--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.SequenceStructureBinding;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+/**
+ * GUI elements for handlnig an external chimera display
+ *
+ * @author jprocter
+ *
+ */
+public class ChimeraViewFrame extends GStructureViewer implements Runnable,
+ ViewSetProvider, JalviewStructureDisplayI
+
+{
+ JalviewChimeraBindingModel jmb;
+
+ AlignmentPanel ap;
+
+ Vector atomsPicked = new Vector();
+
+ private boolean addingStructures = false;
+
+ ViewSelectionMenu seqColourBy;
+
+ /**
+ *
+ * @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 ChimeraViewFrame(String[] files, String[] ids,
+ * SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour,
+ * boolean useToAlign, boolean leaveColouringToJmol, String
+ * loadStatus, Rectangle bounds, String viewid) { 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
+ * JalviewChimeraBindingModel(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() { 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)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ 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(MessageManager
+ .formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[]
+ { new Integer(_alignwith.size()).toString() }));
+ }
+ });
+ 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
+
+ }
+ });
+ }
+
+ IProgressIndicator progressBar = null;
+
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentPanel ap)
+ {
+ progressBar = ap.alignFrame;
+ // ////////////////////////////////
+ // Is the pdb file already loaded?
+ String alreadyMapped = ap.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
+
+ if (alreadyMapped != null)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new String[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new String[]
+ { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
+
+ if (option == JOptionPane.YES_OPTION)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ ap.getStructureSelectionManager().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 ChimeraViewFrame)
+ {
+ final ChimeraViewFrame topJmol = ((ChimeraViewFrame) 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);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
+ topJmol.buildChimeraActionMenu();
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
+ break;
+ }
+ }
+ }
+ }
+
+ 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())
+ {
+ ChimeraViewFrame topJmol = (ChimeraViewFrame) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.add_pdbentry_to_view", new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.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;
+ }
+ }
+ }
+ // /////////////////////////////////
+ openNewJmol(ap, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq });
+ }
+
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ progressBar = ap.alignFrame;
+ jmb = new JalviewChimeraBindingModel(this,
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length > 1)
+ {
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
+ }
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ worker = null;
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+ }
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+
+ }
+
+ /**
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
+ SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
+
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ 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>();
+
+ /**
+ * 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)
+ {
+ 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)
+ {
+ buildChimeraActionMenu();
+ }
+ }
+
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_alignwith.contains(nap))
+ {
+ _alignwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ if (_alignwith.contains(nap))
+ {
+ _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))
+ {
+ _colourwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
+
+ /**
+ * 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)
+ {
+ if (worker != null && worker.isAlive())
+ {
+ // a retrieval is in progress, wait around and add ourselves to the
+ // queue.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ while (worker != null && worker.isAlive() && _started)
+ {
+ try
+ {
+ Thread.sleep(100 + ((int) Math.random() * 100));
+
+ } catch (Exception e)
+ {
+ }
+
+ }
+ // and call ourselves again.
+ addStructure(pdbentry, seq, chains, b, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // 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 ChimeraViewFrame)
+ {
+ ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
+ if (topJmol.isLinkedWith(ap2))
+ {
+ otherJmols.addElement(topJmol);
+ }
+ }
+ }
+ return otherJmols;
+ }
+
+ void initChimera(String command)
+ {
+ jmb.setFinishedInit(false);
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ if (command == null)
+ {
+ command = "";
+ }
+ jmb.evalStateCommand(command);
+ jmb.setFinishedInit(true);
+ }
+
+ void setChainMenuItems(Vector chains)
+ {
+ chainMenu.removeAll();
+ if (chains == null)
+ {
+ return;
+ }
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ 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++)
+ {
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ centerViewer();
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
+
+ void centerViewer()
+ {
+ 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);
+ }
+
+ public void closeViewer()
+ {
+ 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;
+ }
+
+ /**
+ * 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();
+ List<String> fileToLoad=new ArrayList<String>();
+ List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
+ List<Integer> filePDBpos =new ArrayList<Integer>();
+ 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 = new File(jmb.pdbentry[pi].getFile())
+ .getAbsoluteFile().getPath();
+ 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
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[pi].setFile(file);
+
+ files.append(" \"" + Platform.escapeString(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)
+ {
+ fileToLoad.add(file);
+ filePDB.add(jmb.pdbentry[pi]);
+ filePDBpos.add(Integer.valueOf(pi));
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
+
+ }
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ if (files.length() > 0)
+ {
+ if (!addingStructures)
+ {
+ try
+ {
+ initChimera("");
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Chimera viewer!", ex);
+ }
+ }
+ int num=-1;
+ for (PDBEntry pe : filePDB)
+ {
+ num++;
+ if (pe.getFile() != null)
+ {
+ try
+ {
+ int pos=filePDBpos.get(num).intValue();
+ jmb.openFile(pe);
+ jmb.addSequence(pos, jmb.sequence[pos]);
+ File fl=new File(pe.getFile());
+ String protocol = AppletFormatAdapter.URL;
+ try
+ {
+ if (fl.exists())
+ {
+ protocol = AppletFormatAdapter.FILE;
+ }
+ } catch (Exception e)
+ {
+ } catch (Error e)
+ {
+ }
+ // Explicitly map to the filename used by Jmol ;
+ jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(),
+ protocol);
+ // pdbentry[pe].getFile(), protocol);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to open and map structures from Chimera!",
+ oomerror);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open " + pe.getFile()
+ + " in Chimera viewer!", ex);
+ } finally
+ {
+ Cache.log.debug("File locations are " + files);
+ }
+ }
+ }
+ // jmb.getPdbFile();
+ jmb.setFinishedInit(true);
+ jmb.setLoadingFromArchive(false);
+
+ // 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();
+ }
+ });
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+ }
+ _started = false;
+ worker = null;
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save PDB File");
+ chooser.setToolTipText(MessageManager.getString("action.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,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ throw new Error("EPS Generation not yet implemented.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ throw new Error("PNG Generation not yet implemented.");
+ }
+
+ 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("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = System.currentTimeMillis() + "." + this.hashCode();
+ }
+ return viewId;
+ }
+
+ public void updateTitleAndMenus()
+ {
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
+
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ jmolActionMenu.setVisible(true);
+ }
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
+
+ protected void buildChimeraActionMenu()
+ {
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : jmolActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ jmolActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_withAllAlignPanels();
+ }
+
+ private void alignStructs_withAllAlignPanels()
+ {
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _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)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ jmb.superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+
+ }
+
+ }
+
+ public void setJalviewColourScheme(ColourSchemeI ucs)
+ {
+ jmb.setJalviewColourScheme(ucs);
+
+ }
+
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (AlignmentPanel ap : getAllAlignmentPanels())
+ {
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
+ }
+ return ap;
+ }
+
+ /**
+ *
+ * @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)
+ {
+
+ 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();
+ }
+
+ public SequenceStructureBinding getBinding()
+ {
+ return jmb;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff