X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=d0817946f6cccae0b1725ace72a4358f8da85e5d;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=b85cb94a9dc9952fe37c0a0d1598a0c03923fa28;hpb=043de9819c2d780cdfa55dc0e278308e2c97aee1;p=jalview.git diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index b85cb94..d081794 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,73 +1,196 @@ -package jalview.gui; - -import jalview.datamodel.*; -import jalview.jbgui.GPairwiseAlignPanel; -import jalview.analysis.*; -import java.awt.event.*; -import javax.swing.*; -import java.util.*; - - -public class PairwiseAlignPanel extends GPairwiseAlignPanel -{ - Vector sequences = new Vector(); - AlignViewport av; - - public PairwiseAlignPanel(AlignViewport av) - { - super(); - this.av = av; - float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()]; - double totscore = 0; - int count = av.getSelection().size(); - - int acount = 0; - for (int i = 1; i < count; i++) - { - for (int j = 0; j < i; j++) - { - acount++; - AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep"); - - as.calcScoreMatrix(); - as.traceAlignment(); - as.printAlignment(); - scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length; - totscore = totscore + scores[i][j]; - - textarea.append(as.getOutput()); - sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) ); - sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) ); - - - } - } - - 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); - } - } - - - protected void viewInEditorButton_actionPerformed(ActionEvent e) - { - - Sequence [] seq = new Sequence[sequences.size()]; - - for (int i=0;i500) - newHeight=500; - - Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", 700,newHeight); - - } - -} +/* + * 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. + * + * 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.gui; + +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.ActionEvent; +import java.util.Vector; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class PairwiseAlignPanel extends GPairwiseAlignPanel +{ + + private static final String DASHES = "---------------------\n"; + + AlignmentViewport av; + + Vector sequences; + + /** + * Creates a new PairwiseAlignPanel object. + * + * @param viewport + * DOCUMENT ME! + */ + public PairwiseAlignPanel(AlignmentViewport viewport) + { + super(); + this.av = viewport; + + sequences = new Vector(); + + 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()); + + SequenceI[] seqs; + if (isSelection) + { + seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport + .getGapCharacter())[0]; + } + else + { + seqs = av.getAlignment().getSequencesArray(); + } + + String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA + : AlignSeq.PEP; + + float[][] scores = new float[seqs.length][seqs.length]; + double totscore = 0D; + int count = seqs.length; + 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); + + if (as.s1str.length() == 0 || as.s2str.length() == 0) + { + continue; + } + + as.calcScoreMatrix(); + as.traceAlignment(); + + if (!first) + { + System.out.println(DASHES); + textarea.append(DASHES); + } + first = false; + as.printAlignment(System.out); + scores[i][j] = as.getMaxScore() + / as.getASeq1().length; + totscore = totscore + scores[i][j]; + + textarea.append(as.getOutput()); + sequences.add(as.getAlignedSeq1()); + sequences.add(as.getAlignedSeq2()); + } + } + + if (count > 2) + { + printScoreMatrix(seqs, scores, totscore); + } + } + + /** + * 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"); + + 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 < seqs.length; i++) + { + System.out.print(String.format("%3d", i + 1)); + for (int j = 0; j < i; j++) + { + /* + * 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(); + } + + System.out.println("\n"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + @Override + protected void viewInEditorButton_actionPerformed(ActionEvent e) + { + SequenceI[] seq = new SequenceI[sequences.size()]; + + for (int i = 0; i < sequences.size(); i++) + { + seq[i] = sequences.elementAt(i); + } + + AlignFrame af = new AlignFrame(new Alignment(seq), + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + Desktop.addInternalFrame(af, + MessageManager.getString("label.pairwise_aligned_sequences"), + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + } +}