X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=77c96913f13795809d21d2139198bee09b2c332d;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=504338acf9161ed4cc80a11a3bd00693fdef8ff1;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 504338a..77c9691 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,129 +1,325 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import java.util.*; - -import java.awt.event.*; - -import jalview.datamodel.*; - -public class RedundancyPanel extends SliderPanel -{ - AlignmentPanel ap; - - SequenceI[] oldAlignment; - - public RedundancyPanel(AlignmentPanel ap) - { - super(ap, 0, false, null); - - this.ap = ap; - - label.setText("Enter the redundancy threshold"); - - slider.addAdjustmentListener(new AdjustmentListener() - { - public void adjustmentValueChanged(AdjustmentEvent evt) - { - valueField.setText(slider.getValue() + ""); - } - }); - - slider.setMinimum(0); - slider.setMaximum(100); - slider.setValue(100); - - } - - public void applyButton_actionPerformed() - { - 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), true); - } - } - - } - 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), true); - } - - } - } - - ap.repaint(); - - } - - public void undoButton_actionPerformed() - { - 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.commands.*; +import jalview.datamodel.*; + +public class RedundancyPanel extends SliderPanel implements Runnable, + WindowListener +{ + AlignmentPanel ap; + + Stack historyList = new Stack(); // simpler than synching with alignFrame. + + float[] redundancy; + + SequenceI[] originalSequences; + + Frame frame; + + Vector redundantSeqs; + + public RedundancyPanel(AlignmentPanel ap) + { + super(ap, 0, false, null); + + redundantSeqs = new Vector(); + this.ap = ap; + undoButton.setVisible(true); + applyButton.setVisible(true); + allGroupsCheck.setVisible(false); + + label.setText("Enter the redundancy threshold"); + valueField.setText("100"); + + slider.setVisibleAmount(1); + slider.setMinimum(0); + slider.setMaximum(100 + slider.getVisibleAmount()); + slider.setValue(100); + + slider.addAdjustmentListener(new AdjustmentListener() + { + public void adjustmentValueChanged(AdjustmentEvent evt) + { + valueField.setText(slider.getValue() + ""); + sliderValueChanged(); + } + }); + + frame = new Frame(); + frame.add(this); + jalview.bin.JalviewLite.addFrame(frame, + "Redundancy threshold selection", 400, 100); + + frame.addWindowListener(this); + + Thread worker = new Thread(this); + worker.start(); + } + + /** + * 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() + { + 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.alignment); + start = sg.getStartRes(); + end = sg.getEndRes(); + } + else + { + originalSequences = ap.av.alignment.getSequencesArray(); + start = 0; + end = ap.av.alignment.getWidth(); + } + + height = originalSequences.length; + + redundancy = new float[height]; + for (int i = 0; i < height; i++) + { + redundancy[i] = 0f; + } + + // if (ap.av.hasHiddenColumns) + { + // omitHidden = ap.av.getSelectionAsString(); + } + + // long start = System.currentTimeMillis(); + + float pid; + String seqi, seqj; + for (int i = 0; i < height; i++) + { + for (int j = 0; j < i; j++) + { + if (i == j) + { + continue; + } + + if (omitHidden == null) + { + seqi = originalSequences[i].getSequenceAsString(start, end); + seqj = originalSequences[j].getSequenceAsString(start, end); + } + else + { + seqi = omitHidden[i]; + seqj = omitHidden[j]; + } + + pid = jalview.util.Comparison.PID(seqi, seqj); + + if (seqj.length() < seqi.length()) + { + redundancy[j] = Math.max(pid, redundancy[j]); + } + else + { + redundancy[i] = Math.max(pid, redundancy[i]); + } + + } + } + + label.setText("Enter the redundancy threshold"); + slider.setVisible(true); + applyButton.setEnabled(true); + valueField.setVisible(true); + + validate(); + // System.out.println("blob done "+ (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.removeElement(originalSequences[i]); + } + else if (!redundantSeqs.contains(originalSequences[i])) + { + redundantSeqs.addElement(originalSequences[i]); + } + } + + ap.idPanel.idCanvas.setHighlighted(redundantSeqs); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); + + } + + public void applyButton_actionPerformed() + { + 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.alignment); + + for (int i = 0; i < del.size(); i++) + { + ap.av.alignment.deleteSequence(deleted[i]); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); + if (sg != null) + { + sg.deleteSequence(deleted[i], false); + } + } + + historyList.push(cut); + + ap.alignFrame.addHistoryItem(cut); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + } + + } + + public void undoButton_actionPerformed() + { + CommandI command = (CommandI) historyList.pop(); + command.undoCommand(null); + + if (ap.av.historyList.contains(command)) + { + ap.av.historyList.removeElement(command); + ap.alignFrame.updateEditMenuBar(); + } + + ap.paintAlignment(true); + + if (historyList.size() == 0) + { + undoButton.setEnabled(false); + } + } + + public void valueField_actionPerformed(ActionEvent e) + { + try + { + int i = Integer.parseInt(valueField.getText()); + slider.setValue(i); + } catch (Exception ex) + { + valueField.setText(slider.getValue() + ""); + } + } + + public void windowOpened(WindowEvent evt) + { + } + + public void windowClosing(WindowEvent evt) + { + ap.idPanel.idCanvas.setHighlighted(null); + } + + public void windowClosed(WindowEvent evt) + { + } + + public void windowActivated(WindowEvent evt) + { + } + + public void windowDeactivated(WindowEvent evt) + { + } + + public void windowIconified(WindowEvent evt) + { + } + + public void windowDeiconified(WindowEvent evt) + { + } +}