X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=09fbbb03ba8aa8eb6d45b19b11d625c448749d59;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=93ffd9cad1df038c975ba53c65e62a71a75773f9;hpb=79f4b175e12f4c16d598b4cb56ffe62532b592a1;p=jalview.git diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 93ffd9c..09fbbb0 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,103 +1,298 @@ -package jalview.gui; - -import jalview.jbgui.*; -import jalview.datamodel.*; -import java.awt.event.*; -import java.util.*; -import javax.swing.event.*; - -public class RedundancyPanel extends GSliderPanel -{ - AlignmentPanel ap; - - SequenceI[] oldAlignment; - - - public RedundancyPanel(AlignmentPanel ap) - { - this.ap = ap; - - label.setText("Enter the redundancy threshold"); - - slider.addChangeListener(new ChangeListener() - { - public void stateChanged(ChangeEvent evt) - { - valueField.setText( slider.getValue()+"" ); - } - }); - - slider.setMinimum(0); - slider.setMaximum(100); - slider.setValue(100 ); - - } - - public void applyButton_actionPerformed(ActionEvent e) - { - float threshold = slider.getValue(); - Vector del; - - oldAlignment = new SequenceI[ap.av.alignment.getHeight()]; - for (int i = 0; i < ap.av.alignment.getHeight(); i++) - { - oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(), - ap.av.alignment.getSequenceAt(i). - getSequence()); - } - - undoButton.setEnabled(true); - - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null && sg.getSize() > 1) - { - - del = ap.av.alignment.removeRedundancy(threshold, sg.sequences); - for (int i = 0; i < del.size(); i++) - if (sg.sequences.contains( (SequenceI) del.elementAt(i))) - sg.deleteSequence( (SequenceI) del.elementAt(i)); - - } - else - { - Vector s = new Vector(); - int i=0; - while(i < ap.av.alignment.getHeight()) - { - s.addElement( ap.av.alignment.getSequenceAt(i) ); - i++; - } - del = ap.av.alignment.removeRedundancy(threshold,s); - for (int j=0; j < del.size(); j++) - { - if (sg.sequences.contains((SequenceI)del.elementAt(j))) - sg.deleteSequence((SequenceI)del.elementAt(j)); - - } - } - - ap.repaint(); - - } - - public void undoButton_actionPerformed(ActionEvent e) - { - undoButton.setEnabled(false); - ap.av.setAlignment( new Alignment(oldAlignment) ); - oldAlignment = null; - ap.repaint(); - } - - - public void valueField_actionPerformed(ActionEvent e) - { - try{ - int i = Integer.parseInt(valueField.getText()); - slider.setValue(i); - } - catch(Exception ex) - { - valueField.setText( slider.getValue()+"" ); - } - } -} +/* + * 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; + +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.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class RedundancyPanel extends GSliderPanel implements Runnable +{ + AlignFrame af; + + AlignmentPanel ap; + + Stack historyList = new Stack(); // simpler than synching with alignFrame. + + float[] redundancy; + + SequenceI[] originalSequences; + + JInternalFrame frame; + + Vector redundantSeqs; + + /** + * Creates a new RedundancyPanel object. + * + * @param ap + * DOCUMENT ME! + * @param af + * DOCUMENT ME! + */ + public RedundancyPanel(final AlignmentPanel ap, AlignFrame af) + { + this.ap = ap; + this.af = af; + redundantSeqs = new Vector(); + + slider.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + valueField.setText(slider.getValue() + ""); + sliderValueChanged(); + } + }); + + applyButton.setText("Remove"); + allGroupsCheck.setVisible(false); + slider.setMinimum(0); + slider.setMaximum(100); + slider.setValue(100); + + Thread worker = new Thread(this); + worker.start(); + + frame = new JInternalFrame(); + frame.setContentPane(this); + Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, + 100, false); + frame.addInternalFrameListener(new InternalFrameAdapter() + { + public void internalFrameClosing(InternalFrameEvent evt) + { + ap.idPanel.idCanvas.setHighlighted(null); + } + }); + + } + + /** + * This is a copy of remove redundancy in jalivew.datamodel.Alignment except + * we dont want to remove redundancy, just calculate once so we can use the + * slider to dynamically hide redundant sequences + * + * @param threshold + * DOCUMENT ME! + * @param sel + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public void run() + { + JProgressBar progress = new JProgressBar(); + progress.setIndeterminate(true); + southPanel.add(progress, java.awt.BorderLayout.SOUTH); + + label.setText("Calculating...."); + + slider.setVisible(false); + applyButton.setEnabled(false); + valueField.setVisible(false); + + validate(); + + String[] omitHidden = null; + + SequenceGroup sg = ap.av.getSelectionGroup(); + int height; + + int start, end; + + if ((sg != null) && (sg.getSize() >= 1)) + { + originalSequences = sg.getSequencesInOrder(ap.av.getAlignment()); + start = sg.getStartRes(); + end = sg.getEndRes(); + } + else + { + originalSequences = ap.av.getAlignment().getSequencesArray(); + start = 0; + end = ap.av.getAlignment().getWidth(); + } + + height = originalSequences.length; + if (ap.av.hasHiddenColumns()) + { + omitHidden = ap.av.getViewAsString(sg != null); + } + redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, + omitHidden, start, end, false); + + progress.setIndeterminate(false); + progress.setVisible(false); + progress = null; + + label.setText("Enter the redundancy threshold"); + slider.setVisible(true); + applyButton.setEnabled(true); + valueField.setVisible(true); + + validate(); + // System.out.println((System.currentTimeMillis()-start)); + } + + void sliderValueChanged() + { + if (redundancy == null) + { + return; + } + + float value = slider.getValue(); + + for (int i = 0; i < redundancy.length; i++) + { + if (value > redundancy[i]) + { + redundantSeqs.remove(originalSequences[i]); + } + else if (!redundantSeqs.contains(originalSequences[i])) + { + redundantSeqs.add(originalSequences[i]); + } + + } + + ap.idPanel.idCanvas.setHighlighted(redundantSeqs); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void applyButton_actionPerformed(ActionEvent e) + { + Vector del = new Vector(); + + undoButton.setEnabled(true); + + float value = slider.getValue(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + for (int i = 0; i < redundancy.length; i++) + { + if (value <= redundancy[i]) + { + del.addElement(originalSequences[i]); + } + } + + // This has to be done before the restoreHistoryItem method of alignFrame + // will + // actually restore these sequences. + if (del.size() > 0) + { + SequenceI[] deleted = new SequenceI[del.size()]; + + int width = 0; + for (int i = 0; i < del.size(); i++) + { + deleted[i] = (SequenceI) del.elementAt(i); + if (deleted[i].getLength() > width) + { + width = deleted[i].getLength(); + } + } + + EditCommand cut = new EditCommand("Remove Redundancy", + EditCommand.CUT, deleted, 0, width, ap.av.getAlignment()); + + for (int i = 0; i < del.size(); i++) + { + ap.av.getAlignment().deleteSequence(deleted[i]); + if (sg != null) + { + sg.deleteSequence(deleted[i], false); + } + } + + historyList.push(cut); + + ap.alignFrame.addHistoryItem(cut); + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); + // ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + // .getSequences()); + } + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void undoButton_actionPerformed(ActionEvent e) + { + CommandI command = (CommandI) historyList.pop(); + command.undoCommand(af.getViewAlignments()); + + if (ap.av.historyList.contains(command)) + { + ap.av.historyList.remove(command); + af.updateEditMenuBar(); + } + + ap.paintAlignment(true); + + if (historyList.size() == 0) + { + undoButton.setEnabled(false); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void valueField_actionPerformed(ActionEvent e) + { + try + { + int i = Integer.parseInt(valueField.getText()); + slider.setValue(i); + } catch (Exception ex) + { + valueField.setText(slider.getValue() + ""); + } + } + +}