X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=7608cb9bbdeac91a8c7c6f6027d1b0b6196aadad;hb=2ac5b6423fe366e093c8f12b0935aefc9aafbe5f;hp=6e22ecb8290d58a5ccc95766d626d12c0b7aeb04;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 6e22ecb..7608cb9 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,102 +1,296 @@ +/* + * 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 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; + +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; + Hashtable originalColours; + Frame frame; public RedundancyPanel(AlignmentPanel ap) { + super(ap, 0, false, null); + 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(40); + 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; + + originalColours = new Hashtable(); + 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++) + { + originalColours.put(originalSequences[i], + originalSequences[i].getColor()); + + 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 = 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]); - public void applyButton_actionPerformed(ActionEvent e) + } + } + + + 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() { - 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(); + if(redundancy==null) + return; + + float value = slider.getValue(); + + for(int i=0; i redundancy[i]) + originalSequences[i].setColor(java.awt.Color.white); + else + originalSequences[i].setColor(java.awt.Color.red); + } + + PaintRefresher.Refresh(null,ap.av.alignment); + + } + public void applyButton_actionPerformed() + { + historyList.push(new HistoryItem("Remove redundancy", + ap.av.alignment, HistoryItem.HIDE)); + + if ((historyList.size() == 1) || + !ap.alignFrame.historyList.contains(historyList.firstElement())) + { + ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement()); + ap.alignFrame.updateEditMenuBar(); + } + + 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]) + { + SequenceI seq = originalSequences[i]; + ap.av.alignment.deleteSequence(seq); + del.addElement(seq); + if (sg != null) + { + sg.deleteSequence(seq, false); + } + } + } + + + // This has to be done before the restoreHistoryItem method of alignFrame will + // actually restore these sequences. + if (del.size() > 0) + { + for (int i = 0, j = del.size(); i < j; i++) + { + SequenceI sq = (SequenceI) del.elementAt(i); + sq.deleteChars(0, sq.getLength()); + } + } + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); + ap.alignFrame.updateEditMenuBar(); } - public void undoButton_actionPerformed(ActionEvent e) + public void undoButton_actionPerformed() { + HistoryItem hi = (HistoryItem) historyList.pop(); + ap.alignFrame.restoreHistoryItem(hi); + + if (historyList.size() == 0) + { undoButton.setEnabled(false); - ap.av.setAlignment( new Alignment(oldAlignment) ); - oldAlignment = null; - ap.repaint(); + } + ap.alignFrame.updateEditMenuBar(); } - 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() + ""); + } + } + + + public void windowOpened(WindowEvent evt) + {} + + public void windowClosing(WindowEvent evt) + { + for(int i=0; i