X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=f48701169722061cb3d6f82f3792f12deb75676d;hb=5640ec0623c6d1205e62f9fe15292f32bfdab7d9;hp=0038939c29455daf9bd8b286dfa57043e12da217;hpb=4cea7a0328724b90a6a7c16ae8c926e0cc12cedd;p=jalview.git
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 0038939..f487011 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,32 +1,45 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 .
+ * 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.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
import jalview.util.MessageManager;
/**
@@ -41,7 +54,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
AlignmentPanel ap;
- Stack historyList = new Stack(); // simpler than synching with alignFrame.
+ Stack historyList = new Stack<>();
+
+ // simpler than synching with alignFrame.
float[] redundancy;
@@ -67,6 +82,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
@@ -84,14 +100,18 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
worker.start();
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager.getString("label.redundancy_threshold_selection"), 400,
- 100, false);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent evt)
{
- ap.idPanel.idCanvas.setHighlighted(null);
+ ap.getIdPanel().getIdCanvas().setHighlighted(null);
}
});
@@ -109,6 +129,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
JProgressBar progress = new JProgressBar();
@@ -155,13 +176,15 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
progress.setVisible(false);
progress = null;
- label.setText("Enter the redundancy threshold");
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
validate();
- // System.out.println((System.currentTimeMillis()-start));
+ sliderValueChanged();
+ // jalview.bin.Console.outPrintln((System.currentTimeMillis()-start));
}
void sliderValueChanged()
@@ -172,21 +195,15 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
float value = slider.getValue();
-
+ List redundantSequences = new ArrayList<>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.remove(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.add(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
-
}
-
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
}
/**
@@ -195,9 +212,10 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
* @param e
* DOCUMENT ME!
*/
+ @Override
public void applyButton_actionPerformed(ActionEvent e)
{
- Vector del = new Vector();
+ List del = new ArrayList<>();
undoButton.setEnabled(true);
@@ -208,13 +226,12 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
{
if (value <= redundancy[i])
{
- del.addElement(originalSequences[i]);
+ del.add(originalSequences[i]);
}
}
// This has to be done before the restoreHistoryItem method of alignFrame
- // will
- // actually restore these sequences.
+ // will actually restore these sequences.
if (del.size() > 0)
{
SequenceI[] deleted = new SequenceI[del.size()];
@@ -222,15 +239,16 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
int width = 0;
for (int i = 0; i < del.size(); i++)
{
- deleted[i] = (SequenceI) del.elementAt(i);
+ deleted[i] = del.get(i);
if (deleted[i].getLength() > width)
{
width = deleted[i].getLength();
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
{
@@ -246,8 +264,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- // ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- // .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
@@ -258,18 +276,26 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
* @param e
* DOCUMENT ME!
*/
+ @Override
public void undoButton_actionPerformed(ActionEvent e)
{
- CommandI command = (CommandI) historyList.pop();
- command.undoCommand(af.getViewAlignments());
+ if (historyList == null || historyList.isEmpty())
+ {
+ undoButton.setEnabled(false);
+ return;
+ }
- if (ap.av.historyList.contains(command))
+ CommandI command = historyList.pop();
+ if (ap.av.getHistoryList().contains(command))
{
- ap.av.historyList.remove(command);
+ command.undoCommand(af.getViewAlignments());
+ ap.av.getHistoryList().remove(command);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
if (historyList.size() == 0)
{
@@ -277,22 +303,4 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void valueField_actionPerformed(ActionEvent e)
- {
- try
- {
- int i = Integer.parseInt(valueField.getText());
- slider.setValue(i);
- } catch (Exception ex)
- {
- valueField.setText(slider.getValue() + "");
- }
- }
-
}