X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=65e17442e4ad6a5010237b038c88458e3ae86761;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=190dcb059c3afbe04efb6927fc9fbc594fc0dcc9;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 190dcb0..65e1744 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,48 +1,53 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 2.8.2b1) + * 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.gui; -import java.util.*; +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 java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.jbgui.*; +import java.awt.event.ActionEvent; +import java.util.Vector; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class PairwiseAlignPanel - extends GPairwiseAlignPanel +public class PairwiseAlignPanel extends GPairwiseAlignPanel { AlignViewport av; + Vector sequences; /** * Creates a new PairwiseAlignPanel object. - * - * @param av DOCUMENT ME! + * + * @param av + * DOCUMENT ME! */ public PairwiseAlignPanel(AlignViewport av) { @@ -56,14 +61,15 @@ public class PairwiseAlignPanel if (av.getSelectionGroup() == null) { - seqs = av.alignment.getSequencesArray(); + seqs = av.getAlignment().getSequencesArray(); } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } - String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP; + String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA + : AlignSeq.PEP; float[][] scores = new float[seqs.length][seqs.length]; double totscore = 0; @@ -76,8 +82,8 @@ 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) { @@ -88,35 +94,25 @@ 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.add(seq); - - seq = new Sequence(as.getS2().getName(), - as.getAStr2(), - as.getS2().getStart(), - as.getS2().getEnd()); - sequences.add(seq); + sequences.add(as.getAlignedSeq1()); + sequences.add(as.getAlignedSeq2()); } } 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"); @@ -125,8 +121,8 @@ 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); } } @@ -136,8 +132,9 @@ public class PairwiseAlignPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void viewInEditorButton_actionPerformed(ActionEvent e) { @@ -149,11 +146,10 @@ public class PairwiseAlignPanel } AlignFrame af = new AlignFrame(new Alignment(seq), - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, + MessageManager.getString("label.pairwise_aligned_sequences"), + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } }