void setConservation(Conservation cons);
+ /**
+ * get a copy of the currently visible alignment annotation
+ * @param selectedOnly if true - trim to selected regions on the alignment
+ * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+ */
+ List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+ boolean selectedOnly);
+
+ FeaturesDisplayedI getFeaturesDisplayed();
+
+ String getSequenceSetId();
+
+ boolean isShowSequenceFeatures();
+
+ void setShowSequenceFeatures(boolean b);
+
}
boolean renderGaps = true;
- boolean showSequenceFeatures = false;
-
boolean showAnnotation = true;
+ SequenceAnnotationOrder sortAnnotationsBy = null;
+
int charHeight;
int charWidth;
--- /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 jalview.ws.dbsources.Pdb;
+
+ 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.IOException;
+ import java.io.PrintWriter;
+ import java.util.ArrayList;
+ 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
+
+ {
+ private JalviewChimeraBindingModel jmb;
+
+ /*
+ * list of sequenceSet ids associated with the view
+ */
+ private ArrayList<String> _aps = new ArrayList<String>();
+
+ /*
+ * list of alignment panels to use for superposition
+ */
+ private Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
+ /*
+ * list of alignment panels that are used for colouring structures by aligned
+ * sequences
+ */
+ private Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
+ private boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
+
+ AlignmentPanel ap;
+
+ /*
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
+
+ private boolean addingStructures = false;
+
+ private IProgressIndicator progressBar = null;
+
+ private String viewId = null;
+
+ /*
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
+
+ /**
+ * Initialise menu options.
+ */
+ private void initMenus()
+ {
+ viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+ viewerColour.setText(MessageManager
+ .getString("label.colour_with_chimera"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_chimera_manage_structure_colours"));
+ helpItem.setText(MessageManager.getString("label.chimera_help"));
+ seqColour.setSelected(jmb.isColourBySequence());
+ viewerColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the Chimera display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+ final ItemListener handler;
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.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 Object[]
+ { new Integer(_alignwith.size()).toString() }));
+ }
+ });
+ handler.itemStateChanged(null);
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.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
+ }
+ });
+ }
+
+ /**
+ * add a single PDB structure to a new or existing Chimera view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentPanel ap)
+ {
+ super();
+ 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 Object[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbentry.getId() }),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
+ 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 ChimeraViewFrame is mapped to new sequences. We must add
+ // them to the existing array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof ChimeraViewFrame)
+ {
+ final ChimeraViewFrame topView = ((ChimeraViewFrame) frame);
+ // JBPNOTE: this looks like a binding routine, rather than a gui
+ // routine
+ for (int pe = 0; pe < topView.jmb.pdbentry.length; pe++)
+ {
+ if (topView.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ {
+ topView.jmb.addSequence(pe, seq);
+ topView.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topView.useAlignmentPanelForColourbyseq(ap);
+ topView.buildChimeraActionMenu();
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
+ break;
+ }
+ }
+ }
+ }
+
+ return;
+ }
+ }
+ // /////////////////////////////////
+ // Check if there are other Chimera views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
+ for (ChimeraViewFrame topView : existingViews)
+ {
+ // TODO: highlight topView in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new Object[]
+ { pdbentry.getId(), topView.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topView.useAlignmentPanelForSuperposition(ap);
+ topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
+ // /////////////////////////////////
+ openNewChimera(ap, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq });
+ }
+
+ private void openNewChimera(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 viewer containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
+ SequenceI[][] seqs)
+ {
+ super();
+ openNewChimera(ap, pe, seqs);
+ }
+
+ 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;
+ }
+
+ /**
+ * 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);
+ viewerColour.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);
+ }
+ }
+
+ /**
+ * 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 List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
+ {
+ List<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof ChimeraViewFrame)
+ {
+ if (((ChimeraViewFrame) frame).isLinkedWith(apanel))
+ {
+ result.add((ChimeraViewFrame) frame);
+ }
+ }
+ }
+ return result;
+ }
+
+ 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(true),
+ getBounds().width, getBounds().height);
+ if (command == null)
+ {
+ command = "";
+ }
+ jmb.evalStateCommand(command, false);
+ jmb.setFinishedInit(true);
+ }
+
+ void setChainMenuItems(List<String> chainNames)
+ {
+ chainMenu.removeAll();
+ if (chainNames == 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 (String chainName : chainNames)
+ {
+ menuItem = new JCheckBoxMenuItem(chainName, true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ {
+ centerViewer();
+ }
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ void centerViewer()
+ {
+ List<String> toshow = new ArrayList<String>();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.add(item.getText());
+ }
+ }
+ }
+ jmb.centerViewer(toshow);
+ }
+
+ /**
+ * Close down this instance of Jalview's Chimera viewer, giving the user the
+ * option to close the associated Chimera window (process). They may wish to
+ * keep it open until they have had an opportunity to save any work.
+ */
+ public void closeViewer()
+ {
+ if (jmb.isChimeraRunning())
+ {
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_chimera", new Object[]
+ { jmb.getViewerTitle(false) });
+ prompt = JvSwingUtils.wrapTooltip(true, prompt);
+ int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ MessageManager.getString("label.close_viewer"),
+ JOptionPane.YES_NO_OPTION);
+ jmb.closeViewer(confirm == JOptionPane.YES_OPTION);
+ }
+ 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;
+ }
+
+ /**
+ * Open any newly added PDB structures in Chimera, having first fetched data
+ * from PDB (if not already saved).
+ */
+ public void run()
+ {
+ _started = true;
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder(128);
+ StringBuilder files = new StringBuilder(128);
+ List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
+ List<Integer> filePDBpos = new ArrayList<Integer>();
+ PDBEntry thePdbEntry = null;
+ try
+ {
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ {
+ String file = null;
+ thePdbEntry = jmb.pdbentry[pi];
+ if (thePdbEntry.getFile() == null)
+ {
+ /*
+ * Retrieve PDB data, save to file, attach to PDBEntry
+ */
+ file = fetchPdbFile(thePdbEntry);
+ if (file == null)
+ {
+ errormsgs.append("'" + thePdbEntry.getId() + "' ");
+ }
+ }
+ else
+ {
+ /*
+ * Got file already - ignore if already loaded in Chimera.
+ */
+ file = new File(thePdbEntry.getFile()).getAbsoluteFile()
+ .getPath();
+ 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)
+ {
+ filePDB.add(thePdbEntry);
+ filePDBpos.add(Integer.valueOf(pi));
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + thePdbEntry.getId(),
+ oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles for '"
+ + thePdbEntry.getId() + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new Object[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ 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 (Throwable e)
+ {
+ }
+ // Explicitly map to the filename used by Chimera ;
+ // TODO: use pe.getId() instead of pe.getFile() ?
+ jmb.ssm.setMapping(jmb.sequence[pos], null, 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.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)
+ {
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ }).start();
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+ }
+ _started = false;
+ worker = null;
+ }
+
+ /**
+ * Fetch PDB data and save to a local file. Returns the full path to the file,
+ * or null if fetch fails.
+ *
+ * @param processingEntry
+ * @return
+ * @throws Exception
+ */
+ private String fetchPdbFile(PDBEntry processingEntry) throws Exception
+ {
+ String filePath = null;
+ Pdb pdbclient = new Pdb();
+ AlignmentI pdbseq = null;
+ String pdbid = processingEntry.getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new Object[]
+ { pdbid }), hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } finally
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"), hdl);
+ }
+ }
+ /*
+ * If PDB data were saved and are not invalid (empty alignment), return the
+ * file path.
+ */
+ if (pdbseq != null && pdbseq.getHeight() > 0)
+ {
+ // just use the file name from the first sequence's first PDBEntry
+ filePath = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ processingEntry.setFile(filePath);
+ }
+ return filePath;
+ }
+
+ @Override
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ BufferedReader in = null;
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ 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();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+ }
+
+ @Override
+ 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);
+ }
+
+ @Override
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.eps_generation_not_implemented"));
+ }
+
+ @Override
+ public void png_actionPerformed(ActionEvent e)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.png_generation_not_implemented"));
+ }
+
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
+
+ @Override
+ 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);
++ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ }
+ }
+ }
+
+ @Override
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour.setSelected(true);
+ jmb.colourByChain();
+ }
+
+ @Override
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
+ }
+
+ @Override
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)
+ {
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
+ }
+
+ @Override
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)
+ {
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
+ }
+
+ @Override
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)
+ {
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
+ }
+
+ @Override
+ public void helixColour_actionPerformed(ActionEvent actionEvent)
+ {
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
+ }
+
+ @Override
+ public void strandColour_actionPerformed(ActionEvent actionEvent)
+ {
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
+ }
+
+ @Override
+ public void turnColour_actionPerformed(ActionEvent actionEvent)
+ {
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
+ }
+
+ @Override
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)
+ {
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
+ }
+
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
+ @Override
+ public void userColour_actionPerformed(ActionEvent actionEvent)
+ {
+ userColour.setSelected(true);
+ new UserDefinedColours(this, null);
+ }
+
+ @Override
+ public void backGround_actionPerformed(ActionEvent actionEvent)
+ {
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
+ if (col != null)
+ {
+ jmb.setBackgroundColour(col);
+ }
+ }
+
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ 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(true));
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ viewerActionMenu.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 : viewerActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ viewerActionMenu.remove((JMenuItem) c);
+ }
+ }
+ }
+
+ /*
+ * (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 Chimera 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 isColouredByChimera()
+ {
+ return !jmb.isColourBySequence();
+ }
+
+ public SequenceStructureBinding getBinding()
+ {
+ return jmb;
+ }
+
+ }
*/
package jalview.gui;
- import java.io.*;
- import java.util.*;
- import java.util.List;
- import java.awt.*;
- import java.awt.event.*;
- import java.beans.PropertyChangeEvent;
- import java.beans.PropertyChangeListener;
-
- import javax.swing.*;
- import javax.swing.event.*;
- import javax.swing.table.*;
-
--import jalview.analysis.AlignmentSorter;
- import jalview.api.FeaturesDisplayedI;
import jalview.bin.Cache;
--import jalview.commands.OrderCommand;
- import jalview.datamodel.*;
- import jalview.io.*;
-import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
+ import jalview.datamodel.SequenceI;
+ import jalview.io.JalviewFileChooser;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
+ import java.awt.BorderLayout;
+ import java.awt.Color;
+ import java.awt.Component;
+ import java.awt.Font;
+ import java.awt.Graphics;
+ import java.awt.GridLayout;
+ import java.awt.Rectangle;
+ import java.awt.event.ActionEvent;
+ import java.awt.event.ActionListener;
+ import java.awt.event.ItemEvent;
+ import java.awt.event.ItemListener;
+ import java.awt.event.MouseAdapter;
+ import java.awt.event.MouseEvent;
+ import java.awt.event.MouseMotionAdapter;
+ import java.beans.PropertyChangeEvent;
+ import java.beans.PropertyChangeListener;
+ import java.io.File;
+ import java.io.FileInputStream;
+ import java.io.FileOutputStream;
+ import java.io.InputStreamReader;
+ import java.io.OutputStreamWriter;
+ import java.io.PrintWriter;
-import java.util.ArrayList;
+ import java.util.Hashtable;
+ import java.util.Iterator;
+ import java.util.List;
++import java.util.Set;
+ import java.util.Vector;
+
+ import javax.swing.AbstractCellEditor;
+ import javax.swing.BorderFactory;
+ import javax.swing.Icon;
+ import javax.swing.JButton;
+ import javax.swing.JCheckBox;
+ import javax.swing.JCheckBoxMenuItem;
+ import javax.swing.JColorChooser;
+ import javax.swing.JDialog;
+ import javax.swing.JInternalFrame;
+ import javax.swing.JLabel;
+ import javax.swing.JLayeredPane;
+ import javax.swing.JMenuItem;
+ import javax.swing.JOptionPane;
+ import javax.swing.JPanel;
+ import javax.swing.JPopupMenu;
+ import javax.swing.JScrollPane;
+ import javax.swing.JSlider;
+ import javax.swing.JTabbedPane;
+ import javax.swing.JTable;
+ import javax.swing.ListSelectionModel;
+ import javax.swing.SwingConstants;
+ import javax.swing.SwingUtilities;
+ import javax.swing.event.ChangeEvent;
+ import javax.swing.event.ChangeListener;
+ import javax.swing.table.AbstractTableModel;
+ import javax.swing.table.TableCellEditor;
+ import javax.swing.table.TableCellRenderer;
+
public class FeatureSettings extends JPanel
{
DasSourceBrowser dassourceBrowser;
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (evt.isPopupTrigger())
+ if (SwingUtilities.isRightMouseButton(evt))
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
- evt.getY());
+ table.getValueAt(selectedRow, 1), fr.getMinMax(),
+ evt.getX(), evt.getY());
}
else if (evt.getClickCount() == 2)
{
(String) table.getValueAt(selectedRow, 0));
}
}
+
+ // isPopupTrigger fires on mouseReleased on Mac
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ selectedRow = table.rowAtPoint(evt.getPoint());
+ if (evt.isPopupTrigger())
+ {
+ popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
++ table.getValueAt(selectedRow, 1), fr.getMinMax(),
++ evt.getX(),
+ evt.getY());
+ }
+ }
});
table.addMouseMotionListener(new MouseMotionAdapter()
{
order[i] = fr.getOrder(data[i][0].toString());
if (order[i] < 0)
++ {
order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
++ }
if (i > 1)
++ {
sort = sort || order[i - 1] > order[i];
++ }
}
if (sort)
++ {
jalview.util.QuickSort.sort(order, data);
++ }
}
void load()
public void orderByAvWidth()
{
if (table == null || table.getModel() == null)
++ {
return;
++ }
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
width[i] = 0;
}
if (max < width[i])
++ {
max = width[i];
++ }
}
boolean sort = false;
for (int i = 0; i < width.length; i++)
fr.setOrder(data[i][0].toString(), width[i]); // store for later
}
if (i > 0)
++ {
sort = sort || width[i - 1] > width[i];
++ }
}
if (sort)
++ {
jalview.util.QuickSort.sort(width, data);
// update global priority order
++ }
updateFeatureRenderer(data, false);
table.repaint();
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
+
AnnotationElement ae;
if (aa[i].annotations != null)
{
{
skipList = skipList2;
}
--
}
*/
package jalview.gui;
- import java.io.*;
- import java.util.*;
- import java.util.jar.*;
+ import jalview.binding.Annotation;
+ import jalview.binding.AnnotationElement;
+ import jalview.binding.Features;
+ import jalview.binding.JGroup;
+ import jalview.binding.JSeq;
+ import jalview.binding.JalviewModel;
+ import jalview.binding.JalviewModelSequence;
+ import jalview.binding.Pdbids;
+ import jalview.binding.Sequence;
+ import jalview.binding.SequenceSet;
+ import jalview.binding.Setting;
+ import jalview.binding.Tree;
+ import jalview.binding.UserColours;
+ import jalview.binding.Viewport;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.ColourSchemeProperty;
+ import jalview.schemes.ResidueProperties;
+ import jalview.structure.StructureSelectionManager;
+ import jalview.util.MessageManager;
+ import jalview.util.jarInputStreamProvider;
- import javax.swing.*;
+ import java.io.InputStreamReader;
+ import java.util.Hashtable;
+ import java.util.Vector;
+ import java.util.jar.JarEntry;
+ import java.util.jar.JarInputStream;
- import org.exolab.castor.xml.*;
+ import javax.swing.JOptionPane;
- import jalview.binding.*;
- import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
+ import org.exolab.castor.xml.IDResolver;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
/**
* DOCUMENT ME!
--- /dev/null
+ package jalview.gui;
+
+ import jalview.api.AlignmentViewPanel;
+ import jalview.datamodel.PDBEntry;
+ import jalview.datamodel.SequenceI;
+ import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+ import jalview.structure.StructureSelectionManager;
+
+ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
+ {
+ private ChimeraViewFrame cvf;
+
+ public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
+ StructureSelectionManager ssm, PDBEntry[] pdbentry,
+ SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, chains, protocol);
+ cvf = chimeraViewFrame;
+ }
+
+ FeatureRenderer fr = null;
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
+ {
+ AlignmentPanel ap = (alignment == null) ? cvf.ap
+ : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
++ if (ap.av.isShowSequenceFeatures())
+ {
+ if (fr == null)
+ {
- fr = ap.cloneFeatureRenderer();
++ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
+ }
+ }
+
+ return fr;
+ }
+
+ @Override
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
+ }
+ @Override
+ public void refreshGUI()
+ {
+ // appJmolWindow.repaint();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ cvf.updateTitleAndMenus();
+ cvf.revalidate();
+ }
+ });
+ }
+
+ public void updateColours(Object source)
+ {
+ AlignmentPanel ap = (AlignmentPanel) source, topap;
+ // ignore events from panels not used to colour this view
+ if (!cvf.isUsedforcolourby(ap))
+ {
+ return;
+ }
+ if (!isLoadingFromArchive())
+ {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
++ colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ }
+ }
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void refreshPdbEntries()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void showUrl(String url, String target)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ }
--- /dev/null
+package jalview.viewmodel.seqfeatures;
+
+import jalview.api.AlignViewportI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.GraduatedColor;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import java.util.Arrays;
- import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
- import java.util.Vector;
+import java.util.concurrent.ConcurrentHashMap;
+
+public abstract class FeatureRendererModel implements
+ jalview.api.FeatureRenderer
+{
+
+ /**
+ * global transparency for feature
+ */
+ protected float transparency = 1.0f;
+
+ protected Map<String, Object> featureColours = new ConcurrentHashMap<String, Object>();
+
+ protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
+
+ protected Object currentColour;
+
+ protected String[] renderOrder;
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ protected AlignmentViewport av;
+
+ public AlignViewportI getViewport()
+ {
+ return av;
+ }
+
+ public FeatureRendererSettings getSettings()
+ {
+ return new FeatureRendererSettings(this);
+ }
+
+ public void transferSettings(FeatureRendererSettings fr)
+ {
+ this.renderOrder = fr.renderOrder;
+ this.featureGroups = fr.featureGroups;
+ this.featureColours = fr.featureColours;
+ this.transparency = fr.transparency;
+ this.featureOrder = fr.featureOrder;
+ }
+
+ /**
+ * update from another feature renderer
+ *
+ * @param fr
+ * settings to copy
+ */
+ public void transferSettings(jalview.api.FeatureRenderer _fr)
+ {
+ FeatureRenderer fr = (FeatureRenderer) _fr;
+ FeatureRendererSettings frs = new FeatureRendererSettings(fr);
+ this.renderOrder = frs.renderOrder;
+ this.featureGroups = frs.featureGroups;
+ this.featureColours = frs.featureColours;
+ this.transparency = frs.transparency;
+ this.featureOrder = frs.featureOrder;
+ if (av != null && av != fr.getViewport())
+ {
+ // copy over the displayed feature settings
+ if (_fr.getFeaturesDisplayed() != null)
+ {
+ FeaturesDisplayedI fd = getFeaturesDisplayed();
+ if (fd == null)
+ {
+ setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
+ }
+ else
+ {
+ synchronized (fd)
+ {
+ fd.clear();
+ java.util.Iterator<String> fdisp = _fr.getFeaturesDisplayed()
+ .getVisibleFeatures();
+ while (fdisp.hasNext())
+ {
+ fd.setVisible(fdisp.next());
+ }
+ }
+ }
+ }
+ }
+ }
+
+ public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
+ {
+ av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
+ }
+
+ @Override
+ public void setVisible(String featureType)
+ {
+ FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
+ if (fdi == null)
+ {
+ av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
+ }
+ if (!fdi.isRegistered(featureType))
+ {
+ pushFeatureType(Arrays.asList(new String[]
+ { featureType }));
+ }
+ fdi.setVisible(featureType);
+ }
+
+ @Override
+ public void setAllVisible(List<String> featureTypes)
+ {
+ FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
+ if (fdi == null)
+ {
+ av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
+ }
+ List<String> nft = new ArrayList<String>();
+ for (String featureType : featureTypes)
+ {
+ if (!fdi.isRegistered(featureType))
+ {
+ nft.add(featureType);
+ }
+ }
+ if (nft.size() > 0)
+ {
+ pushFeatureType(nft);
+ }
+ fdi.setAllVisible(featureTypes);
+ }
+
+ /**
+ * push a set of new types onto the render order stack. Note - this is a
+ * direct mechanism rather than the one employed in updateRenderOrder
+ *
+ * @param types
+ */
+ private void pushFeatureType(List<String> types)
+ {
+
+ int ts = types.size();
+ String neworder[] = new String[(renderOrder == null ? 0
+ : renderOrder.length) + ts];
+ types.toArray(neworder);
+ if (renderOrder != null)
+ {
+ System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
+ System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
+ }
+ renderOrder = neworder;
+ }
+
+ protected Hashtable minmax = new Hashtable();
+
+ public Hashtable getMinMax()
+ {
+ return minmax;
+ }
+
+ /**
+ * normalise a score against the max/min bounds for the feature type.
+ *
+ * @param sequenceFeature
+ * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
+ * (0-255) value.
+ */
+ protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
+ {
+ float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
+ final byte[] r = new byte[]
+ { 0, (byte) 255 };
+ if (mm != null)
+ {
+ if (r[0] != 0 || mm[0] < 0.0)
+ {
+ r[0] = 1;
+ r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+ }
+ else
+ {
+ r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
+ }
+ }
+ return r;
+ }
+
+ boolean newFeatureAdded = false;
+
+ boolean findingFeatures = false;
+
+ protected boolean updateFeatures()
+ {
+ if (av.getFeaturesDisplayed() == null || renderOrder == null
+ || newFeatureAdded)
+ {
+ findAllFeatures();
+ if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
+ {
+ return false;
+ }
+ }
+ // TODO: decide if we should check for the visible feature count first
+ return true;
+ }
+
+ /**
+ * search the alignment for all new features, give them a colour and display
+ * them. Then fires a PropertyChangeEvent on the changeSupport object.
+ *
+ */
+ protected void findAllFeatures()
+ {
+ synchronized (firing)
+ {
+ if (firing.equals(Boolean.FALSE))
+ {
+ firing = Boolean.TRUE;
+ findAllFeatures(true); // add all new features as visible
+ changeSupport.firePropertyChange("changeSupport", null, null);
+ firing = Boolean.FALSE;
+ }
+ }
+ }
+
+ @Override
+ public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (!av.areFeaturesDisplayed()
+ || !av.getFeaturesDisplayed().isVisible(
+ features[i].getType()))
+ {
+ continue;
+ }
+
+ if (features[i].featureGroup != null
+ && featureGroups != null
+ && featureGroups.containsKey(features[i].featureGroup)
- && !((Boolean) featureGroups.get(features[i].featureGroup))
++ && !featureGroups.get(features[i].featureGroup)
+ .booleanValue())
++ {
+ continue;
++ }
+
+ if ((features[i].getBegin() <= res)
+ && (features[i].getEnd() >= res))
+ {
+ tmp.add(features[i]);
+ }
+ }
+ }
+ return tmp;
+ }
+
+ /**
+ * Searches alignment for all features and updates colours
+ *
+ * @param newMadeVisible
+ * if true newly added feature types will be rendered immediatly
+ * TODO: check to see if this method should actually be proxied so
+ * repaint events can be propagated by the renderer code
+ */
+ @Override
+ public synchronized void findAllFeatures(boolean newMadeVisible)
+ {
+ newFeatureAdded = false;
+
+ if (findingFeatures)
+ {
+ newFeatureAdded = true;
+ return;
+ }
+
+ findingFeatures = true;
+ if (av.getFeaturesDisplayed() == null)
+ {
+ av.setFeaturesDisplayed(new FeaturesDisplayed());
+ }
+ FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
+
+ ArrayList<String> allfeatures = new ArrayList<String>();
+ ArrayList<String> oldfeatures = new ArrayList<String>();
+ if (renderOrder != null)
+ {
+ for (int i = 0; i < renderOrder.length; i++)
+ {
+ if (renderOrder[i] != null)
+ {
+ oldfeatures.add(renderOrder[i]);
+ }
+ }
+ }
+ if (minmax == null)
+ {
+ minmax = new Hashtable();
+ }
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ SequenceI asq = alignment.getSequenceAt(i);
+ SequenceI dasq = asq.getDatasetSequence();
+ SequenceFeature[] features = dasq != null ? dasq
+ .getSequenceFeatures() : asq.getSequenceFeatures();
+
+ if (features == null)
+ {
+ continue;
+ }
+
+ int index = 0;
+ while (index < features.length)
+ {
+ if (!featuresDisplayed.isRegistered(features[index].getType()))
+ {
+ String fgrp = features[index].getFeatureGroup();
+ if (fgrp != null)
+ {
+ Boolean groupDisplayed = featureGroups.get(fgrp);
+ if (groupDisplayed == null)
+ {
+ groupDisplayed = Boolean.valueOf(newMadeVisible);
+ featureGroups.put(fgrp, groupDisplayed);
+ }
- if (!((Boolean) groupDisplayed).booleanValue())
++ if (!groupDisplayed.booleanValue())
+ {
+ index++;
+ continue;
+ }
+ }
+ if (!(features[index].begin == 0 && features[index].end == 0))
+ {
+ // If beginning and end are 0, the feature is for the whole sequence
+ // and we don't want to render the feature in the normal way
+
+ if (newMadeVisible
+ && !oldfeatures.contains(features[index].getType()))
+ {
+ // this is a new feature type on the alignment. Mark it for
+ // display.
+ featuresDisplayed.setVisible(features[index].getType());
+ setOrder(features[index].getType(), 0);
+ }
+ }
+ }
+ if (!allfeatures.contains(features[index].getType()))
+ {
+ allfeatures.add(features[index].getType());
+ }
+ if (features[index].score != Float.NaN)
+ {
+ int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
+ float[][] mm = (float[][]) minmax.get(features[index].getType());
+ if (mm == null)
+ {
+ mm = new float[][]
+ { null, null };
+ minmax.put(features[index].getType(), mm);
+ }
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
+ }
+ else
+ {
+ if (mm[nonpos][0] > features[index].score)
+ {
+ mm[nonpos][0] = features[index].score;
+ }
+ if (mm[nonpos][1] < features[index].score)
+ {
+ mm[nonpos][1] = features[index].score;
+ }
+ }
+ }
+ index++;
+ }
+ }
+ updateRenderOrder(allfeatures);
+ findingFeatures = false;
+ }
+
+ protected Boolean firing = Boolean.FALSE;
+
+ /**
+ * replaces the current renderOrder with the unordered features in
+ * allfeatures. The ordering of any types in both renderOrder and allfeatures
+ * is preserved, and all new feature types are rendered on top of the existing
+ * types, in the order given by getOrder or the order given in allFeatures.
+ * Note. this operates directly on the featureOrder hash for efficiency. TODO:
+ * eliminate the float storage for computing/recalling the persistent ordering
+ * New Cability: updates min/max for colourscheme range if its dynamic
+ *
+ * @param allFeatures
+ */
+ private void updateRenderOrder(List<String> allFeatures)
+ {
+ List<String> allfeatures = new ArrayList<String>(allFeatures);
+ String[] oldRender = renderOrder;
+ renderOrder = new String[allfeatures.size()];
+ Object mmrange, fc = null;
+ boolean initOrders = (featureOrder == null);
+ int opos = 0;
+ if (oldRender != null && oldRender.length > 0)
+ {
+ for (int j = 0; j < oldRender.length; j++)
+ {
+ if (oldRender[j] != null)
+ {
+ if (initOrders)
+ {
+ setOrder(oldRender[j], (1 - (1 + (float) j)
- / (float) oldRender.length));
++ / oldRender.length));
+ }
+ if (allfeatures.contains(oldRender[j]))
+ {
+ renderOrder[opos++] = oldRender[j]; // existing features always
+ // appear below new features
+ allfeatures.remove(oldRender[j]);
+ if (minmax != null)
+ {
+ mmrange = minmax.get(oldRender[j]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(oldRender[j]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(
+ ((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ if (allfeatures.size() == 0)
+ {
+ // no new features - leave order unchanged.
+ return;
+ }
+ int i = allfeatures.size() - 1;
+ int iSize = i;
+ boolean sort = false;
+ String[] newf = new String[allfeatures.size()];
+ float[] sortOrder = new float[allfeatures.size()];
+ for (String newfeat : allfeatures)
+ {
+ newf[i] = newfeat;
+ if (minmax != null)
+ {
+ // update from new features minmax if necessary
+ mmrange = minmax.get(newf[i]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(newf[i]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
+ if (initOrders || !featureOrder.containsKey(newf[i]))
+ {
+ int denom = initOrders ? allfeatures.size() : featureOrder.size();
+ // new unordered feature - compute persistent ordering at head of
+ // existing features.
+ setOrder(newf[i], i / (float) denom);
+ }
+ // set order from newly found feature from persisted ordering.
+ sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
+ if (i < iSize)
+ {
+ // only sort if we need to
+ sort = sort || sortOrder[i] > sortOrder[i + 1];
+ }
+ i--;
+ }
+ if (iSize > 1 && sort)
+ {
+ jalview.util.QuickSort.sort(sortOrder, newf);
+ }
+ sortOrder = null;
+ System.arraycopy(newf, 0, renderOrder, opos, newf.length);
+ }
+
+ /**
+ * get a feature style object for the given type string. Creates a
+ * java.awt.Color for a featureType with no existing colourscheme. TODO:
+ * replace return type with object implementing standard abstract colour/style
+ * interface
+ *
+ * @param featureType
+ * @return java.awt.Color or GraduatedColor
+ */
+ public Object getFeatureStyle(String featureType)
+ {
+ Object fc = featureColours.get(featureType);
+ if (fc == null)
+ {
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+ Color col = ucs.createColourFromName(featureType);
+ featureColours.put(featureType, fc = col);
+ }
+ return fc;
+ }
+
+ /**
+ * return a nominal colour for this feature
+ *
+ * @param featureType
+ * @return standard color, or maximum colour for graduated colourscheme
+ */
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + featureType);
+ }
+
+ /**
+ * calculate the render colour for a specific feature using current feature
+ * settings.
+ *
+ * @param feature
+ * @return render colour for the given feature
+ */
+ public Color getColour(SequenceFeature feature)
+ {
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).findColor(feature);
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + feature.getType());
+ }
+
+ protected boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ protected boolean showFeatureOfType(String type)
+ {
+ return av.getFeaturesDisplayed().isVisible(type);
+ }
+
+ public void setColour(String featureType, Object col)
+ {
+ // overwrite
+ // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
+ // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
+ // Object c = featureColours.get(featureType);
+ // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
+ // !((GraduatedColor)c).getMaxColor().equals(_col)))
+ {
+ featureColours.put(featureType, col);
+ }
+ }
+
+ public void setTransparency(float value)
+ {
+ transparency = value;
+ }
+
+ public float getTransparency()
+ {
+ return transparency;
+ }
+
+ Map featureOrder = null;
+
+ /**
+ * analogous to colour - store a normalized ordering for all feature types in
+ * this rendering context.
+ *
+ * @param type
+ * Feature type string
+ * @param position
+ * normalized priority - 0 means always appears on top, 1 means
+ * always last.
+ */
+ public float setOrder(String type, float position)
+ {
+ if (featureOrder == null)
+ {
+ featureOrder = new Hashtable();
+ }
+ featureOrder.put(type, new Float(position));
+ return position;
+ }
+
+ /**
+ * get the global priority (0 (top) to 1 (bottom))
+ *
+ * @param type
+ * @return [0,1] or -1 for a type without a priority
+ */
+ public float getOrder(String type)
+ {
+ if (featureOrder != null)
+ {
+ if (featureOrder.containsKey(type))
+ {
+ return ((Float) featureOrder.get(type)).floatValue();
+ }
+ }
+ return -1;
+ }
+
+ @Override
- public Map getFeatureColours()
++ public Map<String, Object> getFeatureColours()
+ {
- return new ConcurrentHashMap<>(featureColours);
++ return new ConcurrentHashMap<String, Object>(featureColours);
+ }
+
+ /**
+ * Replace current ordering with new ordering
+ *
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
+ */
+ public void setFeaturePriority(Object[][] data)
+ {
+ setFeaturePriority(data, true);
+ }
+
+ /**
+ *
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
+ * @param visibleNew
+ * when true current featureDisplay list will be cleared
+ */
+ public void setFeaturePriority(Object[][] data, boolean visibleNew)
+ {
+ FeaturesDisplayedI av_featuresdisplayed = null;
+ if (visibleNew)
+ {
+ if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
+ {
+ av.getFeaturesDisplayed().clear();
+ }
+ else
+ {
+ av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+ }
+ }
+ else
+ {
+ av_featuresdisplayed = av.getFeaturesDisplayed();
+ }
+ if (data == null)
+ {
+ return;
+ }
+ // The feature table will display high priority
+ // features at the top, but theses are the ones
+ // we need to render last, so invert the data
+ renderOrder = new String[data.length];
+
+ if (data.length > 0)
+ {
+ for (int i = 0; i < data.length; i++)
+ {
+ String type = data[i][0].toString();
+ setColour(type, data[i][1]); // todo : typesafety - feature color
+ // interface object
+ if (((Boolean) data[i][2]).booleanValue())
+ {
+ av_featuresdisplayed.setVisible(type);
+ }
+
+ renderOrder[data.length - i - 1] = type;
+ }
+ }
+
+ }
+
+ /**
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ public Set getAllFeatureColours()
+ {
+ return featureColours.keySet();
+ }
+
+ public void clearRenderOrder()
+ {
+ renderOrder = null;
+ }
+
+ public boolean hasRenderOrder()
+ {
+ return renderOrder != null;
+ }
+
+ public List<String> getRenderOrder()
+ {
+ if (renderOrder == null)
+ {
+ return Arrays.asList(new String[]
+ {});
+ }
+ return Arrays.asList(renderOrder);
+ }
+
+ public int getFeatureGroupsSize()
+ {
+ return featureGroups != null ? 0 : featureGroups.size();
+ }
+
+ @Override
+ public List<String> getFeatureGroups()
+ {
+ // conflict between applet and desktop - featureGroups returns the map in
+ // the desktop featureRenderer
+ return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
+ .asList(featureGroups.keySet().toArray(new String[0]));
+ }
+
+ public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
+ {
+ if (featureGroups == null)
+ {
+ // then an exception happens next..
+ }
+ if (featureGroups.containsKey(group))
+ {
- return ((Boolean) featureGroups.get(group)).booleanValue();
++ return featureGroups.get(group).booleanValue();
+ }
+ if (newGroupsVisible)
+ {
+ featureGroups.put(group, new Boolean(true));
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * get visible or invisible groups
+ *
+ * @param visible
+ * true to return visible groups, false to return hidden ones.
+ * @return list of groups
+ */
+ @Override
+ public List getGroups(boolean visible)
+ {
+ if (featureGroups != null)
+ {
+ ArrayList gp = new ArrayList();
+
+ for (Object grp : featureGroups.keySet())
+ {
- Boolean state = (Boolean) featureGroups.get(grp);
++ Boolean state = featureGroups.get(grp);
+ if (state.booleanValue() == visible)
+ {
+ gp.add(grp);
+ }
+ }
+ return gp;
+ }
+ return null;
+ }
+
+ @Override
+ public void setGroupVisibility(String group, boolean visible)
+ {
+ featureGroups.put(group, new Boolean(visible));
+ }
+
+ @Override
+ public void setGroupVisibility(List<String> toset, boolean visible)
+ {
+ if (toset != null && toset.size() > 0 && featureGroups != null)
+ {
+ boolean rdrw = false;
+ for (String gst : toset)
+ {
+ Boolean st = featureGroups.get(gst);
+ featureGroups.put(gst, new Boolean(visible));
+ if (st != null)
+ {
- rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
++ rdrw = rdrw || (visible != st.booleanValue());
+ }
+ }
+ if (rdrw)
+ {
+ // set local flag indicating redraw needed ?
+ }
+ }
+ }
+
+ @Override
+ public Hashtable getDisplayedFeatureCols()
+ {
+ Hashtable fcols = new Hashtable();
+ if (getViewport().getFeaturesDisplayed() == null)
+ {
+ return fcols;
+ }
+ Iterator<String> en = getViewport().getFeaturesDisplayed()
+ .getVisibleFeatures();
+ while (en.hasNext())
+ {
+ String col = en.next();
+ fcols.put(col, getColour(col));
+ }
+ return fcols;
+ }
+
+ @Override
+ public FeaturesDisplayedI getFeaturesDisplayed()
+ {
+ return av.getFeaturesDisplayed();
+ }
+
+ @Override
+ public String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ typ = getRenderOrder().toArray(new String[0]);
+ FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
+ if (feature_disp != null)
+ {
+ synchronized (feature_disp)
+ {
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (feature_disp.isVisible(typ[i]))
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ }
+ return typ;
+ }
+
+ @Override
+ public String[] getDisplayedFeatureGroups()
+ {
+ String[] gps = null;
+ ArrayList<String> _gps = new ArrayList<String>();
+ Iterator en = getFeatureGroups().iterator();
+ int g = 0;
+ boolean valid = false;
+ while (en.hasNext())
+ {
+ String gp = (String) en.next();
+ if (checkGroupVisibility(gp, false))
+ {
+ valid = true;
+ _gps.add(gp);
+ }
+ if (!valid)
+ {
+ return null;
+ }
+ else
+ {
+ gps = new String[_gps.size()];
+ _gps.toArray(gps);
+ }
+ }
+ return gps;
+ }
+
+}
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+ import jalview.util.MessageManager;
public abstract class AWSThread extends Thread
{
git://source.jalview.org / jalview.git / commitdiff