/*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
-import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
+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 javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
-public class AppVarna extends GStructureViewer implements Runnable,
- SequenceStructureBinding, ViewSetProvider
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+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.RNA;
+
+public class AppVarna extends JInternalFrame implements
+ InterfaceVARNAListener, SelectionListener,
+ SecondaryStructureListener// implements
+ // Runnable,SequenceStructureBinding,
+ // ViewSetProvider
+ , InterfaceVARNASelectionListener, VamsasSource
{
- AppJmolBinding jmb;
-
- JPanel scriptWindow;
-
- JSplitPane splitPane;
+ AppVarnaBinding vab;
- RenderPanel renderPanel;
+ VARNAPanel varnaPanel;
- AlignmentPanel ap;
-
- Vector atomsPicked = new Vector();
-
- private boolean addingStructures = false;
+ public String name;
- /**
- *
- * @param file
- * @param id
- * @param seq
- * @param ap
- * @param loadStatus
- * @param bounds
- * @deprecated defaults to AppJmol(String[] files, ... , viewid);
- */
- public AppVarna(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
- {
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
+ public StructureSelectionManager ssm;
- /**
- * @deprecated
+ /*
+ * public AppVarna(){ vab = new AppVarnaBinding(); initVarna(); }
*/
- public AppVarna(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
- {
- this(new String[]
- { file }, new String[]
- { id }, new SequenceI[][]
- { seq }, ap, true, true, false, loadStatus, bounds, viewid);
- }
- ViewSelectionMenu seqColourBy;
+ AlignmentPanel ap;
- /**
- *
- * @param files
- * @param ids
- * @param seqs
- * @param ap
- * @param usetoColour
- * - add the alignment panel to the list used for colouring these
- * structures
- * @param useToAlign
- * - add the alignment panel to the list used for aligning these
- * structures
- * @param leaveColouringToJmol
- * - do not update the colours from any other source. Jmol is handling them
- * @param loadStatus
- * @param bounds
- * @param viewid
- */
- public AppVarna(String[] files, String[] ids, SequenceI[][] seqs,
- AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol,
- String loadStatus, Rectangle bounds, String viewid)
+ public AppVarna(String sname, SequenceI seq, String strucseq,
+ String struc, String name, AlignmentPanel ap)
{
- PDBEntry[] pdbentrys = new PDBEntry[files.length];
- for (int i = 0; i < pdbentrys.length; i++)
- {
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(files[i]);
- pdbentry.setId(ids[i]);
- pdbentrys[i] = pdbentry;
- }
- // / TODO: check if protocol is needed to be set, and if chains are
- // autodiscovered.
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
-
- jmb.setLoadingFromArchive(true);
- addAlignmentPanel(ap);
- if (useToAlign)
- {
- useAlignmentPanelForSuperposition(ap);
- }
- if (leaveColouringToJmol || !usetoColour)
- {
- jmb.setColourBySequence(false);
- seqColour.setSelected(false);
- jmolColour.setSelected(true);
- }
- if (usetoColour)
- {
- useAlignmentPanelForColourbyseq(ap);
- jmb.setColourBySequence(true);
- seqColour.setSelected(true);
- jmolColour.setSelected(false);
- }
- this.setBounds(bounds);
- initMenus();
- viewId = viewid;
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- // bounds.width,bounds.height);
- this.addInternalFrameListener(new InternalFrameAdapter()
+ // 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<RNA> rnaList = new ArrayList<RNA>();
+ RNA rna1 = new RNA(name);
+ try
{
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
- }
- private void initMenus()
- {
- seqColour.setSelected(jmb.isColourBySequence());
- jmolColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith==null)
+ rna1.setRNA(strucseq, replaceOddGaps(struc));
+ // System.out.println("The sequence is :"+rna1.getSeq());
+ // System.out.println("The sequence is:"+struc);
+ // System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
+ } catch (ExceptionUnmatchedClosingParentheses e2)
{
- _colourwith=new Vector<AlignmentPanel>();
- }
- if (_alignwith==null)
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3)
{
- _alignwith=new Vector<AlignmentPanel>();
+ e3.printStackTrace();
}
-
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
- new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
- _alignwith, handler = new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
- }
- });
- handler.itemStateChanged(null);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ RNA trim = trimRNA(rna1, "trimmed " + sname);
+ rnaList.add(trim);
+ rnaList.add(rna1);
- }
- });
- }
- IProgressIndicator progressBar = null;
-
- public AppVarna(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
- {
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = jmb.ssm.alreadyMappedToFile(
- pdbentry.getId());
-
- if (alreadyMapped != null)
- {
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- pdbentry.getId() + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: " + pdbentry.getId(),
- JOptionPane.YES_NO_OPTION);
-
- if (option == JOptionPane.YES_OPTION)
- {
- jmb.ssm.setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
-
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppVarna)
- {
- AppVarna topJmol = ((AppVarna) frames[i]);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
- {
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
- topJmol.buildJmolActionMenu();
- break;
- }
- }
- }
- }
+ rnas.put(seq, rna1);
+ rnas.put(seq, trim);
+ rna1.setName(sname + " (with gaps)");
- return;
- }
- }
- // /////////////////////////////////
- // Check if there are other Jmol views involving this alignment
- // and prompt user about adding this molecule to one of them
- Vector existingViews = getJmolsFor(ap);
- if (existingViews.size() > 0)
{
- Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements())
- {
- AppVarna topJmol = (AppVarna) jm.nextElement();
- // TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "Do you want to add " + pdbentry.getId()
- + " to the view called\n'" + topJmol.getTitle()
- + "'\n", "Align to existing structure view",
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
- }
- }
- // /////////////////////////////////
+ seqs.put(trim, seq);
+ seqs.put(rna1, seq);
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, null, null);
- addAlignmentPanel(ap);
- useAlignmentPanelForColourbyseq(ap);
- jmb.setColourBySequence(true);
- setSize(400, 400); // probably should be a configurable/dynamic default here
- initMenus();
-
- if (pdbentry.getFile() != null)
- {
- initJmol("load \"" + pdbentry.getFile() + "\"");
- }
- else
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
+ /**
+ * 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);
+ this.name = sname + " trimmed to " + name;
+ initVarna();
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
-
+ ssm = ap.getStructureSelectionManager();
+ // System.out.println(ssm.toString());
+ ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
}
- /**
- * list of sequenceSet ids associated with the view
- */
- ArrayList<String> _aps = new ArrayList();
-
- public AlignmentPanel[] getAllAlignmentPanels()
+ public void initVarna()
{
- AlignmentPanel[] t, list = new AlignmentPanel[0];
- for (String setid : _aps)
- {
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
- if (panels != null)
- {
- t = new AlignmentPanel[list.length + panels.length];
- System.arraycopy(list, 0, t, 0, list.length);
- System.arraycopy(panels, 0, t, list.length, panels.length);
- list = t;
- }
- }
-
- return list;
- }
-
- /**
- * list of alignment panels to use for superposition
- */
- Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
- /**
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+ // 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,
+ MessageManager.formatMessage("label.varna_params", new String[]
+ { name }), getBounds().width, getBounds().height);
+ this.pack();
+ showPanel(true);
- /**
- * set the primary alignmentPanel reference and add another alignPanel to the
- * list of ones to use for colouring and aligning
- *
- * @param nap
- */
- public void addAlignmentPanel(AlignmentPanel nap)
- {
- if (ap == null)
- {
- ap = nap;
- }
- if (!_aps.contains(nap.av.getSequenceSetId()))
- {
- _aps.add(nap.av.getSequenceSetId());
- }
}
- /**
- * remove any references held to the given alignment panel
- *
- * @param nap
- */
- public void removeAlignmentPanel(AlignmentPanel nap)
+ public String replaceOddGaps(String oldStr)
{
- try
- {
- _alignwith.remove(nap);
- _colourwith.remove(nap);
- if (ap == nap)
- {
- ap = null;
- for (AlignmentPanel aps : getAllAlignmentPanels())
- {
- if (aps != nap)
- {
- ap = aps;
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- }
- if (ap != null)
- {
- buildJmolActionMenu();
- }
+ String patternStr = "[^([{<>}])]";
+ String replacementStr = ".";
+ Pattern pattern = Pattern.compile(patternStr);
+ Matcher matcher = pattern.matcher(oldStr);
+ String newStr = matcher.replaceAll(replacementStr);
+ return newStr;
}
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ public RNA trimRNA(RNA rna, String name)
{
- addAlignmentPanel(nap);
- if (!_alignwith.contains(nap))
- {
- _alignwith.add(nap);
- }
- }
+ ShiftList offset = new ShiftList();
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- if (_alignwith.contains(nap))
+ RNA rnaTrim = new RNA(name);
+ try
{
- _alignwith.remove(nap);
- }
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
- {
- useAlignmentPanelForColourbyseq(nap);
- jmb.setColourBySequence(enableColourBySeq);
- seqColour.setSelected(enableColourBySeq);
- jmolColour.setSelected(!enableColourBySeq);
- }
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_colourwith.contains(nap))
+ rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
+ } catch (ExceptionUnmatchedClosingParentheses e2)
{
- _colourwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
+ e2.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e3)
{
- _colourwith.remove(nap);
+ e3.printStackTrace();
}
- }
-
- /**
- * pdb retrieval thread.
- */
- private Thread worker = null;
- /**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param alignFrame
- * @param align
- * if true, new structure(s) will be align using associated alignment
- */
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
- {
- if (pdbentry.getFile() == null)
+ 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++)
{
- if (worker != null && worker.isAlive())
+ // TODO: Jalview utility for gap detection java.utils.isGap()
+ // TODO: Switch to jalview rna datamodel
+ if (jalview.util.Comparison.isGap(seq.charAt(i)))
{
- // a retrieval is in progress, wait around and add ourselves to the
- // queue.
- new Thread(new Runnable()
+ if (ofstart == -1)
{
- public void run()
- {
- while (worker != null && worker.isAlive() && _started)
- {
- try
- {
- Thread.sleep(100 + ((int) Math.random() * 100));
-
- } catch (Exception e)
- {
- }
+ ofstart = i;
+ }
+ if (!rnaTrim.findPair(i).isEmpty())
+ {
+ int m = rnaTrim.findPair(i).get(1);
+ int l = rnaTrim.findPair(i).get(0);
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
+ struc.replace(m, m + 1, "*");
+ struc.replace(l, l + 1, "*");
+ }
+ else
+ {
+ struc.replace(i, i + 1, "*");
+ }
}
- }
- // otherwise, start adding the structure.
- jmb.addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- addingStructures = true;
- _started = false;
- alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
- (worker = new Thread(this)).start();
- return;
- }
-
- private Vector getJmolsFor(AlignmentPanel ap2)
- {
- Vector otherJmols = new Vector();
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppVarna)
+ else
{
- AppVarna topJmol = ((AppVarna) frames[i]);
- if (topJmol.isLinkedWith(ap2))
+ if (ofstart > -1)
{
- otherJmols.addElement(topJmol);
+ offset.addShift(offset.shift(ofstart), ofstart - i);
+ ofstart = -1;
}
}
}
- return otherJmols;
- }
-
- void initJmol(String command)
- {
- jmb.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, jmb.getViewerTitle(),
- getBounds().width, getBounds().height);
- if (scriptWindow == null)
- {
- BorderLayout bl = new BorderLayout();
- bl.setHgap(0);
- bl.setVgap(0);
- scriptWindow = new JPanel(bl);
- scriptWindow.setVisible(false);
- }
- ;
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
- null);
- jmb.newJmolPopup(true, "Jmol", true);
- if (command==null)
+ // final gap
+ if (ofstart > -1)
{
- command="";
+ offset.addShift(offset.shift(ofstart), ofstart - sleng);
+ ofstart = -1;
}
- jmb.evalStateCommand(command);
- jmb.setFinishedInit(true);
- }
+ String newSeq = rnaTrim.getSeq().replace("-", "");
+ rnaTrim.getSeq().replace(".", "");
+ String newStruc = struc.toString().replace("*", "");
- void setChainMenuItems(Vector chains)
- {
- chainMenu.removeAll();
- if (chains == null)
+ try
{
- return;
- }
- JMenuItem menuItem = new JMenuItem("All");
- menuItem.addActionListener(new ActionListener()
+ rnaTrim.setRNA(newSeq, newStruc);
+ registerOffset(rnaTrim, offset);
+ } catch (ExceptionUnmatchedClosingParentheses e)
{
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- centerViewer();
- allChainsSelected = false;
- }
- });
-
- chainMenu.add(menuItem);
-
- for (int c = 0; c < chains.size(); c++)
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
- menuItem.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- centerViewer();
- }
- });
-
- chainMenu.add(menuItem);
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
+ return rnaTrim;
}
- boolean allChainsSelected = false;
+ // needs to be many-many
+ Map<RNA, SequenceI> seqs = new Hashtable<RNA, SequenceI>();
- private boolean alignAddedStructures = false;
+ Map<SequenceI, RNA> rnas = new Hashtable<SequenceI, RNA>();
- void centerViewer()
+ Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>();
+
+ Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>();
+
+ private void registerOffset(RNA rnaTrim, ShiftList offset)
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if (item.isSelected())
- {
- toshow.addElement(item.getText());
- }
- }
- }
- jmb.centerViewer(toshow);
+ offsets.put(rnaTrim, offset);
+ offsetsInv.put(rnaTrim, offset.getInverse());
}
- void closeViewer()
+ public void showPanel(boolean show)
{
- jmb.closeViewer();
- ap = null;
- _aps.clear();
- _alignwith.clear();
- _colourwith.clear();
- // TODO: check for memory leaks where instance isn't finalised because jmb
- // holds a reference to the window
- jmb = null;
+ this.setVisible(show);
}
- /**
- * state flag for PDB retrieval thread
- */
private boolean _started = false;
public void run()
{
_started = true;
- String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
+
try
{
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
- {
- String file = jmb.pdbentry[pi].getFile();
- if (file == null)
- {
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.pdbentry[pi].getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
- {
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
- }
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
- {
- progressBar.setProgressBar("Finished.", hdl);
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
- .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
- files.append(" \"" + file + "\"");
- }
- else
- {
- errormsgs.append("'" + pdbid + "' ");
- }
- }
- else
- {
- if (curfiles != null && curfiles.length > 0)
- {
- addingStructures = true; // already files loaded.
- for (int c = 0; c < curfiles.length; c++)
- {
- if (curfiles[c].equals(file))
- {
- file = null;
- break;
- }
- }
- }
- if (file != null)
- {
- files.append(" \"" + file + "\"");
- }
- }
- }
+ initVarna();
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ new OOMWarning("When trying to open the Varna viewer!", oomerror);
} catch (Exception ex)
{
- ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
+ Cache.log.error("Couldn't open Varna viewer!", ex);
}
- if (errormsgs.length() > 0)
- {
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
- }
- if (files.length() > 0)
- {
- if (!addingStructures)
- {
-
- try
- {
- initJmol("load FILES " + files.toString());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't open Jmol viewer!", ex);
- }
- }
- else
- {
- StringBuffer cmd = new StringBuffer();
- cmd.append("loadingJalviewdata=true\nload APPEND ");
- cmd.append(files.toString());
- cmd.append("\nloadingJalviewdata=null");
- final String command = cmd.toString();
- cmd = null;
- long lastnotify = jmb.getLoadNotifiesHandled();
- try
- {
- jmb.evalStateCommand(command);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning(
- "When trying to add structures to the Jmol viewer!",
- oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
- }
- // need to wait around until script has finished
- while (lastnotify >= jmb.getLoadNotifiesHandled())
- ;
- {
- try
- {
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
- // refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.updateColours(ap);
- }
- // do superposition if asked to
- if (alignAddedStructures)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- alignStructs_withAllAlignPanels();
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
- }
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
- }
- }
- _started = false;
- worker = null;
}
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void onUINewStructure(VARNAConfig v, RNA r)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- try
- {
- // TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
- {
- cap.appendText(jmb.printMapping(
- jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
- }
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
+ @Override
+ public void onWarningEmitted(String s)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
- }
+ // TODO Auto-generated method stub
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
}
- void makePDBImage(int type)
+ private class VarnaHighlighter
{
- int width = getWidth();
- int height = getHeight();
+ private HighlightRegionAnnotation _lastHighlight;
- jalview.util.ImageMaker im;
+ private RNA _lastRNAhighlighted = null;
- if (type == jalview.util.ImageMaker.PNG)
+ public void highlightRegion(RNA rna, int start, int end)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Make PNG image from view", width, height, null, null);
- }
- else
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null,
- this.getTitle());
- }
+ clearSelection(null);
+ HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(
+ rna.getBasesBetween(start, end));
+ rna.addHighlightRegion(highlight);
+ _lastHighlight = highlight;
+ _lastRNAhighlighted = rna;
- if (im.getGraphics() != null)
- {
- Rectangle rect = new Rectangle(width, height);
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
- im.writeImage();
- }
- }
- public void jmolColour_actionPerformed(ActionEvent actionEvent)
- {
- if (jmolColour.isSelected()) {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
}
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size()==0 && ap!=null) {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
- }
- }
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
- {
- try
- {
- jalview.util.BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
- } catch (Exception ex)
+ public HighlightRegionAnnotation getLastHighlight()
{
+ return _lastHighlight;
}
- }
-
- public void showConsole(boolean showConsole)
- {
-
- if (showConsole)
- {
- if (splitPane == null)
- {
- splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
- splitPane.setTopComponent(renderPanel);
- splitPane.setBottomComponent(scriptWindow);
- this.getContentPane().add(splitPane, BorderLayout.CENTER);
- splitPane.setDividerLocation(getHeight() - 200);
- scriptWindow.setVisible(true);
- scriptWindow.validate();
- splitPane.validate();
- }
- }
- else
+ public RNA getLastRNA()
{
- if (splitPane != null)
- {
- splitPane.setVisible(false);
- }
-
- splitPane = null;
-
- this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ return _lastRNAhighlighted;
}
- validate();
- }
-
- class RenderPanel extends JPanel
- {
- final Dimension currentSize = new Dimension();
-
- final Rectangle rectClip = new Rectangle();
-
- public void paintComponent(Graphics g)
+ public void clearSelection(AppVarnaBinding vab)
{
- getSize(currentSize);
- g.getClipBounds(rectClip);
-
- if (jmb.fileLoadingError != null)
+ if (_lastRNAhighlighted != null)
{
- g.setColor(Color.black);
- g.fillRect(0, 0, currentSize.width, currentSize.height);
- g.setColor(Color.white);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20, currentSize.height / 2);
- StringBuffer sb = new StringBuffer();
- int lines = 0;
- for (int e = 0; e < jmb.pdbentry.length; e++)
+ _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
+ if (vab != null)
{
- sb.append(jmb.pdbentry[e].getId());
- if (e < jmb.pdbentry.length - 1)
- {
- sb.append(",");
- }
-
- if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
- {
- lines++;
- g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
- * g.getFontMetrics().getHeight());
- }
+ vab.updateSelectedRNA(_lastRNAhighlighted);
}
- }
- else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
- {
- g.setColor(Color.black);
- g.fillRect(0, 0, currentSize.width, currentSize.height);
- g.setColor(Color.white);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else
- {
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ _lastRNAhighlighted = null;
+ _lastHighlight = null;
+
}
}
}
- String viewId = null;
+ VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter(),
+ selectionHighlighter = new VarnaHighlighter();
- public String getViewId()
+ /**
+ * 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)
{
- if (viewId == null)
+ RNA rna = vab.getSelectedRNA();
+ if (seqs.get(rna) == sequence)
{
- viewId = System.currentTimeMillis() + "." + this.hashCode();
+ ShiftList shift = offsets.get(rna);
+ if (shift != null)
+ {
+ // System.err.print("Orig pos:"+index);
+ index = shift.shift(index);
+ // System.err.println("\nFinal pos:"+index);
+ }
+ mouseOverHighlighter.highlightRegion(rna, index, index);
+ vab.updateSelectedRNA(rna);
}
- return viewId;
}
- public void updateTitleAndMenus()
+ @Override
+ public void onStructureRedrawn()
{
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
+ // TODO Auto-generated method stub
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
- {
- jmolActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
}
- protected void buildJmolActionMenu()
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
{
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
+ if (source != ap.av)
{
- _alignwith.add(ap);
+ // ignore events from anything but our parent alignpanel
+ // TODO - reuse many-one panel-view system in jmol viewer
+ return;
}
- ;
- for (Component c : jmolActionMenu.getMenuComponents())
+ if (seqsel != null && seqsel.getSize() > 0)
{
- if (c != alignStructs)
+ int start = seqsel.getStartRes(), end = seqsel.getEndRes();
+ RNA rna = vab.getSelectedRNA();
+ ShiftList shift = offsets.get(rna);
+ if (shift != null)
{
- jmolActionMenu.remove((JMenuItem) c);
+ 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);
}
- final ItemListener handler;
}
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
@Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
{
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (ap == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
+ RNA rna = vab.getSelectedRNA();
+ ShiftList shift = offsetsInv.get(rna);
+ SequenceI seq = seqs.get(rna);
+ if (arg1 != null && seq != null)
{
- _alignwith.add(ap);
- }
- ;
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
+ if (shift != null)
{
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
+ int i = shift.shift(arg1.getIndex());
+ // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+ ssm.mouseOverVamsasSequence(seq, i, this);
}
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
+ else
{
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
}
-
}
- public void setJalviewColourScheme(ColourSchemeI ucs)
+ @Override
+ public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
{
- jmb.setJalviewColourScheme(ucs);
+ // TODO translate selected regions in VARNA to a selection on the
+ // alignpanel.
}
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ @Override
+ public void onTranslationChanged()
{
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return ap;
- }
+ // TODO Auto-generated method stub
- /**
- *
- * @param ap2
- * @return true if this Jmol instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
- {
- return _aps.contains(ap2.av.getSequenceSetId());
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ @Override
+ public void onZoomLevelChanged()
{
+ // TODO Auto-generated method stub
- return (_alignwith != null) && _alignwith.contains(ap2);
- }
-
- public boolean isUsedforcolourby(AlignmentPanel ap2)
- {
- return (_colourwith != null) && _colourwith.contains(ap2);
}
- /**
- *
- * @return TRUE if the view is NOT being coloured by sequence associations.
- */
- public boolean isColouredByJmol()
- {
- return !jmb.isColourBySequence();
- }
-
-
}
git://source.jalview.org / jalview.git / blobdiff