X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=c4d7e3b366da37054c023dd8fb31291da349add2;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=ec896d596f591b07148f892554478e05e3750da8;hpb=8b7b2e3d4893991f29ab603c20ae826f7e3c8ffb;p=jalview.git diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index ec896d5..c4d7e3b 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,326 +1,341 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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.gui; - -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.util.Comparison; -import jalview.commands.*; - -import java.awt.event.*; - -import java.util.*; - -import javax.swing.event.*; - -import javax.swing.*; - - -/** - * 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(false) >= 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.getViewAsString(sg!=null); - } - - - // 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].getSequence(start, end); - seqj = originalSequences[j].getSequence(start, end); - } - else - { - seqi = omitHidden[i]; - seqj = omitHidden[j]; - } - - pid = Comparison.PID( seqi, seqj ); - - if(seqj.length() < seqi.length()) - redundancy[j] = Math.max(pid, redundancy[j]); - else - redundancy[i] = Math.max(pid, redundancy[i]); - - } - } - - 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[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.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()); - } - - - } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void undoButton_actionPerformed(ActionEvent e) - { - CommandI command = (CommandI) historyList.pop(); - command.undoCommand(); - - if (ap.av.historyList.contains(command)) - { - ap.av.historyList.remove(command); - af.updateEditMenuBar(); - } - - ap.repaint(); - - 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() + ""); - } - } - - -} +/* + * 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.gui; + +import java.util.*; + +import java.awt.event.*; +import javax.swing.*; +import javax.swing.event.*; + +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.jbgui.*; +import jalview.util.*; + +/** + * 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.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.getViewAsString(sg != null); + } + + // 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 = Comparison.PID(seqi, seqj); + + if (seqj.length() < seqi.length()) + { + redundancy[j] = Math.max(pid, redundancy[j]); + } + else + { + redundancy[i] = Math.max(pid, redundancy[i]); + } + + } + } + + 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.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()); + } + + } + + /** + * 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() + ""); + } + } + +}