X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=248a54c4ba013bb37b28942ab6bd2b654341e975;hb=4ef2163fcc47ef807e841fd21949e63c54f8bb11;hp=28254671cd7299834066912e7b1026ced2780b06;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 2825467..248a54c 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,98 +1,160 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -* 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. -* -* 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 -*/ - + * 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 + * 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. + * + * 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 + */ package jalview.gui; -import jalview.datamodel.*; -import jalview.jbgui.GPairwiseAlignPanel; import jalview.analysis.*; + +import jalview.datamodel.*; + +import jalview.jbgui.*; + import java.awt.event.*; -import javax.swing.*; + import java.util.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class PairwiseAlignPanel extends GPairwiseAlignPanel { - Vector sequences = new Vector(); + AlignViewport av; + Vector sequences; + /** + * Creates a new PairwiseAlignPanel object. + * + * @param av DOCUMENT ME! + */ public PairwiseAlignPanel(AlignViewport av) { - super(); - this.av = av; - Vector selsubset = new Vector(); - for (int i=0, j=av.getSelectionGroup().getSize(); i 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)+" "+((SequenceI) selsubset.elementAt(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"); - - } - } + else + { + seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + } + + float[][] scores = new float[seqs.length][seqs.length]; + double totscore = 0; + int count = seqs.length; - protected void viewInEditorButton_actionPerformed(ActionEvent e) - { + Sequence seq; - Sequence [] seq = new Sequence[sequences.size()]; + 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], "pep"); + + 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); + } + } - for (int i=0;i 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()]; - AlignFrame af = new AlignFrame(new Alignment(seq)); - Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", - AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_HEIGHT); + 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, "Pairwise Aligned Sequences", + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + } }