-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PairwiseAlignPanel extends GPairwiseAlignPanel\r
-{\r
- Vector sequences = new Vector();\r
- AlignViewport av;\r
-\r
- /**\r
- * Creates a new PairwiseAlignPanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public PairwiseAlignPanel(AlignViewport av)\r
- {\r
- super();\r
- this.av = av;\r
-\r
- Vector selsubset = new Vector();\r
-\r
- for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)\r
- {\r
- if (av.getAlignment().getSequences().contains(av.getSelectionGroup()\r
- .getSequenceAt(i)))\r
- {\r
- selsubset.add(av.getSelectionGroup().getSequenceAt(i));\r
- }\r
- }\r
-\r
- float[][] scores = new float[selsubset.size()][selsubset.size()];\r
- double totscore = 0;\r
- int count = selsubset.size();\r
-\r
- int acount = 0;\r
-\r
- for (int i = 1; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- acount++;\r
-\r
- AlignSeq as = new AlignSeq((SequenceI) selsubset.elementAt(i),\r
- (SequenceI) selsubset.elementAt(j), "pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
- totscore = totscore + scores[i][j];\r
-\r
- textarea.append(as.getOutput());\r
- sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
- sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
- }\r
- }\r
-\r
- if (count > 2)\r
- {\r
- System.out.println(\r
- "Pairwise alignment scaled similarity score matrix\n");\r
-\r
- for (int i = 0; i < count; i++)\r
- {\r
- jalview.util.Format.print(System.out, "%s \n",\r
- ("" + i) + " " +\r
- ((SequenceI) selsubset.elementAt(i)).getName());\r
- }\r
-\r
- System.out.println("\n");\r
-\r
- for (int i = 0; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- jalview.util.Format.print(System.out, "%7.3f",\r
- scores[i][j] / totscore);\r
- }\r
- }\r
-\r
- System.out.println("\n");\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
- {\r
- Sequence[] seq = new Sequence[sequences.size()];\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- seq[i] = (Sequence) sequences.elementAt(i);\r
- }\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(seq));\r
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
- AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
+{
+
+ AlignmentViewport av;
+
+ Vector sequences;
+
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public PairwiseAlignPanel(AlignmentViewport av)
+ {
+ super();
+ this.av = av;
+
+ sequences = new Vector();
+
+ SequenceI[] seqs;
+ String[] seqStrings = av.getViewAsString(true);
+
+ if (av.getSelectionGroup() == null)
+ {
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ }
+
+ String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
+ : AlignSeq.PEP;
+
+ float[][] scores = new float[seqs.length][seqs.length];
+ double totscore = 0;
+ int count = seqs.length;
+
+ 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);
+
+ 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());
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
+ }
+ }
+
+ if (count > 2)
+ {
+ 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");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void viewInEditorButton_actionPerformed(ActionEvent e)
+ {
+ Sequence[] seq = new Sequence[sequences.size()];
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seq[i] = (Sequence) sequences.elementAt(i);
+ }
+
+ AlignFrame af = new AlignFrame(new Alignment(seq),
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ Desktop.addInternalFrame(af,
+ MessageManager.getString("label.pairwise_aligned_sequences"),
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff