X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=294bb9d3eb18afd6a72c17d29b9f5c983f48efb9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=69789b9c46e499bec5838ecdce516ff1792e115b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 69789b9..294bb9d 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,118 +1,156 @@ -/* - * 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 - */ -package jalview.gui; - -import java.util.*; - -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.jbgui.*; - -public class PairwiseAlignPanel - extends GPairwiseAlignPanel -{ - Vector sequences = new Vector(); - AlignViewport av; - - public PairwiseAlignPanel(AlignViewport av) - { - super(); - this.av = av; - - Vector selsubset = new Vector(); - - for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++) - { - if (av.getAlignment().getSequences().contains(av.getSelectionGroup() - .getSequenceAt(i))) - { - selsubset.add(av.getSelectionGroup().getSequenceAt(i)); - } - } - - float[][] scores = new float[selsubset.size()][selsubset.size()]; - double totscore = 0; - int count = selsubset.size(); - - int acount = 0; - - for (int i = 1; i < count; i++) - { - for (int j = 0; j < i; j++) - { - acount++; - - AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i), - (SequenceI) selsubset.elementAt(j), "pep"); - as.calcScoreMatrix(); - as.traceAlignment(); - as.printAlignment(); - scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length; - totscore = totscore + scores[i][j]; - - textarea.append(as.getOutput()); - sequences.add(new Sequence(as.getS1().getName(), as.getAStr1())); - sequences.add(new Sequence(as.getS2().getName(), as.getAStr2())); - } - } - - 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) + " " + - ( (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"); - } - } - - 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)); - Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", - AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_HEIGHT); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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.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); + } +}