X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=f237e72a8eb5aad0860536a47252fd16dd321382;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=30effb79fdb3779ca9055a14d8efc181744883fe;hpb=a442f71fc61f1b8b41cedd2c2fd78a5c5323bafb;p=jalview.git diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 30effb7..f237e72 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,161 +1,155 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import jalview.analysis.*; +import java.util.*; +import java.awt.event.*; +import jalview.analysis.*; import jalview.datamodel.*; - import jalview.jbgui.*; - -import java.awt.event.*; - -import java.util.*; - +import jalview.util.MessageManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public class PairwiseAlignPanel extends GPairwiseAlignPanel { - AlignViewport av; - Vector sequences; + AlignViewport av; + + Vector sequences; + + /** + * Creates a new PairwiseAlignPanel object. + * + * @param av + * DOCUMENT ME! + */ + public PairwiseAlignPanel(AlignViewport av) + { + super(); + this.av = av; + + sequences = new Vector(); + + SequenceI[] seqs; + String[] seqStrings = av.getViewAsString(true); - /** - * Creates a new PairwiseAlignPanel object. - * - * @param av DOCUMENT ME! - */ - public PairwiseAlignPanel(AlignViewport av) + if (av.getSelectionGroup() == null) { - super(); - this.av = av; + seqs = av.getAlignment().getSequencesArray(); + } + else + { + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); + } - sequences = new Vector(); + String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA + : AlignSeq.PEP; - SequenceI [] seqs; - String [] seqStrings = av.getViewAsString(true); + float[][] scores = new float[seqs.length][seqs.length]; + double totscore = 0; + int count = seqs.length; - if(av.getSelectionGroup()==null) - { - seqs = av.alignment.getSequencesArray(); - } - else - { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); - } + Sequence seq; - String type=(av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP; - - float[][] scores = new float[seqs.length][seqs.length]; - double totscore = 0; - int count = seqs.length; + for (int i = 1; i < count; i++) + { + for (int j = 0; j < i; j++) + { - Sequence seq; + 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) - { - 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"); - } + 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); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void viewInEditorButton_actionPerformed(ActionEvent e) + if (count > 2) { - Sequence[] seq = new Sequence[sequences.size()]; + System.out + .println("Pairwise alignment scaled similarity score matrix\n"); - for (int i = 0; i < sequences.size(); i++) + 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++) { - seq[i] = (Sequence) sequences.elementAt(i); + 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); + 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); - } + } }