X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=ec896d596f591b07148f892554478e05e3750da8;hb=7cf75b5b379dd71b3480726419c7dc55d8e01f0e;hp=e4ef46ec1dfa274f5a1cebbcb16f59898eeefcdc;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index e4ef46e..ec896d5 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,148 +1,326 @@ /* -* 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 -*/ - + * 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.jbgui.*; import jalview.datamodel.*; +import jalview.jbgui.*; +import jalview.util.Comparison; +import jalview.commands.*; + import java.awt.event.*; + import java.util.*; + import javax.swing.event.*; -public class RedundancyPanel - extends GSliderPanel -{ - AlignFrame af; - AlignmentPanel ap; - Stack historyList = new Stack(); // simpler than synching with alignFrame. +import javax.swing.*; + - public RedundancyPanel(AlignmentPanel ap, AlignFrame af) - { - this.ap = ap; - this.af = af; - label.setText("Enter the redundancy threshold"); +/** + * 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; - slider.addChangeListener(new ChangeListener() + /** + * Creates a new RedundancyPanel object. + * + * @param ap DOCUMENT ME! + * @param af DOCUMENT ME! + */ + public RedundancyPanel(final AlignmentPanel ap, AlignFrame af) { - 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; - HistoryItem it; - historyList.push(it=new HistoryItem("Remove redundancy", - ap.av.alignment, HistoryItem.HIDE)); - if (historyList.size()==1 - || !af.historyList.contains(historyList.firstElement())) { - af.addHistoryItem((HistoryItem) historyList.firstElement()); - af.updateEditMenuBar(); + 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); + } + } + ); + } - undoButton.setEnabled(true); - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null && sg.getSize() >= 1) + + + /** + * 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); - del = ap.av.alignment.removeRedundancy(threshold, sg.sequences); - for (int i = 0; i < del.size(); i++) - { - if (sg.sequences.contains( (SequenceI) del.elementAt(i))) + 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)) { - sg.deleteSequence( (SequenceI) del.elementAt(i)); + 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)); } - else + + void sliderValueChanged() { - Vector s = new Vector(); - int i = 0; - while (i < ap.av.alignment.getHeight()) + 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]); + } - del = ap.av.alignment.removeRedundancy(threshold, s); + + ap.idPanel.idCanvas.setHighlighted(redundantSeqs); } - // This has to be done before the restoreHistoryItem method of alignFrame will - // actually restore these sequences. + /** + * 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()); + } - if (del.size()>0) - for (int i=0,j=del.size(); i