From 7928c1a7fab123e9e8baa935f37ab08a965341e7 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 7 Jul 2006 12:56:57 +0000 Subject: [PATCH] Highlight sequences to be deleted before deleting, and apply button exists --- src/jalview/appletgui/RedundancyPanel.java | 248 +++++++++++++++++++++++----- 1 file changed, 206 insertions(+), 42 deletions(-) diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 504338a..2732612 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -23,95 +23,232 @@ import java.util.*; import java.awt.event.*; +import java.awt.*; + import jalview.datamodel.*; +import jalview.appletgui.PaintRefresher; -public class RedundancyPanel extends SliderPanel +public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener { AlignmentPanel ap; + Stack historyList = new Stack(); // simpler than synching with alignFrame. + Vector originalSequences; + Hashtable originalColours; SequenceI[] oldAlignment; + float [] redundancy; + 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() + ""); + 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); - public void applyButton_actionPerformed() + 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() { - float threshold = slider.getValue(); - Vector del; + label.setText("Calculating...."); - 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()); - } + slider.setVisible(false); + applyButton.setEnabled(false); + valueField.setVisible(false); - undoButton.setEnabled(true); + validate(); - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null && sg.getSize() > 1) - { + Vector sel = new Vector(); + SequenceGroup sg = ap.av.getSelectionGroup(); + int height; + originalSequences = new Vector(); + originalColours = new Hashtable(); - del = ap.av.alignment.removeRedundancy(threshold, sg.sequences); - for (int i = 0; i < del.size(); i++) + if ( (sg != null) && (sg.getSize() >= 1)) { - if (sg.sequences.contains( (SequenceI) del.elementAt(i))) + height = sg.getSize(); + for (int i = 0; i < sg.getSize(); i++) { - sg.deleteSequence( (SequenceI) del.elementAt(i), true); + sel.addElement(sg.getSequenceAt(i)); + } + } + else + { + height = ap.av.alignment.getHeight(); + for (int i = 0; i < ap.av.alignment.getHeight(); i++) + { + sel.addElement(ap.av.alignment.getSequenceAt(i)); } } - } - else - { - Vector s = new Vector(); - int i = 0; - while (i < ap.av.alignment.getHeight()) + redundancy = new float[height]; + for (int i = 0; i < height; i++) { - s.addElement(ap.av.alignment.getSequenceAt(i)); - i++; + redundancy[i] = 0f; } - del = ap.av.alignment.removeRedundancy(threshold, s); - for (int j = 0; j < del.size(); j++) + + + // long start = System.currentTimeMillis(); + + float pid; + SequenceI seqi, seqj; + for (int i = 0; i < sel.size(); i++) { - if (sg.sequences.contains( (SequenceI) del.elementAt(j))) - { - sg.deleteSequence( (SequenceI) del.elementAt(j), true); - } + originalSequences.addElement(sel.elementAt(i)); + originalColours.put(sel.elementAt(i), + ((SequenceI) sel.elementAt(i)).getColor()); + + for (int j = 0; j < i; j++) + { + if(i==j) + continue; + + seqi = (SequenceI) sel.elementAt(i); + seqj = (SequenceI) sel.elementAt(j); + if (sg != null) + { + pid = jalview.util.Comparison.PID(seqi, + seqj, + sg.getStartRes(), sg.getEndRes()); + } + else + pid = jalview.util.Comparison.PID( seqi, seqj ); + + + if(seqj.getLength() < seqi.getLength()) + 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[i]) + ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white); + else + ((SequenceI)originalSequences.elementAt(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 = (SequenceI) originalSequences.elementAt(i); + ap.av.alignment.deleteSequence(seq); + del.addElement(seq); + if (sg != null) + { + sg.deleteSequence(seq, false); + } + } + } - ap.repaint(); + + // 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() { - undoButton.setEnabled(false); - ap.av.setAlignment(new Alignment(oldAlignment)); - oldAlignment = null; - ap.repaint(); + HistoryItem hi = (HistoryItem) historyList.pop(); + ap.alignFrame.restoreHistoryItem(hi); + + if (historyList.size() == 0) + { + undoButton.setEnabled(false); + } + ap.alignFrame.updateEditMenuBar(); } public void valueField_actionPerformed(ActionEvent e) @@ -126,4 +263,31 @@ public class RedundancyPanel extends SliderPanel valueField.setText(slider.getValue() + ""); } } + + + public void windowOpened(WindowEvent evt) + {} + + public void windowClosing(WindowEvent evt) + { + for(int i=0; i