X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=d25cf7fcb2f6f5851acb5c46ec37a89513f14808;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=d0b0c986e7bae3c1c8f2b1df8b8a3380830f0d55;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java old mode 100755 new mode 100644 index d0b0c98..d25cf7f --- a/src/jalview/appletgui/PairwiseAlignPanel.java +++ b/src/jalview/appletgui/PairwiseAlignPanel.java @@ -1,140 +1,177 @@ -/* - * 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.appletgui; - -import java.util.*; - -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import java.awt.*; - -public class PairwiseAlignPanel - extends Panel implements ActionListener -{ - Vector sequences = new Vector(); - AlignmentPanel ap; - - public PairwiseAlignPanel(AlignmentPanel ap) - { - try - { - jbInit(); - } - catch (Exception e) - { - e.printStackTrace(); - } - this.ap = ap; - float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment. - getHeight()]; - double totscore = 0; - int count = ap.av.getSelectionGroup().getSize(false); - - int acount = 0; - Sequence seq; - for (int i = 1; i < count; i++) - { - for (int j = 0; j < i; j++) - { - acount++; - AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i), - ap.av.getSelectionGroup().getSequenceAt(j), - "pep"); - - 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.addElement(seq); - - seq = new Sequence(as.getS2().getName(), - as.getAStr2(), - as.getS2().getStart(), as.getS2().getEnd() - ); - - sequences.addElement(seq); - } - } - - if (count > 2) - { - 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); - } - } - } - } - - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==viewInEditorButton) - viewInEditorButton_actionPerformed(); - } - - protected void viewInEditorButton_actionPerformed() - { - - Sequence[] seq = new Sequence[sequences.size()]; - - for (int i = 0; i < sequences.size(); i++) - { - seq[i] = (Sequence) sequences.elementAt(i); - } - - new AlignFrame(new Alignment(seq), - ap.alignFrame.applet, - "Pairwise Aligned Sequences", - false); - - } - protected ScrollPane scrollPane = new ScrollPane(); - protected TextArea textarea = new TextArea(); - protected Button viewInEditorButton = new Button(); - Panel jPanel1 = new Panel(); - BorderLayout borderLayout1 = new BorderLayout(); - - private void jbInit() throws Exception { - this.setLayout(borderLayout1); - textarea.setFont(new java.awt.Font("Monospaced", 0, 12)); - textarea.setText(""); - viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12)); - viewInEditorButton.setLabel("View in alignment editor"); - viewInEditorButton.addActionListener(this); - this.add(scrollPane, BorderLayout.CENTER); - scrollPane.add(textarea); - this.add(jPanel1, BorderLayout.SOUTH); - jPanel1.add(viewInEditorButton, null); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * 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.appletgui; + +import jalview.analysis.AlignSeq; +import jalview.datamodel.Alignment; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Panel; +import java.awt.ScrollPane; +import java.awt.TextArea; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Vector; + +public class PairwiseAlignPanel extends Panel implements ActionListener +{ + Vector sequences = new Vector(); + + AlignmentPanel ap; + + public PairwiseAlignPanel(AlignmentPanel ap) + { + try + { + jbInit(); + } catch (Exception e) + { + e.printStackTrace(); + } + this.ap = ap; + sequences = new Vector(); + + SequenceI[] seqs; + String[] seqStrings = ap.av.getViewAsString(true); + + if (ap.av.getSelectionGroup() == null) + { + seqs = ap.av.getAlignment().getSequencesArray(); + } + else + { + seqs = ap.av.getSelectionGroup().getSequencesInOrder( + ap.av.getAlignment()); + } + + float scores[][] = new float[seqs.length][seqs.length]; + double totscore = 0; + int count = ap.av.getSelectionGroup().getSize(); + String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA + : AlignSeq.PEP; + 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.getAlignedSeq1()); + } + } + + 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"); + } + } + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == viewInEditorButton) + { + viewInEditorButton_actionPerformed(); + } + } + + protected void viewInEditorButton_actionPerformed() + { + + Sequence[] seq = new Sequence[sequences.size()]; + + for (int i = 0; i < sequences.size(); i++) + { + seq[i] = (Sequence) sequences.elementAt(i); + } + + new AlignFrame(new Alignment(seq), ap.av.applet, + "Pairwise Aligned Sequences", false); + + } + + protected ScrollPane scrollPane = new ScrollPane(); + + protected TextArea textarea = new TextArea(); + + protected Button viewInEditorButton = new Button(); + + Panel jPanel1 = new Panel(); + + BorderLayout borderLayout1 = new BorderLayout(); + + private void jbInit() throws Exception + { + this.setLayout(borderLayout1); + textarea.setFont(new java.awt.Font("Monospaced", 0, 12)); + textarea.setText(""); + viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12)); + viewInEditorButton.setLabel(MessageManager + .getString("label.view_alignment_editor")); + viewInEditorButton.addActionListener(this); + this.add(scrollPane, BorderLayout.CENTER); + scrollPane.add(textarea); + this.add(jPanel1, BorderLayout.SOUTH); + jPanel1.add(viewInEditorButton, null); + } + +}