X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=70e68eea770bf2fc884f20e8d8988bf8db13fd20;hb=33b4764ff9d75a0e966c3c8b4b7956f54431221f;hp=cbb3f95d431f3ed2f6fa28ce1be7728793b012b4;hpb=973ebf84c9968d596886729c9b5bfa52b51e3521;p=jalview.git diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index cbb3f95..70e68ee 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -1,13 +1,13 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 @@ -17,30 +17,30 @@ */ package jalview.gui; -import java.util.*; +import jalview.bin.Cache; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.structure.SecondaryStructureListener; +import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.ShiftList; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.Map; import java.util.regex.Matcher; import java.util.regex.Pattern; -import java.awt.*; - -import javax.swing.*; -import javax.swing.event.*; -import java.awt.event.*; -import java.io.*; +import javax.swing.JInternalFrame; +import javax.swing.JSplitPane; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.SequenceStructureBinding; -import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.structure.*; -import jalview.io.*; -import jalview.schemes.*; -import jalview.util.ShiftList; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; -import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener; @@ -48,7 +48,6 @@ import fr.orsay.lri.varna.models.BaseList; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; -import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; import fr.orsay.lri.varna.models.rna.RNA; public class AppVarna extends JInternalFrame implements @@ -73,15 +72,26 @@ public class AppVarna extends JInternalFrame implements AlignmentPanel ap; - public AppVarna(SequenceI seq, String strucseq, String struc, - String name, AlignmentPanel ap) + public AppVarna(String sname, SequenceI seq, String strucseq, + String struc, String name, AlignmentPanel ap) { - this.ap=ap; + System.out.println("je suis là (AppVarna!!"); + System.out.println("1:"+sname); + System.out.println("2:"+seq); + System.out.println("3:"+strucseq); + System.out.println("4:"+struc); + System.out.println("5:"+name); + System.out.println("6:"+ap); + this.ap = ap; ArrayList rnaList = new ArrayList(); RNA rna1 = new RNA(name); try { + System.out.println("ou ici ?"); rna1.setRNA(strucseq, replaceOddGaps(struc)); + System.out.println("La séquence est :"+rna1.getSeq()); + System.out.println("La séquence est :"+struc); + System.out.println("La séquence est :"+replaceOddGaps(struc).toString()); } catch (ExceptionUnmatchedClosingParentheses e2) { e2.printStackTrace(); @@ -89,17 +99,18 @@ public class AppVarna extends JInternalFrame implements { e3.printStackTrace(); } - RNA trim = trimRNA(rna1); + RNA trim = trimRNA(rna1, "trimmed " + sname); rnaList.add(trim); rnaList.add(rna1); + rnas.put(seq, rna1); rnas.put(seq, trim); - rna1.setName("consensus_" + rna1.getName()); + rna1.setName(sname + " (with gaps)"); { seqs.put(trim, seq); seqs.put(rna1, seq); - + /** * if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList * shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift, @@ -110,15 +121,18 @@ public class AppVarna extends JInternalFrame implements vab = new AppVarnaBinding(rnaList); // vab = new AppVarnaBinding(seq,struc); // System.out.println("Hallo: "+name); - this.name = name; + this.name = sname + " trimmed to " + name; initVarna(); + ssm = ap.getStructureSelectionManager(); + System.out.println(ssm.toString()); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } public void initVarna() { + System.out.println("initialisation VANRA"); // vab.setFinishedInit(false); varnaPanel = vab.get_varnaPanel(); setBackground(Color.white); @@ -133,6 +147,7 @@ public class AppVarna extends JInternalFrame implements getBounds().width, getBounds().height); this.pack(); showPanel(true); + System.out.println("Sortie initialisation VANRA"); } public String replaceOddGaps(String oldStr) @@ -145,10 +160,11 @@ public class AppVarna extends JInternalFrame implements return newStr; } - public RNA trimRNA(RNA rna) + public RNA trimRNA(RNA rna, String name) { ShiftList offset = new ShiftList(); - RNA rnaTrim = new RNA("trim_" + rna.getName()); + + RNA rnaTrim = new RNA(name); try { rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN())); @@ -304,12 +320,13 @@ public class AppVarna extends JInternalFrame implements if (_lastRNAhighlighted != null) { _lastRNAhighlighted.removeHighlightRegion(_lastHighlight); - if (vab!=null) { + if (vab != null) + { vab.updateSelectedRNA(_lastRNAhighlighted); } _lastRNAhighlighted = null; _lastHighlight = null; - + } } } @@ -332,9 +349,9 @@ public class AppVarna extends JInternalFrame implements ShiftList shift = offsets.get(rna); if (shift != null) { - // System.err.print("Orig pos:"+index); - index = shift.shift(index); - // System.err.println("\nFinal pos:"+index); + // System.err.print("Orig pos:"+index); + index = shift.shift(index); + // System.err.println("\nFinal pos:"+index); } mouseOverHighlighter.highlightRegion(rna, index, index); vab.updateSelectedRNA(rna); @@ -391,7 +408,7 @@ public class AppVarna extends JInternalFrame implements if (shift != null) { int i = shift.shift(arg1.getIndex()); - // System.err.println("shifted "+(arg1.getIndex())+" to "+i); + // System.err.println("shifted "+(arg1.getIndex())+" to "+i); ssm.mouseOverVamsasSequence(seq, i, this); } else @@ -404,7 +421,22 @@ public class AppVarna extends JInternalFrame implements @Override public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2) { - // TODO translate selected regions in VARNA to a selection on the alignpanel. + // TODO translate selected regions in VARNA to a selection on the + // alignpanel. + + } + + @Override + public void onTranslationChanged() + { + // TODO Auto-generated method stub + + } + + @Override + public void onZoomLevelChanged() + { + // TODO Auto-generated method stub }