From 16963d1109bb0989757ed5200baaeb5d59b2203f Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 7 Jul 2006 13:07:32 +0000 Subject: [PATCH] Highlight sequences before seleting --- src/jalview/gui/RedundancyPanel.java | 228 +++++++++++++++++++++++++++------- 1 file changed, 183 insertions(+), 45 deletions(-) diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 3901b1f..5dd2fc4 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -27,6 +27,8 @@ import java.awt.event.*; import java.util.*; import javax.swing.event.*; +import jalview.util.Comparison; +import javax.swing.*; /** @@ -35,11 +37,15 @@ import javax.swing.event.*; * @author $author$ * @version $Revision$ */ -public class RedundancyPanel extends GSliderPanel +public class RedundancyPanel extends GSliderPanel implements Runnable { AlignFrame af; AlignmentPanel ap; Stack historyList = new Stack(); // simpler than synching with alignFrame. + float [] redundancy; + Vector originalSequences; + Hashtable originalColours; + JInternalFrame frame; /** * Creates a new RedundancyPanel object. @@ -51,19 +57,160 @@ public class RedundancyPanel extends GSliderPanel { this.ap = ap; this.af = af; - label.setText("Enter the redundancy threshold"); slider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent evt) { valueField.setText(slider.getValue() + ""); + sliderValueChanged(); } }); - slider.setMinimum(0); + applyButton.setText("Remove"); + allGroupsCheck.setVisible(false); + slider.setMinimum(60); 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) + { + resetColours(); + } + } + ); + + } + + + /** + * 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(); + + Vector sel = new Vector(); + SequenceGroup sg = ap.av.getSelectionGroup(); + int height; + originalSequences = new Vector(); + originalColours = new Hashtable(); + + if ( (sg != null) && (sg.getSize() >= 1)) + { + height = sg.getSize(); + for (int i = 0; i < sg.getSize(); i++) + { + 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)); + } + } + + redundancy = new float[height]; + for (int i = 0; i < height; i++) + { + redundancy[i] = 0f; + } + + + // long start = System.currentTimeMillis(); + + float pid; + SequenceI seqi, seqj; + for (int i = 0; i < sel.size(); i++) + { + 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 = Comparison.PID( seqi, + seqj, + sg.getStartRes(), sg.getEndRes()); + else + pid = Comparison.PID( seqi, seqj ); + + + if(seqj.getLength() < seqi.getLength()) + 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("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); + } /** @@ -73,8 +220,6 @@ public class RedundancyPanel extends GSliderPanel */ public void applyButton_actionPerformed(ActionEvent e) { - float threshold = slider.getValue(); - Vector del; historyList.push(new HistoryItem("Remove redundancy", ap.av.alignment, HistoryItem.HIDE)); @@ -85,35 +230,27 @@ public class RedundancyPanel extends GSliderPanel af.updateEditMenuBar(); } + Vector del = new Vector(); + undoButton.setEnabled(true); + float value = slider.getValue(); SequenceGroup sg = ap.av.getSelectionGroup(); - if ((sg != null) && (sg.getSize() >= 1)) + for (int i = 0; i < redundancy.length; i++) { - del = ap.av.alignment.removeRedundancy(threshold, sg.sequences); - - for (int i = 0; i < del.size(); i++) + if (value <= redundancy[i]) + { + SequenceI seq = (SequenceI) originalSequences.elementAt(i); + ap.av.alignment.deleteSequence(seq); + del.add(seq); + if (sg != null) { - if (sg.sequences.contains((SequenceI) del.elementAt(i))) - { - sg.deleteSequence((SequenceI) del.elementAt(i), true); - } + sg.deleteSequence(seq, false); } + } } - 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); - } // This has to be done before the restoreHistoryItem method of alignFrame will // actually restore these sequences. @@ -128,18 +265,17 @@ public class RedundancyPanel extends GSliderPanel ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); af.updateEditMenuBar(); + } + void resetColours() + { + for(int i=0; i