X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=c4b53675abfa3830ed371f5826ebe175d5207ba6;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=190dcb059c3afbe04efb6927fc9fbc594fc0dcc9;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 190dcb0..c4b5367 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,83 +1,98 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.AlignmentView; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GPairwiseAlignPanel; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; -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; + private static final String DASHES = "---------------------\n"; + + AlignmentViewport av; + + Vector sequences; /** * Creates a new PairwiseAlignPanel object. - * - * @param av DOCUMENT ME! + * + * @param viewport + * DOCUMENT ME! */ - public PairwiseAlignPanel(AlignViewport av) + public PairwiseAlignPanel(AlignmentViewport viewport) { super(); - this.av = av; + this.av = viewport; - sequences = new Vector(); + sequences = new Vector(); - SequenceI[] seqs; - String[] seqStrings = av.getViewAsString(true); + SequenceGroup selectionGroup = viewport.getSelectionGroup(); + boolean isSelection = selectionGroup != null + && selectionGroup.getSize() > 0; + AlignmentView view = viewport.getAlignmentView(isSelection); + // String[] seqStrings = viewport.getViewAsString(true); + String[] seqStrings = view + .getSequenceStrings(viewport.getGapCharacter()); - if (av.getSelectionGroup() == null) + SequenceI[] seqs; + if (isSelection) { - seqs = av.alignment.getSequencesArray(); + seqs = (SequenceI[]) view + .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0]; } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = av.getAlignment().getSequencesArray(); } - String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP; + String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA + : AlignSeq.PEP; float[][] scores = new float[seqs.length][seqs.length]; - double totscore = 0; + double totscore = 0D; int count = seqs.length; - - Sequence seq; + boolean first = true; 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); + AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j], + seqStrings[j], type); if (as.s1str.length() == 0 || as.s2str.length() == 0) { @@ -87,73 +102,94 @@ public class PairwiseAlignPanel as.calcScoreMatrix(); as.traceAlignment(); + if (!first) + { + System.out.println(DASHES); + textarea.append(DASHES); + } + first = false; as.printAlignment(System.out); - scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length; + scores[i][j] = as.getMaxScore() / 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"); + printScoreMatrix(seqs, scores, totscore); + } + } - for (int i = 0; i < count; i++) - { - jalview.util.Format.print(System.out, "%s \n", - ("" + i) + " " + - seqs[i].getName()); - } + /** + * Prints a matrix of seqi-seqj pairwise alignment scores to sysout + * + * @param seqs + * @param scores + * @param totscore + */ + protected void printScoreMatrix(SequenceI[] seqs, float[][] scores, + double totscore) + { + System.out + .println("Pairwise alignment scaled similarity score matrix\n"); - System.out.println("\n"); + for (int i = 0; i < seqs.length; i++) + { + System.out.println( + String.format("%3d %s", i + 1, seqs[i].getDisplayId(true))); + } + + /* + * table heading columns for sequences 1, 2, 3... + */ + System.out.print("\n "); + for (int i = 0; i < seqs.length; i++) + { + System.out.print(String.format("%7d", i + 1)); + } + System.out.println(); - for (int i = 0; i < count; i++) + for (int i = 0; i < seqs.length; i++) + { + System.out.print(String.format("%3d", i + 1)); + for (int j = 0; j < i; j++) { - for (int j = 0; j < i; j++) - { - jalview.util.Format.print(System.out, "%7.3f", - scores[i][j] / totscore); - } + /* + * as a fraction of tot score, outputs are 0 <= score <= 1 + */ + System.out.print(String.format("%7.3f", scores[i][j] / totscore)); } - - System.out.println("\n"); + System.out.println(); } + + System.out.println("\n"); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void viewInEditorButton_actionPerformed(ActionEvent e) { - Sequence[] seq = new Sequence[sequences.size()]; + SequenceI[] seq = new SequenceI[sequences.size()]; for (int i = 0; i < sequences.size(); i++) { - seq[i] = (Sequence) sequences.elementAt(i); + seq[i] = sequences.elementAt(i); } 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); } }