X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=e59005f52512e11de4b08524b750067418cf102f;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=f951acf7474b276deb6962a48023e710671cd250;hpb=3e9eba89979511361b51f1c78882c9877874f2ba;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index f951acf..e59005f 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.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; @@ -24,7 +25,6 @@ import java.awt.event.*; import java.awt.print.*; import javax.swing.*; -import jalview.analysis.*; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.viewmodel.PCAModel; @@ -35,17 +35,19 @@ 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 +63,12 @@ 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(); } @@ -99,7 +102,7 @@ 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); @@ -123,11 +126,12 @@ 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); @@ -139,45 +143,48 @@ 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, "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(); + Thread worker = new Thread(this); + worker.start(); } - + } + @Override protected void protSetting_actionPerfomed(ActionEvent arg0) { - + if (pcaModel.isNucleotide()) { pcaModel.setNucleotide(false); @@ -298,7 +305,8 @@ 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) { @@ -512,7 +520,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getPointsasCsv(false, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); + cap.setText(pcaModel.getPointsasCsv(false, + xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), + zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500); } catch (OutOfMemoryError oom) { @@ -521,8 +531,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } - - /* * (non-Javadoc) * @@ -535,7 +543,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getPointsasCsv(true, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); + cap.setText(pcaModel.getPointsasCsv(true, + xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), + zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(), 500, 500); } catch (OutOfMemoryError oom) @@ -551,7 +561,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator /* * (non-Javadoc) - * + * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override @@ -635,7 +645,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } /** - * + * * @return true if any progress bars are still active */ @Override @@ -647,14 +657,15 @@ 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); } }