X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=fd85ce7b3636f75017dafa2fd18566435ac448f3;hb=c766c1829042b039ea2ff56fc05f4a0100c2a73d;hp=735a5790459e23fe66ca837be501531211ec7378;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 735a579..fd85ce7 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,121 +1,304 @@ /* -* 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.appletgui; -import jalview.jbappletgui.*; -import jalview.datamodel.*; -import java.awt.event.*; import java.util.*; -public class RedundancyPanel extends GSliderPanel +import java.awt.event.*; + +import java.awt.*; + +import jalview.datamodel.*; +import jalview.appletgui.PaintRefresher; +import jalview.commands.*; + +public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener { AlignmentPanel ap; - SequenceI[] oldAlignment; - + 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()+"" ); + valueField.setText(slider.getValue() + ""); + sliderValueChanged(); } }); - slider.setMinimum(0); - slider.setMaximum(100); - slider.setValue(100 ); + 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(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.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)); } - public void applyButton_actionPerformed(ActionEvent e) + void sliderValueChanged() { - float threshold = slider.getValue(); - Vector del; + if(redundancy==null) + return; - 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()); - } + float value = slider.getValue(); + + for(int i=0; i 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(); - 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(); + + 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(ActionEvent e) + public void undoButton_actionPerformed() { + CommandI command = (CommandI) historyList.pop(); + command.undoCommand(); + + if (ap.av.historyList.contains(command)) + { + ap.av.historyList.removeElement(command); + ap.alignFrame.updateEditMenuBar(); + } + + ap.repaint(); + + if (historyList.size() == 0) + { undoButton.setEnabled(false); - ap.av.setAlignment( new Alignment(oldAlignment) ); - oldAlignment = null; - ap.repaint(); + } } - public void valueField_actionPerformed(ActionEvent e) { - try{ + try + { int i = Integer.parseInt(valueField.getText()); slider.setValue(i); } - catch(Exception ex) + catch (Exception ex) { - valueField.setText( slider.getValue()+"" ); + 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) + {} }