X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=5e65f1e23ac186f5de13599d194dcddbb5644deb;hb=f4fd7b0e74572c8fddbfe9e3e55bc624f8ba0c6a;hp=65f40c351ca2fd4ba72ddc375feb5a4e3f733bac;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java index 65f40c3..5e65f1e 100755 --- a/src/jalview/appletgui/PairwiseAlignPanel.java +++ b/src/jalview/appletgui/PairwiseAlignPanel.java @@ -1,90 +1,170 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 + * 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 + */ package jalview.appletgui; -import jalview.datamodel.*; -import jalview.jbappletgui.GPairwiseAlignPanel; -import jalview.analysis.*; -import java.awt.event.*; import java.util.*; +import java.awt.event.*; + +import jalview.analysis.*; +import jalview.datamodel.*; +import java.awt.*; -public class PairwiseAlignPanel extends GPairwiseAlignPanel +public class PairwiseAlignPanel + extends Panel implements ActionListener { - Vector sequences = new Vector(); - AlignViewport av; + Vector sequences = new Vector(); + AlignmentPanel ap; - public PairwiseAlignPanel(AlignViewport av) + public PairwiseAlignPanel(AlignmentPanel ap) + { + try { - super(); - this.av = av; - float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()]; - double totscore = 0; - int count = av.getSelectionGroup().getSize(); - - int acount = 0; - for (int i = 1; i < count; i++) - { - for (int j = 0; j < i; j++) - { - acount++; - AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i), - av.getSelectionGroup().getSequenceAt(j),"pep"); + jbInit(); + } + catch (Exception e) + { + e.printStackTrace(); + } + this.ap = ap; + sequences = new Vector(); - as.calcScoreMatrix(); - as.traceAlignment(); - as.printAlignment(); - scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length; - totscore = totscore + scores[i][j]; + SequenceI[] seqs; + String[] seqStrings = ap.av.getViewAsString(true); - textarea.append(as.getOutput()); - sequences.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) ); - sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) ); + if (ap.av.getSelectionGroup() == null) + { + seqs = ap.av.alignment.getSequencesArray(); + } + else + { + seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment); + } + float scores[][] = new float[seqs.length][seqs.length]; + double totscore = 0; + int count = ap.av.getSelectionGroup().getSize(false); - } - } + Sequence seq; + + for (int i = 1; i < count; i++) + { + for (int j = 0; j < i; j++) + { - if (count > 2) + AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], + seqs[j], seqStrings[j], "pep"); + + if (as.s1str.length() == 0 || as.s2str.length() == 0) { - 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); + continue; } + + as.calcScoreMatrix(); + as.traceAlignment(); + + as.printAlignment(System.out); + 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); } + } + if (count > 2) + { + 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()); + } + + System.out.println("\n"); + + 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) + System.out.println("\n"); + } + } + public void actionPerformed(ActionEvent evt) { + if(evt.getSource()==viewInEditorButton) + viewInEditorButton_actionPerformed(); + } - Sequence [] seq = new Sequence[sequences.size()]; + protected void viewInEditorButton_actionPerformed() + { - for (int i=0;i