X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=7b489a79e1cf2a4986af7e37f52fc7a47cdae9e2;hb=854fa199e6dd89266237dc803ddc88bf7ba5bdcc;hp=1b84d9fe6be990f2bc630c850ec8b90889bdbfee;hpb=45ce9dae1ec917b16d753b664ff804c9f6f84f02;p=jalview.git
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1b84d9f..7b489a7 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,19 +1,20 @@
/*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 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.
- *
+ *
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -27,7 +28,7 @@ import jalview.analysis.AlignSeq;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
-import jalview.util.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -74,7 +75,7 @@ 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);
@@ -85,7 +86,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.redundancy_threshold_selection"), 400,
100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
@@ -115,7 +116,7 @@ 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);
@@ -148,7 +149,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
{
omitHidden = ap.av.getViewAsString(sg != null);
}
- redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, omitHidden, start, end, false);
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ omitHidden, start, end, false);
progress.setIndeterminate(false);
progress.setVisible(false);
@@ -160,6 +162,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println((System.currentTimeMillis()-start));
}
@@ -171,21 +174,15 @@ 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.idPanel.idCanvas.setHighlighted(redundantSequences);
}
/**
@@ -245,8 +242,8 @@ 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());
}
}