X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=354d8bfdc0dc9eabe9f5e521d9eb4da27f32838c;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=480f719283bd3f63da9d9d5efd027156ffbec2bb;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java index 480f719..354d8bf 100755 --- a/src/jalview/appletgui/PairwiseAlignPanel.java +++ b/src/jalview/appletgui/PairwiseAlignPanel.java @@ -1,36 +1,34 @@ /* - * 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . */ - package jalview.appletgui; import java.util.*; +import java.awt.*; import java.awt.event.*; import jalview.analysis.*; import jalview.datamodel.*; -import java.awt.*; -public class PairwiseAlignPanel - extends Panel implements ActionListener +public class PairwiseAlignPanel extends Panel implements ActionListener { Vector sequences = new Vector(); + AlignmentPanel ap; public PairwiseAlignPanel(AlignmentPanel ap) @@ -38,8 +36,7 @@ public class PairwiseAlignPanel try { jbInit(); - } - catch (Exception e) + } catch (Exception e) { e.printStackTrace(); } @@ -61,7 +58,8 @@ public class PairwiseAlignPanel float scores[][] = new float[seqs.length][seqs.length]; double totscore = 0; int count = ap.av.getSelectionGroup().getSize(); - String type=(ap.av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP; + String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA + : AlignSeq.PEP; Sequence seq; for (int i = 1; i < count; i++) @@ -69,8 +67,8 @@ 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 +79,30 @@ 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() - ); + 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()); + seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2() + .getStart(), as.getS2().getEnd()); sequences.addElement(seq); } } 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 +111,21 @@ 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 +138,33 @@ 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("View in alignment editor"); + viewInEditorButton.addActionListener(this); + this.add(scrollPane, BorderLayout.CENTER); + scrollPane.add(textarea); + this.add(jPanel1, BorderLayout.SOUTH); + jPanel1.add(viewInEditorButton, null); } }