X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=5423dc96e02598a42b843b47256bee816224958c;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=17b5dfa87b9cedfe1f2c4033a312ab81c8b03fa1;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 17b5dfa..5423dc9 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; + SequenceI [] originalSequences; + JInternalFrame frame; + Vector redundantSeqs; /** * Creates a new RedundancyPanel object. @@ -47,23 +53,167 @@ public class RedundancyPanel extends GSliderPanel * @param ap DOCUMENT ME! * @param af DOCUMENT ME! */ - public RedundancyPanel(AlignmentPanel ap, AlignFrame af) + public RedundancyPanel(final AlignmentPanel ap, AlignFrame af) { this.ap = ap; this.af = af; - label.setText("Enter the redundancy threshold"); + 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); + } + } + ); + + } + + + /** + * 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(); + + 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.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)); + } + + void sliderValueChanged() + { + 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]); + + } + + ap.idPanel.idCanvas.setHighlighted(redundantSeqs); } /** @@ -73,10 +223,7 @@ public class RedundancyPanel extends GSliderPanel */ public void applyButton_actionPerformed(ActionEvent e) { - float threshold = slider.getValue(); - Vector del; - HistoryItem it; - historyList.push(it = new HistoryItem("Remove redundancy", + historyList.push(new HistoryItem("Remove redundancy", ap.av.alignment, HistoryItem.HIDE)); if ((historyList.size() == 1) || @@ -86,35 +233,27 @@ 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 = originalSequences[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. @@ -127,27 +266,11 @@ public class RedundancyPanel extends GSliderPanel } } - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - - if (ap.av.getAlignment().getHeight() < 1) - { - try - { - af.setClosed(true); - } - catch (Exception ex) - { - } - } - - ap.av.updateConservation(); - ap.av.updateConsensus(); + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); af.updateEditMenuBar(); - ap.repaint(); } + /** * DOCUMENT ME! * @@ -155,19 +278,19 @@ public class RedundancyPanel extends GSliderPanel */ public void undoButton_actionPerformed(ActionEvent e) { - HistoryItem hi = (HistoryItem) historyList.pop(); - af.restoreHistoryItem(hi); + HistoryItem hi = (HistoryItem) historyList.pop(); + af.restoreHistoryItem(hi); - if (historyList.size() == 0) - { - undoButton.setEnabled(false); + if (historyList.size() == 0) + { + undoButton.setEnabled(false); - if (af.historyList.contains(hi)) - { - af.historyList.remove(hi); - af.updateEditMenuBar(); - } + if (af.historyList.contains(hi)) + { + af.historyList.remove(hi); + af.updateEditMenuBar(); } + } } /** @@ -187,4 +310,6 @@ public class RedundancyPanel extends GSliderPanel valueField.setText(slider.getValue() + ""); } } + + }