/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ResidueShaderI;
import jalview.util.MessageManager;
-public class SliderPanel extends Panel implements ActionListener,
- AdjustmentListener, MouseListener
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+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.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.List;
+
+public class SliderPanel extends Panel
+ implements ActionListener, AdjustmentListener, MouseListener
{
+ private static final String BACKGROUND = "Background";
+
AlignmentPanel ap;
boolean forConservation = true;
- ColourSchemeI cs;
+ ResidueShaderI cs;
static Frame conservationSlider;
static Frame PIDSlider;
public static int setConservationSlider(AlignmentPanel ap,
- ColourSchemeI cs, String source)
+ ResidueShaderI ccs, String source)
{
SliderPanel sp = null;
if (conservationSlider == null)
{
- sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+ sp = new SliderPanel(ap, ccs.getConservationInc(), true, ccs);
conservationSlider = new Frame();
conservationSlider.add(sp);
}
else
{
sp = (SliderPanel) conservationSlider.getComponent(0);
- sp.cs = cs;
+ sp.cs = ccs;
+ sp.valueField.setText(String.valueOf(ccs.getConservationInc()));
}
- conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
- if (ap.av.getAlignment().getGroups() != null)
+ conservationSlider.setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment", new String[]
+ { source == null ? BACKGROUND : source }));
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ if (groups != null && !groups.isEmpty())
{
sp.setAllGroupsCheckEnabled(true);
}
conservationSlider.getTitle(), 420, 100);
conservationSlider.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
conservationSlider = null;
}
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
- String source)
+ public static int setPIDSliderSource(AlignmentPanel ap,
+ ResidueShaderI ccs, String source)
{
SliderPanel pid = null;
if (PIDSlider == null)
{
- pid = new SliderPanel(ap, 50, false, cs);
+ pid = new SliderPanel(ap, ccs.getThreshold(), false, ccs);
PIDSlider = new Frame();
PIDSlider.add(pid);
}
else
{
pid = (SliderPanel) PIDSlider.getComponent(0);
- pid.cs = cs;
+ pid.cs = ccs;
+ pid.valueField.setText(String.valueOf(ccs.getThreshold()));
}
- PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
+ PIDSlider.setTitle(MessageManager.formatMessage(
+ "label.percentage_identity_threshold", new String[]
+ { source == null ? BACKGROUND : source }));
if (ap.av.getAlignment().getGroups() != null)
{
if (!PIDSlider.isVisible())
{
- jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
- 420, 100);
+ jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,
+ 100);
PIDSlider.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
PIDSlider = null;
}
+ /**
+ * Hides the PID slider panel if it is shown
+ */
+ public static void hidePIDSlider()
+ {
+ if (PIDSlider != null)
+ {
+ PIDSlider.setVisible(false);
+ PIDSlider = null;
+ }
+ }
+
+ /**
+ * Hides the Conservation slider panel if it is shown
+ */
+ public static void hideConservationSlider()
+ {
+ if (conservationSlider != null)
+ {
+ conservationSlider.setVisible(false);
+ conservationSlider = null;
+ }
+ }
+
public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
- ColourSchemeI cs)
+ ResidueShaderI shader)
{
try
{
e.printStackTrace();
}
this.ap = ap;
- this.cs = cs;
+ this.cs = shader;
forConservation = forConserve;
undoButton.setVisible(false);
applyButton.setVisible(false);
else
{
label.setText(MessageManager
- .getString("label.colour_residues_above_occurence"));
+ .getString("label.colour_residues_above_occurrence"));
slider.setMinimum(0);
slider.setMaximum(100 + slider.getVisibleAmount());
slider.setBlockIncrement(1);
{
return;
}
-
- ColourSchemeI toChange = cs;
- Iterator<SequenceGroup> allGroups = null;
-
- if (allGroupsCheck.getState())
+ if (forConservation)
+ {
+ cs.setConservationApplied(true);
+ cs.setConservationInc(i);
+ }
+ else
{
- allGroups = ap.av.getAlignment().getGroups().listIterator();
+ cs.setThreshold(i, ap.av.isIgnoreGapsConsensus());
}
- while (toChange != null)
+ if (allGroupsCheck.getState())
{
- if (forConservation)
- {
- toChange.setConservationInc(i);
- }
- else
- {
- toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
- }
- if (allGroups != null && allGroups.hasNext())
- {
- while ((toChange = allGroups.next().cs) == null
- && allGroups.hasNext())
- ;
- }
- else
+ for (SequenceGroup group : ap.av.getAlignment().getGroups())
{
- toChange = null;
+ ResidueShaderI groupColourScheme = group.getGroupColourScheme();
+ if (forConservation)
+ {
+ if (!groupColourScheme.conservationApplied())
+ {
+ /*
+ * first time the colour scheme has had Conservation shading applied
+ * - compute conservation
+ */
+ Conservation c = new Conservation("Group",
+ group.getSequences(null), group.getStartRes(),
+ group.getEndRes());
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ group.cs.setConservation(c);
+
+ }
+ groupColourScheme.setConservationApplied(true);
+ groupColourScheme.setConservationInc(i);
+ }
+ else
+ {
+ groupColourScheme.setThreshold(i, ap.av.isIgnoreGapsConsensus());
+ }
}
}
ap.seqPanel.seqCanvas.repaint();
-
}
public void setAllGroupsCheckEnabled(boolean b)
{
+ allGroupsCheck.setState(ap.av.getColourAppliesToAllGroups());
allGroupsCheck.setEnabled(b);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == applyButton)
}
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
valueField.setText(slider.getValue() + "");
{
try
{
- int i = Integer.parseInt(valueField.getText());
+ int i = Integer.valueOf(valueField.getText());
slider.setValue(i);
- } catch (Exception ex)
+ } catch (NumberFormatException ex)
{
- valueField.setText(slider.getValue() + "");
+ valueField.setText(String.valueOf(slider.getValue()));
}
}
valueField.setText(" ");
valueField.addActionListener(this);
valueField.setColumns(3);
+ valueField.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ valueField_actionPerformed();
+ valueChanged(slider.getValue());
+ }
+ });
+
label.setFont(new java.awt.Font("Verdana", 0, 11));
label.setText(MessageManager.getString("label.set_this_label_text"));
jPanel1.setLayout(borderLayout1);
undoButton.addActionListener(this);
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
- allGroupsCheck.setLabel(MessageManager
- .getString("action.apply_threshold_all_groups"));
- allGroupsCheck.setName(MessageManager
- .getString("action.apply_all_groups"));
+ allGroupsCheck.setLabel(
+ MessageManager.getString("action.apply_threshold_all_groups"));
+ allGroupsCheck
+ .setName(MessageManager.getString("action.apply_all_groups"));
this.setBackground(Color.white);
this.setForeground(Color.black);
jPanel2.add(label, null);
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
ap.paintAlignment(true);
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
git://source.jalview.org / jalview.git / blobdiff