X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=1bbc39732d3b95dce1f121579c90ec80c54f4d89;hb=aa643d0f2f5f506df2771e216af1618549d32050;hp=e084417b02d632f29f08d34b41e0766f6b1fe0a2;hpb=0ca159283d6fdd7b76b033421393209ee8c0c8a8;p=jalview.git diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index e084417..1bbc397 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -20,25 +20,6 @@ */ package jalview.gui; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.StructureViewer.ViewerType; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.io.DataSourceType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GStructureViewer; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemes; -import jalview.structure.StructureMapping; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Component; import java.awt.event.ActionEvent; @@ -53,6 +34,7 @@ import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; +import java.util.Random; import java.util.Vector; import javax.swing.ButtonGroup; @@ -64,6 +46,24 @@ import javax.swing.JRadioButtonMenuItem; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.io.DataSourceType; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GStructureViewer; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.structure.StructureMapping; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.MessageManager; +import jalview.ws.dbsources.Pdb; + /** * Base class with common functionality for JMol, Chimera or other structure * viewers. @@ -90,13 +90,13 @@ public abstract class StructureViewerBase extends GStructureViewer /** * list of alignment panels to use for superposition */ - protected Vector _alignwith = new Vector<>(); + protected Vector _alignwith = new Vector<>(); /** * list of alignment panels that are used for colouring structures by aligned * sequences */ - protected Vector _colourwith = new Vector<>(); + protected Vector _colourwith = new Vector<>(); private String viewId = null; @@ -121,6 +121,10 @@ public abstract class StructureViewerBase extends GStructureViewer */ protected volatile boolean seqColoursApplied = false; + private IProgressIndicator progressBar = null; + + private Random random = new Random(); + /** * Default constructor */ @@ -130,6 +134,26 @@ public abstract class StructureViewerBase extends GStructureViewer } /** + * @return true if added structures should be aligned to existing one(s) + */ + @Override + public boolean isAlignAddedStructures() + { + return alignAddedStructures; + } + + /** + * + * @param true + * if added structures should be aligned to existing one(s) + */ + @Override + public void setAlignAddedStructures(boolean alignAdded) + { + alignAddedStructures = alignAdded; + } + + /** * * @param ap2 * @return true if this Jmol instance is linked with the given alignPanel @@ -139,13 +163,14 @@ public abstract class StructureViewerBase extends GStructureViewer return _aps.contains(ap2.av.getSequenceSetId()); } - public boolean isUsedforaligment(AlignmentPanel ap2) + public boolean isUsedforaligment(AlignmentViewPanel ap2) { return (_alignwith != null) && _alignwith.contains(ap2); } - public boolean isUsedforcolourby(AlignmentPanel ap2) + @Override + public boolean isUsedForColourBy(AlignmentViewPanel ap2) { return (_colourwith != null) && _colourwith.contains(ap2); } @@ -173,8 +198,6 @@ public abstract class StructureViewerBase extends GStructureViewer this.viewId = viewId; } - public abstract String getStateInfo(); - protected void buildActionMenu() { if (_alignwith == null) @@ -195,6 +218,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } + @Override public AlignmentPanel getAlignmentPanel() { return ap; @@ -247,7 +271,8 @@ public abstract class StructureViewerBase extends GStructureViewer * * @param nap */ - public void removeAlignmentPanel(AlignmentPanel nap) + @Override + public void removeAlignmentPanel(AlignmentViewPanel nap) { try { @@ -319,8 +344,6 @@ public abstract class StructureViewerBase extends GStructureViewer public abstract ViewerType getViewerType(); - protected abstract IProgressIndicator getIProgressIndicator(); - /** * add a new structure (with associated sequences and chains) to this viewer, * retrieving it if necessary first. @@ -335,7 +358,7 @@ public abstract class StructureViewerBase extends GStructureViewer */ protected void addStructure(final PDBEntry pdbentry, final SequenceI[] seqs, final String[] chains, - final boolean align, final IProgressIndicator alignFrame) + final IProgressIndicator alignFrame) { if (pdbentry.getFile() == null) { @@ -359,7 +382,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } // and call ourselves again. - addStructure(pdbentry, seqs, chains, align, alignFrame); + addStructure(pdbentry, seqs, chains, alignFrame); } }).start(); return; @@ -371,33 +394,11 @@ public abstract class StructureViewerBase extends GStructureViewer { seqs }, new String[][] { chains }); addingStructures = true; _started = false; - alignAddedStructures = align; worker = new Thread(this); worker.start(); return; } - /** - * Presents a dialog with the option to add an align a structure to an - * existing structure view - * - * @param pdbId - * @param view - * @return YES, NO or CANCEL JvOptionPane code - */ - protected int chooseAlignStructureToViewer(String pdbId, - StructureViewerBase view) - { - int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage("label.add_pdbentry_to_view", - new Object[] - { pdbId, view.getTitle() }), - MessageManager - .getString("label.align_to_existing_structure_view"), - JvOptionPane.YES_NO_CANCEL_OPTION); - return option; - } - protected boolean hasPdbId(String pdbId) { return getBinding().hasPdbId(pdbId); @@ -412,35 +413,23 @@ public abstract class StructureViewerBase extends GStructureViewer return Desktop.instance.getStructureViewers(alp, this.getClass()); } - - /** - * Check for any existing views involving this alignment and give user the - * option to add and align this molecule to one of them - * - * @param pdbentry - * @param seq - * @param chains - * @param apanel - * @param pdbId - * @return true if user adds to a view, or cancels entirely, else false - */ @Override - public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, + public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentViewPanel apanel, String pdbId) { /* * JAL-1742 exclude view with this structure already mapped (don't offer - * to align chain B to chain A of the same structure) + * to align chain B to chain A of the same structure); code may defend + * against this possibility before we reach here */ if (hasPdbId(pdbId)) { - return false; + return; } - AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this + AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this // cast fails - useAlignmentPanelForSuperposition(ap); - addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return true; + useAlignmentPanelForSuperposition(alignPanel); + addStructure(pdbentry, seq, chains, alignPanel.alignFrame); } /** @@ -463,7 +452,7 @@ public abstract class StructureViewerBase extends GStructureViewer * create the mappings */ apanel.getStructureSelectionManager().setMapping(seq, chains, - pdbFilename, DataSourceType.FILE, getIProgressIndicator()); + pdbFilename, DataSourceType.FILE, getProgressIndicator()); /* * alert the FeatureRenderer to show new (PDB RESNUM) features @@ -504,33 +493,20 @@ public abstract class StructureViewerBase extends GStructureViewer } } - /** - * Check if the PDB file is already loaded, if so offer to add it to the - * existing viewer - * - * @param seq - * @param chains - * @param apanel - * @param pdbId - * @return true if the user chooses to add to a viewer, or to cancel entirely - */ @Override public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains, final AlignmentViewPanel apanel, String pdbId) { - boolean finished = false; String alreadyMapped = apanel.getStructureSelectionManager() .alreadyMappedToFile(pdbId); - if (alreadyMapped != null) + if (alreadyMapped == null) { - /* - * the PDB file is already loaded - */ - addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); - finished = true; + return false; } - return finished; + + addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); + return true; } void setChainMenuItems(List chainNames) @@ -581,8 +557,6 @@ public abstract class StructureViewerBase extends GStructureViewer } } - abstract void showSelectedChains(); - /** * Action on selecting one of Jalview's registered colour schemes */ @@ -591,8 +565,9 @@ public abstract class StructureViewerBase extends GStructureViewer { AlignmentI al = getAlignmentPanel().av.getAlignment(); ColourSchemeI cs = ColourSchemes.getInstance() - .getColourScheme(colourSchemeName, al, null); - getBinding().setJalviewColourScheme(cs); + .getColourScheme(colourSchemeName, getAlignmentPanel().av, al, + null); + getBinding().colourByJalviewColourScheme(cs); } /** @@ -626,7 +601,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - viewerColour_actionPerformed(actionEvent); + viewerColour_actionPerformed(); } }); colourMenu.add(viewerColour); @@ -642,7 +617,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - background_actionPerformed(actionEvent); + background_actionPerformed(); } }); colourMenu.add(backGround); @@ -673,7 +648,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - seqColour_actionPerformed(actionEvent); + seqColour_actionPerformed(); } }); @@ -685,7 +660,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - chainColour_actionPerformed(actionEvent); + chainColour_actionPerformed(); } }); @@ -697,12 +672,15 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - chargeColour_actionPerformed(actionEvent); + chargeColour_actionPerformed(); } }); viewerColour = new JRadioButtonMenuItem(); - // text is set in overrides of this method + viewerColour + .setText(MessageManager.getString("label.colour_with_viewer")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_viewer_manage_structure_colours")); viewerColour.setName(ViewerColour.ByViewer.name()); viewerColour.setSelected(!binding.isColourBySequence()); @@ -729,7 +707,7 @@ public abstract class StructureViewerBase extends GStructureViewer else { // update the Chimera display now. - seqColour_actionPerformed(null); + seqColour_actionPerformed(); } } }); @@ -740,10 +718,18 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void itemStateChanged(ItemEvent e) { - alignStructs.setEnabled(!_alignwith.isEmpty()); - alignStructs.setToolTipText(MessageManager.formatMessage( - "label.align_structures_using_linked_alignment_views", - _alignwith.size())); + if (_alignwith.isEmpty()) + { + alignStructs.setEnabled(false); + alignStructs.setToolTipText(null); + } + else + { + alignStructs.setEnabled(true); + alignStructs.setToolTipText(MessageManager.formatMessage( + "label.align_structures_using_linked_alignment_views", + _alignwith.size())); + } } }; viewSelectionMenu = new ViewSelectionMenu( @@ -773,24 +759,13 @@ public abstract class StructureViewerBase extends GStructureViewer buildColourMenu(); } - @Override - public void setJalviewColourScheme(ColourSchemeI cs) - { - getBinding().setJalviewColourScheme(cs); - } - /** * Sends commands to the structure viewer to superimpose structures based on * currently associated alignments. May optionally return an error message for * the operation. */ @Override - protected String alignStructs_actionPerformed(ActionEvent actionEvent) - { - return alignStructs_withAllAlignPanels(); - } - - protected String alignStructs_withAllAlignPanels() + protected String alignStructsWithAllAlignPanels() { if (getAlignmentPanel() == null) { @@ -805,19 +780,8 @@ public abstract class StructureViewerBase extends GStructureViewer String reply = null; try { - AlignmentI[] als = new Alignment[_alignwith.size()]; - HiddenColumns[] alc = new HiddenColumns[_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.getAlignment().getHiddenColumns(); - } - reply = getBinding().superposeStructures(als, alm, alc); - if (reply != null) + reply = getBinding().superposeStructures(_alignwith); + if (reply != null && !reply.isEmpty()) { String text = MessageManager .formatMessage("error.superposition_failed", reply); @@ -826,9 +790,9 @@ public abstract class StructureViewerBase extends GStructureViewer } catch (Exception e) { StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) + for (AlignmentViewPanel alignPanel : _alignwith) { - sp.append("'" + ap.alignFrame.getTitle() + "' "); + sp.append("'" + alignPanel.getViewName() + "' "); } Cache.log.info("Couldn't align structures with the " + sp.toString() + "associated alignment panels.", e); @@ -837,7 +801,7 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void background_actionPerformed(ActionEvent actionEvent) + public void background_actionPerformed() { Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_background_colour"), @@ -849,7 +813,7 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) + public void viewerColour_actionPerformed() { if (viewerColour.isSelected()) { @@ -859,21 +823,21 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void chainColour_actionPerformed(ActionEvent actionEvent) + public void chainColour_actionPerformed() { chainColour.setSelected(true); getBinding().colourByChain(); } @Override - public void chargeColour_actionPerformed(ActionEvent actionEvent) + public void chargeColour_actionPerformed() { chargeColour.setSelected(true); getBinding().colourByCharge(); } @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) + public void seqColour_actionPerformed() { AAStructureBindingModel binding = getBinding(); binding.setColourBySequence(seqColour.isSelected()); @@ -892,16 +856,16 @@ public abstract class StructureViewerBase extends GStructureViewer } } // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) + for (AlignmentViewPanel alignPanel : _colourwith) { - binding.colourBySequence(ap); + binding.colourBySequence(alignPanel); } seqColoursApplied = true; } } @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) + public void pdbFile_actionPerformed() { JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); @@ -952,7 +916,7 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void viewMapping_actionPerformed(ActionEvent actionEvent) + public void viewMapping_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -976,6 +940,7 @@ public abstract class StructureViewerBase extends GStructureViewer /** * Configures the title and menu items of the viewer panel. */ + @Override public void updateTitleAndMenus() { AAStructureBindingModel binding = getBinding(); @@ -1013,11 +978,17 @@ public abstract class StructureViewerBase extends GStructureViewer if (!binding.isLoadingFromArchive()) { - seqColour_actionPerformed(null); + seqColour_actionPerformed(); } } @Override + public String toString() + { + return getTitle(); + } + + @Override public boolean hasMapping() { if (worker != null && (addingStructures || _started)) @@ -1054,4 +1025,141 @@ public abstract class StructureViewerBase extends GStructureViewer return seqColoursApplied; } + @Override + public void raiseViewer() + { + toFront(); + } + + @Override + public long startProgressBar(String msg) + { + // TODO would rather have startProgress/stopProgress as the + // IProgressIndicator interface + long tm = random.nextLong(); + if (progressBar != null) + { + progressBar.setProgressBar(msg, tm); + } + return tm; + } + + @Override + public void stopProgressBar(String msg, long handle) + { + if (progressBar != null) + { + progressBar.setProgressBar(msg, handle); + } + } + + protected IProgressIndicator getProgressIndicator() + { + return progressBar; + } + + protected void setProgressIndicator(IProgressIndicator pi) + { + progressBar = pi; + } + + protected void setProgressMessage(String message, long id) + { + if (progressBar != null) + { + progressBar.setProgressBar(message, id); + } + } + + @Override + public void showConsole(boolean show) + { + // default does nothing + } + + /** + * Show only the selected chain(s) in the viewer + */ + protected void showSelectedChains() + { + List toshow = new ArrayList<>(); + 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()); + } + } + } + getBinding().showChains(toshow); + } + + /** + * Tries to fetch a PDB file and save to a temporary local file. Returns the + * saved file path if successful, or null if not. + * + * @param processingEntry + * @return + */ + protected String fetchPdbFile(PDBEntry processingEntry) + { + String filePath = null; + Pdb pdbclient = new Pdb(); + AlignmentI pdbseq = null; + String pdbid = processingEntry.getId(); + long handle = System.currentTimeMillis() + + Thread.currentThread().hashCode(); + + /* + * Write 'fetching PDB' progress on AlignFrame as we are not yet visible + */ + String msg = MessageManager.formatMessage("status.fetching_pdb", + new Object[] + { pdbid }); + getAlignmentPanel().alignFrame.setProgressBar(msg, handle); + // long hdl = startProgressBar(MessageManager.formatMessage( + // "status.fetching_pdb", new Object[] + // { pdbid })); + try + { + pdbseq = pdbclient.getSequenceRecords(pdbid); + } catch (Exception e) + { + System.err.println( + "Error retrieving PDB id " + pdbid + ": " + e.getMessage()); + } finally + { + msg = pdbid + " " + MessageManager.getString("label.state_completed"); + getAlignmentPanel().alignFrame.setProgressBar(msg, handle); + // stopProgressBar(msg, 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(pdbseq.getSequenceAt(0).getAllPDBEntries() + .elementAt(0).getFile()).getAbsolutePath(); + processingEntry.setFile(filePath); + } + return filePath; + } + + /** + * If supported, saves the state of the structure viewer to a temporary file + * and returns the file, else returns null + * + * @return + */ + public File saveSession() + { + // TODO: a wait loop to ensure the file is written fully before returning? + return getBinding() == null ? null : getBinding().saveSession(); + } + }