X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=f07993ca7130c3f41250c5f4eb15e3b2af1144a1;hb=c2214808f64b811a25cec10399dcff38db0c592c;hp=f951acf7474b276deb6962a48023e710671cd250;hpb=3e9eba89979511361b51f1c78882c9877874f2ba;p=jalview.git
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
old mode 100755
new mode 100644
index f951acf..f07993c
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,32 +1,36 @@
/*
- * 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 2.8.2)
+ * 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.
- *
+ * 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.*;
import java.awt.event.*;
import java.awt.print.*;
+
import javax.swing.*;
-import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
import jalview.viewmodel.PCAModel;
/**
@@ -35,17 +39,19 @@ import jalview.viewmodel.PCAModel;
* @author $author$
* @version $Revision$
*/
-public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
+public class PCAPanel extends GPCAPanel implements Runnable,
+ IProgressIndicator
{
-
RotatableCanvas rc;
AlignmentPanel ap;
AlignViewport av;
+
PCAModel pcaModel;
- int top=0;
+
+ int top = 0;
/**
* Creates a new PCAPanel object.
@@ -61,11 +67,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
this.ap = ap;
boolean sameLength = true;
-
- AlignmentView seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
- boolean nucleotide=av.getAlignment().isNucleotide();
+ boolean selected = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 0;
+ AlignmentView seqstrings = av.getAlignmentView(selected);
+ boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
- if (av.getSelectionGroup() == null)
+ if (!selected)
{
seqs = av.getAlignment().getSequencesArray();
}
@@ -99,13 +106,51 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
}
pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
PaintRefresher.Register(this, av.getSequenceSetId());
-
+
rc = new RotatableCanvas(ap);
this.getContentPane().add(rc, BorderLayout.CENTER);
Thread worker = new Thread(this);
worker.start();
}
+ @Override
+ protected void scoreMatrix_menuSelected()
+ {
+ scoreMatrixMenu.removeAll();
+ for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ {
+ if (ResidueProperties.getScoreMatrix(sm) != null)
+ {
+ // create an entry for this score matrix for use in PCA
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+ jm.setText(MessageManager
+ .getStringOrReturn("label.score_model", sm));
+ jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+ if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+ .get(sm).isProtein())
+ || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
+ .get(sm).isDNA())
+ {
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!pcaModel.getScore_matrix().equals((String) sm))
+ {
+ pcaModel.setScore_matrix((String) sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
+ }
+ });
+ scoreMatrixMenu.add(jm);
+ }
+ }
+ }
+ }
+
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this, "Select Background Colour",
@@ -123,11 +168,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
*/
public void run()
{
- long progId=System.currentTimeMillis();
- IProgressIndicator progress=this;
- String message="Recalculating PCA";
- if (getParent()==null) {
- progress=ap.alignFrame;
+ long progId = System.currentTimeMillis();
+ IProgressIndicator progress = this;
+ String message = "Recalculating PCA";
+ if (getParent() == null)
+ {
+ progress = ap.alignFrame;
message = "Calculating PCA";
}
progress.setProgressBar(message, progId);
@@ -139,48 +185,53 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
-
+
pcaModel.updateRc(rc);
// rc.invalidate();
nuclSetting.setSelected(pcaModel.isNucleotide());
protSetting.setSelected(!pcaModel.isNucleotide());
- top=pcaModel.getTop();
jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
+ top = pcaModel.getTop();
} catch (OutOfMemoryError er)
{
new OOMWarning("calculating PCA", er);
return;
- }
- finally {
+ } finally
+ {
progress.setProgressBar("", progId);
}
calcSettings.setEnabled(true);
repaint();
- if (getParent()==null)
+ if (getParent() == null)
{
addKeyListener(rc);
- Desktop.addInternalFrame(this, "Principal component analysis", 475, 450);
+ Desktop.addInternalFrame(this, MessageManager
+ .getString("label.principal_component_analysis"), 475, 450);
}
}
+
@Override
protected void nuclSetting_actionPerfomed(ActionEvent arg0)
{
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
- Thread worker = new Thread(this);
- worker.start();
+ pcaModel.setScore_matrix("DNA");
+ Thread worker = new Thread(this);
+ worker.start();
}
-
+
}
+
@Override
protected void protSetting_actionPerfomed(ActionEvent arg0)
{
-
+
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
+ pcaModel.setScore_matrix("BLOSUM62");
Thread worker = new Thread(this);
worker.start();
}
@@ -253,7 +304,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
try
{
cap.setText(pcaModel.getDetails());
- Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pca_details"), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("opening PCA details", oom);
@@ -298,7 +350,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
{
}
;
- Object[] alAndColsel = pcaModel.getSeqtrings().getAlignmentAndColumnSelection(gc);
+ Object[] alAndColsel = pcaModel.getSeqtrings()
+ .getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
@@ -326,8 +379,10 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
}
/*
@@ -512,8 +567,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pcaModel.getPointsasCsv(false, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
+ cap.setText(pcaModel.getPointsasCsv(false,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
@@ -521,8 +580,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
}
}
-
-
/*
* (non-Javadoc)
*
@@ -535,9 +592,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pcaModel.getPointsasCsv(true, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
- 500, 500);
+ cap.setText(pcaModel.getPointsasCsv(true,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
@@ -551,7 +611,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
/*
* (non-Javadoc)
- *
+ *
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
@@ -615,7 +675,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
@@ -635,7 +696,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
}
/**
- *
+ *
* @return true if any progress bars are still active
*/
@Override
@@ -647,14 +708,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
}
return false;
}
+
@Override
protected void resetButton_actionPerformed(ActionEvent e)
{
- int t=top;
- top=0; // ugly - prevents dimensionChanged events from being processed
+ int t = top;
+ top = 0; // ugly - prevents dimensionChanged events from being processed
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
- top=t;
+ top = t;
zCombobox.setSelectedIndex(2);
}
}