X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=a9d26908a1cac6d286d066e2aaceea292bb1b16f;hb=32e495296239f89190828a16d8893c1e143e0a12;hp=46cf18fcfda15398690645e8ed0e9f1b1f8559bf;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 46cf18f..a9d2690 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,33 +1,46 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.*;
+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;
+
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+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;
/**
* DOCUMENT ME!
@@ -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;
@@ -74,7 +89,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
});
- applyButton.setText("Remove");
+ applyButton.setText(MessageManager.getString("action.remove"));
allGroupsCheck.setVisible(false);
slider.setMinimum(0);
slider.setMaximum(100);
@@ -85,13 +100,14 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
- 100, false);
+ Desktop.addInternalFrame(frame, MessageManager
+ .getString("label.redundancy_threshold_selection"), 400, 100,
+ false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent evt)
{
- ap.idPanel.idCanvas.setHighlighted(null);
+ ap.getIdPanel().getIdCanvas().setHighlighted(null);
}
});
@@ -115,7 +131,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
progress.setIndeterminate(true);
southPanel.add(progress, java.awt.BorderLayout.SOUTH);
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
@@ -155,12 +171,14 @@ 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();
+ sliderValueChanged();
// System.out.println((System.currentTimeMillis()-start));
}
@@ -172,21 +190,15 @@ 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);
}
/**
@@ -229,8 +241,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
}
- 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 +259,8 @@ 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());
}
}
@@ -260,12 +273,19 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
*/
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();
}