/*
- * 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 ($$Version-Rel$$)
+ * 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 <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 jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.schemes.ColourSchemeI;
+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.Iterator;
-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;
/**
* DOCUMENT ME!
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);
sp.cs = cs;
}
- conservationSlider.setTitle("Conservation Colour Increment (" + source
- + ")");
+ conservationSlider
+ .setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment",
+ new String[] { source }));
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
sp.setAllGroupsCheckEnabled(true);
}
}
/**
+ * Hides the PID slider panel if it is shown
+ */
+ public static void hidePIDSlider()
+ {
+ if (PIDSlider != null)
+ {
+ 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()
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()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent e)
{
pid.cs = cs;
}
- PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+ PIDSlider
+ .setTitle(MessageManager.formatMessage(
+ "label.percentage_identity_threshold",
+ new String[] { source }));
- if (ap.av.alignment.getGroups() != null)
+ if (ap.av.getAlignment().getGroups() != null)
{
pid.setAllGroupsCheckEnabled(true);
}
PIDSlider
.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent e)
{
return;
}
- ColourSchemeI toChange = null;
- Vector allGroups = null;
- int groupIndex = 0;
+ ColourSchemeI toChange = cs;
+ Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.isSelected())
{
- allGroups = ap.av.alignment.getGroups();
- groupIndex = allGroups.size() - 1;
- }
- else
- {
- toChange = cs;
+ allGroups = ap.av.getAlignment().getGroups().listIterator();
}
- while (groupIndex > -1)
+ while (toChange != null)
{
- if (allGroups != null)
+ if (forConservation)
{
- toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
-
- if (toChange == null)
- {
- groupIndex--;
-
- continue;
- }
+ toChange.setConservationInc(i);
}
-
- if (forConservation)
+ else
+ {
+ toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
+ }
+ if (allGroups != null && allGroups.hasNext())
{
- if (toChange.conservationApplied())
+ while ((toChange = allGroups.next().cs) == null
+ && allGroups.hasNext())
{
- toChange.setConservationInc(i);
+ ;
}
}
else
{
- toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+ toChange = null;
}
-
- groupIndex--;
}
- ap.seqPanel.seqCanvas.repaint();
+ ap.getSeqPanel().seqCanvas.repaint();
}
/**
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
- */
- public void valueField_actionPerformed(ActionEvent e)
- {
- try
- {
- int i = Integer.parseInt(valueField.getText());
- slider.setValue(i);
- } catch (NumberFormatException ex)
- {
- valueField.setText(slider.getValue() + "");
- }
- }
-
- /**
- * DOCUMENT ME!
- *
* @param value
* DOCUMENT ME!
*/
return Integer.parseInt(valueField.getText());
}
+ @Override
public void slider_mouseReleased(MouseEvent e)
{
if (ap.overviewPanel != null)
git://source.jalview.org / jalview.git / blobdiff