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package jalview.gui; |
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import jalview.analysis.AlignSeq; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.jbgui.GPairwiseAlignPanel; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.AlignmentViewport; |
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import java.awt.event.ActionEvent; |
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import java.util.Vector; |
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@author |
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@version |
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| 52.5% |
Uncovered Elements: 38 (80) |
Complexity: 16 |
Complexity Density: 0.3 |
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public class PairwiseAlignPanel extends GPairwiseAlignPanel |
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{ |
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private static final String DASHES = "---------------------\n"; |
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AlignmentViewport av; |
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Vector<SequenceI> sequences; |
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@param |
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| 83.7% |
Uncovered Elements: 8 (49) |
Complexity: 9 |
Complexity Density: 0.26 |
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public PairwiseAlignPanel(AlignmentViewport viewport)... |
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{ |
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super(); |
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this.av = viewport; |
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sequences = new Vector<SequenceI>(); |
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SequenceGroup selectionGroup = viewport.getSelectionGroup(); |
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boolean isSelection = selectionGroup != null |
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&& selectionGroup.getSize() > 0; |
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AlignmentView view = viewport.getAlignmentView(isSelection); |
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String[] seqStrings = view.getSequenceStrings(viewport |
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.getGapCharacter()); |
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SequenceI[] seqs; |
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if (isSelection) |
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{ |
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seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport |
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.getGapCharacter())[0]; |
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} |
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else |
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{ |
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seqs = av.getAlignment().getSequencesArray(); |
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} |
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String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA |
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: AlignSeq.PEP; |
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float[][] scores = new float[seqs.length][seqs.length]; |
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double totscore = 0D; |
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int count = seqs.length; |
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boolean first = true; |
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for (int i = 1; i < count; i++) |
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{ |
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for (int j = 0; j < i; j++) |
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{ |
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AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j], |
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seqStrings[j], type); |
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if (as.s1str.length() == 0 || as.s2str.length() == 0) |
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{ |
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continue; |
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} |
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as.calcScoreMatrix(); |
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as.traceAlignment(); |
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if (!first) |
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{ |
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System.out.println(DASHES); |
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textarea.append(DASHES); |
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} |
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first = false; |
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as.printAlignment(System.out); |
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scores[i][j] = as.getMaxScore() |
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/ as.getASeq1().length; |
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totscore = totscore + scores[i][j]; |
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textarea.append(as.getOutput()); |
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sequences.add(as.getAlignedSeq1()); |
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sequences.add(as.getAlignedSeq2()); |
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} |
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} |
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if (count > 2) |
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{ |
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printScoreMatrix(seqs, scores, totscore); |
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} |
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} |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 21 (21) |
Complexity: 5 |
Complexity Density: 0.38 |
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protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,... |
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double totscore) |
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{ |
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System.out |
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.println("Pairwise alignment scaled similarity score matrix\n"); |
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for (int i = 0; i < seqs.length; i++) |
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{ |
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System.out.println(String.format("%3d %s", i + 1, |
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seqs[i].getDisplayId(true))); |
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} |
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System.out.print("\n "); |
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for (int i = 0; i < seqs.length; i++) |
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{ |
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System.out.print(String.format("%7d", i + 1)); |
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} |
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System.out.println(); |
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for (int i = 0; i < seqs.length; i++) |
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{ |
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System.out.print(String.format("%3d", i + 1)); |
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for (int j = 0; j < i; j++) |
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{ |
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System.out.print(String.format("%7.3f", scores[i][j] / totscore)); |
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} |
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System.out.println(); |
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} |
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System.out.println("\n"); |
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} |
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@param |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
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@Override... |
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protected void viewInEditorButton_actionPerformed(ActionEvent e) |
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{ |
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SequenceI[] seq = new SequenceI[sequences.size()]; |
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for (int i = 0; i < sequences.size(); i++) |
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{ |
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seq[i] = sequences.elementAt(i); |
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} |
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AlignFrame af = new AlignFrame(new Alignment(seq), |
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AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
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Desktop.addInternalFrame(af, |
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MessageManager.getString("label.pairwise_aligned_sequences"), |
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AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
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} |
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} |