X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=00670aa98d6f4fa59f5901604d5cd65b59b7da38;hb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;hp=d0173d064701d3fee17a3a0873e4e6ef6cc5de47;hpb=320535ad94888c5397646cb942001086540f8939;p=jalview.git diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index d0173d0..00670aa 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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 * * This file is part of Jalview. * @@ -18,13 +18,18 @@ package jalview.gui; import java.util.*; +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 jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; import jalview.datamodel.*; @@ -32,55 +37,396 @@ 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; +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 Runnable,SequenceStructureBinding, ViewSetProvider +public class AppVarna extends JInternalFrame implements + InterfaceVARNAListener, SelectionListener, + SecondaryStructureListener// implements + // Runnable,SequenceStructureBinding, + // ViewSetProvider + , InterfaceVARNASelectionListener, VamsasSource { AppVarnaBinding vab; - JPanel scriptWindow; + VARNAPanel varnaPanel; + + public String name; - JSplitPane splitPane; + public StructureSelectionManager ssm; - //RenderPanel renderPanel; + /* + * public AppVarna(){ vab = new AppVarnaBinding(); initVarna(); } + */ AlignmentPanel ap; - Vector atomsPicked = new Vector(); - - public AppVarna(){ - initVarna(); + public AppVarna(String sname, SequenceI seq, String strucseq, String struc, + String name, AlignmentPanel 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(); + } catch (ExceptionFileFormatOrSyntax e3) + { + e3.printStackTrace(); + } + + RNA trim = trimRNA(rna1, "trimmed "+sname); + rnaList.add(trim); + rnaList.add(rna1); + + rnas.put(seq, rna1); + rnas.put(seq, trim); + + 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, + * shift=new ShiftList());} shift.addShift(1, seq.getStart()-1); + * offsetsInv.put(rshift, shift.getInverse()); } } + **/ + } + vab = new AppVarnaBinding(rnaList); + // vab = new AppVarnaBinding(seq,struc); + // System.out.println("Hallo: "+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); + JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true, + vab.getListPanel(), varnaPanel); + getContentPane().setLayout(new BorderLayout()); + getContentPane().add(split, BorderLayout.CENTER); + // getContentPane().add(vab.getTools(), BorderLayout.NORTH); + varnaPanel.addVARNAListener(this); + varnaPanel.addSelectionListener(this); + jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name, + getBounds().width, getBounds().height); + this.pack(); + showPanel(true); + System.out.println("Sortie initialisation VANRA"); + } + + public String replaceOddGaps(String oldStr) + { + String patternStr = "[^([{<>}])]"; + String replacementStr = "."; + Pattern pattern = Pattern.compile(patternStr); + Matcher matcher = pattern.matcher(oldStr); + String newStr = matcher.replaceAll(replacementStr); + return newStr; + } + + public RNA trimRNA(RNA rna, String name) + { + ShiftList offset = new ShiftList(); + + RNA rnaTrim = new RNA(name); + try + { + rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN())); + } catch (ExceptionUnmatchedClosingParentheses e2) + { + e2.printStackTrace(); + } catch (ExceptionFileFormatOrSyntax e3) + { + e3.printStackTrace(); + } + + StringBuffer seq = new StringBuffer(rnaTrim.getSeq()); + StringBuffer struc = new StringBuffer(rnaTrim.getStructDBN()); + int ofstart = -1, sleng = rnaTrim.getSeq().length(); + for (int i = 0; i < sleng; i++) + { + // TODO: Jalview utility for gap detection java.utils.isGap() + // TODO: Switch to jalview rna datamodel + if (jalview.util.Comparison.isGap(seq.charAt(i))) + { + if (ofstart == -1) + { + ofstart = i; + } + if (!rnaTrim.findPair(i).isEmpty()) + { + int m = rnaTrim.findPair(i).get(1); + int l = rnaTrim.findPair(i).get(0); + + struc.replace(m, m + 1, "*"); + struc.replace(l, l + 1, "*"); + } + else + { + struc.replace(i, i + 1, "*"); + } + } + else + { + if (ofstart > -1) + { + offset.addShift(offset.shift(ofstart), ofstart - i); + ofstart = -1; + } + } + } + // final gap + if (ofstart > -1) + { + offset.addShift(offset.shift(ofstart), ofstart - sleng); + ofstart = -1; + } + String newSeq = rnaTrim.getSeq().replace("-", ""); + rnaTrim.getSeq().replace(".", ""); + String newStruc = struc.toString().replace("*", ""); + + try + { + rnaTrim.setRNA(newSeq, newStruc); + registerOffset(rnaTrim, offset); + } catch (ExceptionUnmatchedClosingParentheses e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } catch (ExceptionFileFormatOrSyntax e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + return rnaTrim; + } + + // needs to be many-many + Map seqs = new Hashtable(); + + Map rnas = new Hashtable(); + + Map offsets = new Hashtable(); + + Map offsetsInv = new Hashtable(); + + private void registerOffset(RNA rnaTrim, ShiftList offset) + { + offsets.put(rnaTrim, offset); + offsetsInv.put(rnaTrim, offset.getInverse()); } - - public void initVarna(){ - //vab.setFinishedInit(false); - //renderPanel = new RenderPanel(); - // TODO: consider waiting until the structure/view is fully loaded before - // displaying - //this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); - //jalview.gui.Desktop.addInternalFrame(this,"test",300,300); - AppVarnaBinding d = new AppVarnaBinding(); - d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - d.pack(); - d.setVisible(true); + + public void showPanel(boolean show) + { + this.setVisible(show); } - + private boolean _started = false; - public void run(){ - _started = true; - - try + public void run() + { + _started = true; + + try + { + initVarna(); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("When trying to open the Varna viewer!", oomerror); + } catch (Exception ex) + { + Cache.log.error("Couldn't open Varna viewer!", ex); + } + } + + @Override + public void onUINewStructure(VARNAConfig v, RNA r) + { + + } + + @Override + public void onWarningEmitted(String s) + { + // TODO Auto-generated method stub + + } + + private class VarnaHighlighter + { + private HighlightRegionAnnotation _lastHighlight; + + private RNA _lastRNAhighlighted = null; + + public void highlightRegion(RNA rna, int start, int end) + { + clearSelection(null); + HighlightRegionAnnotation highlight = new HighlightRegionAnnotation( + rna.getBasesBetween(start, end)); + rna.addHighlightRegion(highlight); + _lastHighlight = highlight; + _lastRNAhighlighted = rna; + + } + + public HighlightRegionAnnotation getLastHighlight() + { + return _lastHighlight; + } + + public RNA getLastRNA() + { + return _lastRNAhighlighted; + } + + public void clearSelection(AppVarnaBinding vab) + { + if (_lastRNAhighlighted != null) { - initVarna(); - } catch (OutOfMemoryError oomerror) + _lastRNAhighlighted.removeHighlightRegion(_lastHighlight); + if (vab != null) + { + vab.updateSelectedRNA(_lastRNAhighlighted); + } + _lastRNAhighlighted = null; + _lastHighlight = null; + + } + } + } + + VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter(), + selectionHighlighter = new VarnaHighlighter(); + + /** + * If a mouseOver event from the AlignmentPanel is noticed the currently + * selected RNA in the VARNA window is highlighted at the specific position. + * To be able to remove it before the next highlight it is saved in + * _lastHighlight + */ + @Override + public void mouseOverSequence(SequenceI sequence, int index) + { + RNA rna = vab.getSelectedRNA(); + if (seqs.get(rna) == sequence) + { + ShiftList shift = offsets.get(rna); + if (shift != null) { - new OOMWarning("When trying to open the Varna viewer!", oomerror); - } catch (Exception ex) + // System.err.print("Orig pos:"+index); + index = shift.shift(index); + // System.err.println("\nFinal pos:"+index); + } + mouseOverHighlighter.highlightRegion(rna, index, index); + vab.updateSelectedRNA(rna); + } + } + + @Override + public void onStructureRedrawn() + { + // TODO Auto-generated method stub + + } + + @Override + public void selection(SequenceGroup seqsel, ColumnSelection colsel, + SelectionSource source) + { + if (source != ap.av) + { + // ignore events from anything but our parent alignpanel + // TODO - reuse many-one panel-view system in jmol viewer + return; + } + if (seqsel != null && seqsel.getSize() > 0) + { + int start = seqsel.getStartRes(), end = seqsel.getEndRes(); + RNA rna = vab.getSelectedRNA(); + ShiftList shift = offsets.get(rna); + if (shift != null) + { + start = shift.shift(start); + end = shift.shift(end); + } + selectionHighlighter.highlightRegion(rna, start, end); + selectionHighlighter.getLastHighlight().setOutlineColor( + seqsel.getOutlineColour()); + // TODO - translate column markings to positions on structure if present. + vab.updateSelectedRNA(rna); + } + else + { + selectionHighlighter.clearSelection(vab); + } + } + + @Override + public void onHoverChanged(ModeleBase arg0, ModeleBase arg1) + { + RNA rna = vab.getSelectedRNA(); + ShiftList shift = offsetsInv.get(rna); + SequenceI seq = seqs.get(rna); + if (arg1 != null && seq != null) + { + if (shift != null) + { + int i = shift.shift(arg1.getIndex()); + // System.err.println("shifted "+(arg1.getIndex())+" to "+i); + ssm.mouseOverVamsasSequence(seq, i, this); + } + else { - Cache.log.error("Couldn't open Varna viewer!", ex); + ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this); } + } + } + + @Override + public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2) + { + // TODO translate selected regions in VARNA to a selection on the + // alignpanel. + } - }