/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
* 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.
- *
+ *
+ * Jalview 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import java.awt.event.*;
-
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.MessageManager;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
- AlignViewport av;
- Vector sequences;
+ private static final String DASHES = "---------------------\n";
- /**
- * Creates a new PairwiseAlignPanel object.
- *
- * @param av DOCUMENT ME!
- */
- public PairwiseAlignPanel(AlignViewport av)
- {
- super();
- this.av = av;
+ AlignViewportI av;
- sequences = new Vector();
+ Vector<SequenceI> sequences;
- SequenceI [] seqs;
- String [] seqStrings = av.getViewAsString(true);
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param viewport
+ */
+ public PairwiseAlignPanel(AlignViewportI viewport)
+ {
+ super();
+ this.av = viewport;
- if(av.getSelectionGroup()==null)
- {
- seqs = av.alignment.getSequencesArray();
- }
- else
- {
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
- }
+ sequences = new Vector<>();
+
+ SequenceGroup selectionGroup = viewport.getSelectionGroup();
+ boolean isSelection = selectionGroup != null
+ && selectionGroup.getSize() > 0;
+ AlignmentView view = viewport.getAlignmentView(isSelection);
+ // String[] seqStrings = viewport.getViewAsString(true);
+ String[] seqStrings = view.getSequenceStrings(viewport
+ .getGapCharacter());
+
+ SequenceI[] seqs;
+ if (isSelection)
+ {
+ seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
+ .getGapCharacter())[0];
+ }
+ else
+ {
+ seqs = av.getAlignment().getSequencesArray();
+ }
+
+ String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
+ : AlignSeq.PEP;
- String type=(av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
-
- float[][] scores = new float[seqs.length][seqs.length];
- double totscore = 0;
- int count = seqs.length;
+ float[][] scores = new float[seqs.length][seqs.length];
+ double totscore = 0D;
+ int count = seqs.length;
+ boolean first = true;
- Sequence seq;
+ for (int i = 1; i < count; i++)
+ {
+ for (int j = 0; j < i; j++)
+ {
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+ seqStrings[j], type);
- for (int i = 1; i < count; i++)
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
- for (int j = 0; j < i; j++)
- {
-
- AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
- seqs[j], seqStrings[j], type);
-
- if(as.s1str.length()==0 || as.s2str.length()==0)
- {
- continue;
- }
-
- as.calcScoreMatrix();
- as.traceAlignment();
-
-
- as.printAlignment(System.out);
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
- totscore = totscore + scores[i][j];
-
- textarea.append(as.getOutput());
- seq = new Sequence(as.getS1().getName(),
- as.getAStr1(),
- as.getS1().getStart(),
- as.getS1().getEnd()
- );
- sequences.add(seq);
-
- seq = new Sequence(as.getS2().getName(),
- as.getAStr2(),
- as.getS2().getStart(),
- as.getS2().getEnd() );
- sequences.add(seq);
- }
+ continue;
}
- if (count > 2)
+ as.calcScoreMatrix();
+ as.traceAlignment();
+
+ if (!first)
{
- System.out.println(
- "Pairwise alignment scaled similarity score matrix\n");
-
- for (int i = 0; i < count; i++)
- {
- jalview.util.Format.print(System.out, "%s \n",
- ("" + i) + " " +
- seqs[i].getName());
- }
-
- System.out.println("\n");
-
- for (int i = 0; i < count; i++)
- {
- for (int j = 0; j < i; j++)
- {
- jalview.util.Format.print(System.out, "%7.3f",
- scores[i][j] / totscore);
- }
- }
-
- System.out.println("\n");
+ System.out.println(DASHES);
+ textarea.append(DASHES);
}
+ first = false;
+ as.printAlignment(System.out);
+ scores[i][j] = as.getMaxScore()
+ / as.getASeq1().length;
+ totscore = totscore + scores[i][j];
+
+ textarea.append(as.getOutput());
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ if (count > 2)
+ {
+ printScoreMatrix(seqs, scores, totscore);
+ }
+ }
+
+ /**
+ * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
+ *
+ * @param seqs
+ * @param scores
+ * @param totscore
+ */
+ protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
+ double totscore)
+ {
+ System.out
+ .println("Pairwise alignment scaled similarity score matrix\n");
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ System.out.println(String.format("%3d %s", i + 1,
+ seqs[i].getDisplayId(true)));
+ }
+
+ /*
+ * table heading columns for sequences 1, 2, 3...
*/
- protected void viewInEditorButton_actionPerformed(ActionEvent e)
+ System.out.print("\n ");
+ for (int i = 0; i < seqs.length; i++)
{
- Sequence[] seq = new Sequence[sequences.size()];
+ System.out.print(String.format("%7d", i + 1));
+ }
+ System.out.println();
- for (int i = 0; i < sequences.size(); i++)
- {
- seq[i] = (Sequence) sequences.elementAt(i);
- }
+ for (int i = 0; i < seqs.length; i++)
+ {
+ System.out.print(String.format("%3d", i + 1));
+ for (int j = 0; j < i; j++)
+ {
+ /*
+ * as a fraction of tot score, outputs are 0 <= score <= 1
+ */
+ System.out.print(String.format("%7.3f", scores[i][j] / totscore));
+ }
+ System.out.println();
+ }
+
+ System.out.println("\n");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void viewInEditorButton_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] seq = new SequenceI[sequences.size()];
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seq[i] = sequences.elementAt(i);
+ }
- AlignFrame af = new AlignFrame(new Alignment(seq),
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(new Alignment(seq),
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+ Desktop.addInternalFrame(af,
+ MessageManager.getString("label.pairwise_aligned_sequences"),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- }
+ }
}
git://source.jalview.org / jalview.git / blobdiff