X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=d0fcd580332cea0617dfd1ca6fb0ddaf93baf309;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=345c906b8c71344aa4e968264f39db971274afb3;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 345c906..d0fcd58 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,33 +1,45 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
public class RedundancyPanel extends SliderPanel implements Runnable,
WindowListener
{
@@ -51,7 +63,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
- label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
+ label.setText(MessageManager
+ .getString("label.enter_redundancy_threshold"));
valueField.setText("100");
slider.setVisibleAmount(1);
@@ -70,8 +83,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.getString("label.redundancy_threshold_selection"), 400, 100);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager
+ .getString("label.redundancy_threshold_selection"), 400, 100);
frame.addWindowListener(this);
@@ -125,12 +138,14 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
omitHidden, start, end, false);
- label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
+ label.setText(MessageManager
+ .getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println("blob done "+ (System.currentTimeMillis()-start));
}
@@ -143,19 +158,16 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
float value = slider.getValue();
+ List redundantSequences = new ArrayList();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.removeElement(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.addElement(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
}
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
}
@@ -194,8 +206,9 @@ public class RedundancyPanel extends SliderPanel 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());
AlignmentI alignment = ap.av.getAlignment();
for (int i = 0; i < del.size(); i++)
{
@@ -211,8 +224,8 @@ public class RedundancyPanel extends SliderPanel 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());
}
}
@@ -222,10 +235,12 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
CommandI command = (CommandI) historyList.pop();
command.undoCommand(null);
- if (ap.av.historyList.contains(command))
+ if (ap.av.getHistoryList().contains(command))
{
- ap.av.historyList.removeElement(command);
+ ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
ap.paintAlignment(true);