/*
- * 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.gui;
-import java.util.*;
+import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.MessageManager;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyVetoException;
+import java.util.List;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
/**
* DOCUMENT ME!
*/
public class SliderPanel extends GSliderPanel
{
+ private static final String BACKGROUND = "Background";
+
static JInternalFrame conservationSlider;
static JInternalFrame PIDSlider;
boolean forConservation = true;
- ColourSchemeI cs;
+ ResidueShaderI cs;
+
+ /**
+ * Returns the currently displayed slider panel (or null if none).
+ *
+ * @return
+ */
+ public static SliderPanel getSliderPanel()
+ {
+ if (conservationSlider != null && conservationSlider.isVisible())
+ {
+ return (SliderPanel) conservationSlider.getContentPane();
+ }
+ if (PIDSlider != null && PIDSlider.isVisible())
+ {
+ return (SliderPanel) PIDSlider.getContentPane();
+ }
+ return null;
+ }
/**
* Creates a new SliderPanel object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param value
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param forConserve
- * DOCUMENT ME!
- * @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
+ * @param scheme
+ * DOCUMENT ME!
*/
public SliderPanel(final AlignmentPanel ap, int value,
- boolean forConserve, ColourSchemeI cs)
+ boolean forConserve, ResidueShaderI scheme)
{
this.ap = ap;
- this.cs = cs;
+ this.cs = scheme;
forConservation = forConserve;
undoButton.setVisible(false);
applyButton.setVisible(false);
if (forConservation)
{
- label.setText("Enter value to increase conservation visibility");
+ label.setText(MessageManager
+ .getString("label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
- label.setText("Enter % identity above which to colour residues");
+ label.setText(MessageManager
+ .getString("label.enter_percentage_identity_above_which_colour_residues"));
slider.setMinimum(0);
slider.setMaximum(100);
}
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
slider.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseReleased(MouseEvent evt)
{
ap.paintAlignment(true);
}
/**
- * DOCUMENT ME!
+ * Method to 'set focus' of the Conservation slider panel
*
* @param ap
- * DOCUMENT ME!
- * @param cs
- * DOCUMENT ME!
+ * the panel to repaint on change of slider
+ * @param rs
+ * the colour scheme to update on change of slider
* @param source
- * DOCUMENT ME!
+ * a text description for the panel's title
*
- * @return DOCUMENT ME!
+ * @return
*/
public static int setConservationSlider(AlignmentPanel ap,
- ColourSchemeI cs, String source)
+ ResidueShaderI rs, String source)
{
- SliderPanel sp = null;
+ SliderPanel sliderPanel = null;
if (conservationSlider == null)
{
- sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+ sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
conservationSlider = new JInternalFrame();
- conservationSlider.setContentPane(sp);
+ conservationSlider.setContentPane(sliderPanel);
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
else
{
- sp = (SliderPanel) conservationSlider.getContentPane();
- sp.cs = cs;
+ sliderPanel = (SliderPanel) conservationSlider.getContentPane();
+ sliderPanel.valueField.setText(String.valueOf(rs.getConservationInc()));
+ sliderPanel.cs = rs;
+ sliderPanel.ap = ap;
+ sliderPanel.slider.setValue(rs.getConservationInc());
}
- conservationSlider.setTitle("Conservation Colour Increment (" + source
- + ")");
+ conservationSlider.setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { source == null ? BACKGROUND : source }));
- if (ap.av.alignment.getGroups() != null)
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ if (groups != null && !groups.isEmpty())
{
- sp.setAllGroupsCheckEnabled(true);
+ sliderPanel.setAllGroupsCheckEnabled(true);
}
else
{
- sp.setAllGroupsCheckEnabled(false);
+ sliderPanel.setAllGroupsCheckEnabled(false);
}
- return sp.getValue();
+ return sliderPanel.getValue();
}
/**
- * DOCUMENT ME!
+ * Hides the PID slider panel if it is shown
*/
- public static void showConservationSlider()
+ public static void hidePIDSlider()
{
- try
+ if (PIDSlider != null)
{
- PIDSlider.setClosed(true);
- PIDSlider = null;
- } catch (Exception ex)
+ try
+ {
+ PIDSlider.setClosed(true);
+ PIDSlider = null;
+ } catch (PropertyVetoException ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * Hides the conservation slider panel if it is shown
+ */
+ public static void hideConservationSlider()
+ {
+ if (conservationSlider != null)
{
+ try
+ {
+ conservationSlider.setClosed(true);
+ conservationSlider = null;
+ } catch (PropertyVetoException ex)
+ {
+ }
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static void showConservationSlider()
+ {
+ hidePIDSlider();
if (!conservationSlider.isVisible())
{
- Desktop.addInternalFrame(conservationSlider, conservationSlider
- .getTitle(), 420, 90, false);
+ Desktop.addInternalFrame(conservationSlider,
+ conservationSlider.getTitle(), 420, 90, false);
conservationSlider
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ .addInternalFrameListener(new InternalFrameAdapter()
{
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent e)
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
{
conservationSlider = null;
}
}
/**
- * DOCUMENT ME!
+ * Method to 'set focus' of the PID slider panel
*
* @param ap
- * DOCUMENT ME!
- * @param cs
- * DOCUMENT ME!
+ * the panel to repaint on change of slider
+ * @param rs
+ * the colour scheme to update on change of slider
* @param source
- * DOCUMENT ME!
+ * a text description for the panel's title
*
- * @return DOCUMENT ME!
+ * @return
*/
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
- String source)
+ public static int setPIDSliderSource(AlignmentPanel ap,
+ ResidueShaderI rs, String source)
{
- SliderPanel pid = null;
+ int threshold = rs.getThreshold();
- int threshold = cs.getThreshold();
+ SliderPanel sliderPanel = null;
if (PIDSlider == null)
{
- pid = new SliderPanel(ap, threshold, false, cs);
+ sliderPanel = new SliderPanel(ap, threshold, false, rs);
PIDSlider = new JInternalFrame();
- PIDSlider.setContentPane(pid);
+ PIDSlider.setContentPane(sliderPanel);
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
else
{
- pid = (SliderPanel) PIDSlider.getContentPane();
- pid.cs = cs;
+ sliderPanel = (SliderPanel) PIDSlider.getContentPane();
+ sliderPanel.cs = rs;
+ sliderPanel.ap = ap;
+ sliderPanel.valueField.setText(String.valueOf(rs.getThreshold()));
+ sliderPanel.slider.setValue(rs.getThreshold());
}
- PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+ PIDSlider.setTitle(MessageManager.formatMessage(
+ "label.percentage_identity_threshold",
+ new String[] { source == null ? BACKGROUND : source }));
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
- pid.setAllGroupsCheckEnabled(true);
+ sliderPanel.setAllGroupsCheckEnabled(true);
}
else
{
- pid.setAllGroupsCheckEnabled(false);
+ sliderPanel.setAllGroupsCheckEnabled(false);
}
- return pid.getValue();
+ return sliderPanel.getValue();
}
/**
* DOCUMENT ME!
+ *
+ * @return
*/
- public static void showPIDSlider()
+ public static JInternalFrame showPIDSlider()
{
- try
- {
- conservationSlider.setClosed(true);
- conservationSlider = null;
- } catch (Exception ex)
- {
- }
+ hideConservationSlider();
if (!PIDSlider.isVisible())
{
Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
false);
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
- PIDSlider
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent e)
- {
- PIDSlider = null;
- }
- });
+ PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ PIDSlider = null;
+ }
+ });
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
+ return PIDSlider;
}
/**
- * DOCUMENT ME!
+ * Updates the colour scheme with the current (identity threshold or
+ * conservation) percentage value. Also updates all groups if 'apply to all
+ * groups' is selected.
*
- * @param i
- * DOCUMENT ME!
+ * @param percent
*/
- public void valueChanged(int i)
+ public void valueChanged(int percent)
{
- if (cs == null)
+ if (!forConservation)
{
- return;
+ ap.av.setThreshold(percent);
}
-
- ColourSchemeI toChange = null;
- Vector allGroups = null;
- int groupIndex = 0;
+ updateColourScheme(percent, cs, null);
if (allGroupsCheck.isSelected())
{
- allGroups = ap.av.alignment.getGroups();
- groupIndex = allGroups.size() - 1;
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ for (SequenceGroup sg : groups)
+ {
+ updateColourScheme(percent, sg.getGroupColourScheme(), sg);
+ }
}
- else
+
+ ap.getSeqPanel().seqCanvas.repaint();
+ }
+
+ /**
+ * Updates the colour scheme (if not null) with the current (identity
+ * threshold or conservation) percentage value
+ *
+ * @param percent
+ * @param scheme
+ * @param sg
+ */
+ protected void updateColourScheme(int percent, ResidueShaderI scheme,
+ SequenceGroup sg)
+ {
+ if (scheme == null)
{
- toChange = cs;
+ return;
}
-
- while (groupIndex > -1)
+ if (forConservation)
{
- if (allGroups != null)
+ if (!scheme.conservationApplied() && sg != null)
{
- toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
+ /*
+ * first time the colour scheme has had Conservation shading applied
+ * - compute conservation
+ */
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ sg.cs.setConservation(c);
- if (toChange == null)
- {
- groupIndex--;
-
- continue;
- }
- }
-
- if (forConservation)
- {
- if (toChange.conservationApplied())
- {
- toChange.setConservationInc(i);
- }
}
- else
- {
- toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
- }
-
- groupIndex--;
+ scheme.setConservationApplied(true);
+ scheme.setConservationInc(percent);
+ }
+ else
+ {
+ scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus());
}
-
- ap.seqPanel.seqCanvas.repaint();
}
/**
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setAllGroupsCheckEnabled(boolean b)
{
allGroupsCheck.setEnabled(b);
+ allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public void valueField_actionPerformed(ActionEvent e)
+ @Override
+ public void valueField_actionPerformed()
{
try
{
* DOCUMENT ME!
*
* @param value
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setValue(int value)
{
return Integer.parseInt(valueField.getText());
}
+ @Override
public void slider_mouseReleased(MouseEvent e)
{
if (ap.overviewPanel != null)
}
}
+ public static int getConservationValue()
+ {
+ return getValue(conservationSlider);
+ }
+
+ static int getValue(JInternalFrame slider)
+ {
+ return slider == null ? 0 : ((SliderPanel) slider.getContentPane())
+ .getValue();
+ }
+
+ public static int getPIDValue()
+ {
+ return getValue(PIDSlider);
+ }
+
+ /**
+ * Answers true if the SliderPanel is for Conservation, false if it is for PID
+ * threshold
+ *
+ * @return
+ */
+ public boolean isForConservation()
+ {
+ return forConservation;
+ }
+
+ /**
+ * Answers the title for the slider panel; this may include 'Background' if
+ * for the alignment, or the group id if for a group
+ *
+ * @return
+ */
+ public String getTitle()
+ {
+ String title = null;
+ if (isForConservation())
+ {
+ if (conservationSlider != null)
+ {
+ title = conservationSlider.getTitle();
+ }
+ }
+ else if (PIDSlider != null)
+ {
+ title = PIDSlider.getTitle();
+ }
+ return title;
+ }
}