / blobdiff