X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=5a3b56ccfe89dbed062b072212f6e6489d47a927;hb=2273eba5668e5340354da60fed329c6c716cc439;hp=792c906ec411d6943b7e9ada626eb7c7180e55c5;hpb=a442f71fc61f1b8b41cedd2c2fd78a5c5323bafb;p=jalview.git diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java old mode 100755 new mode 100644 index 792c906..5a3b56c --- a/src/jalview/appletgui/PairwiseAlignPanel.java +++ b/src/jalview/appletgui/PairwiseAlignPanel.java @@ -1,36 +1,44 @@ /* - * 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 + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ - 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 +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) @@ -38,8 +46,7 @@ public class PairwiseAlignPanel try { jbInit(); - } - catch (Exception e) + } catch (Exception e) { e.printStackTrace(); } @@ -51,17 +58,19 @@ public class PairwiseAlignPanel if (ap.av.getSelectionGroup() == null) { - seqs = ap.av.alignment.getSequencesArray(); + seqs = ap.av.getAlignment().getSequencesArray(); } else { - seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment); + 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(false); - String type=(ap.av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP; + 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++) @@ -69,8 +78,8 @@ public class PairwiseAlignPanel for (int j = 0; j < i; j++) { - AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], - seqs[j], seqStrings[j], type); + AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j], + seqStrings[j], type); if (as.s1str.length() == 0 || as.s2str.length() == 0) { @@ -81,35 +90,25 @@ public class PairwiseAlignPanel as.traceAlignment(); as.printAlignment(System.out); - scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length; + 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); + sequences.add(as.getAlignedSeq1()); + sequences.add(as.getAlignedSeq1()); } } if (count > 2) { - System.out.println( - "Pairwise alignment scaled similarity score matrix\n"); + 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()); + jalview.util.Format.print(System.out, "%s \n", ("" + i) + " " + + seqs[i].getName()); } System.out.println("\n"); @@ -118,18 +117,21 @@ public class PairwiseAlignPanel { for (int j = 0; j < i; j++) { - jalview.util.Format.print(System.out, "%7.3f", - scores[i][j] / totscore); + 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) + if (evt.getSource() == viewInEditorButton) + { viewInEditorButton_actionPerformed(); + } } protected void viewInEditorButton_actionPerformed() @@ -142,29 +144,34 @@ public class PairwiseAlignPanel seq[i] = (Sequence) sequences.elementAt(i); } - new AlignFrame(new Alignment(seq), - ap.av.applet, - "Pairwise Aligned Sequences", - false); + 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("View in alignment editor"); - viewInEditorButton.addActionListener(this); - this.add(scrollPane, BorderLayout.CENTER); - scrollPane.add(textarea); - this.add(jPanel1, BorderLayout.SOUTH); - jPanel1.add(viewInEditorButton, null); + 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); } }