X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=6dd7d502467bba44e8e9a5c3fa587cf0dc5deea1;hb=9c1a9d682a2664d525bfd0f38bae861292dc3921;hp=31c20ed098d55338973deabb3724e2a01d5f000c;hpb=4ed4e90803e3a463458410be06b678ff3154937f;p=jalview.git diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 31c20ed..6dd7d50 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -20,10 +20,9 @@ */ 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; @@ -34,6 +33,7 @@ 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; @@ -51,6 +51,7 @@ 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; @@ -88,13 +89,13 @@ 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; @@ -102,9 +103,9 @@ public abstract class StructureViewerBase extends GStructureViewer protected boolean alignAddedStructures = false; - protected boolean _started = false; + protected volatile boolean _started = false; - protected boolean addingStructures = false; + protected volatile boolean addingStructures = false; protected Thread worker = null; @@ -113,6 +114,17 @@ public abstract class StructureViewerBase extends GStructureViewer protected JMenu viewSelectionMenu; /** + * set after sequence colouring has been applied for this structure viewer. + * used to determine if the final sequence/structure mapping has been + * determined + */ + protected volatile boolean seqColoursApplied = false; + + private IProgressIndicator progressBar = null; + + private Random random = new Random(); + + /** * Default constructor */ public StructureViewerBase() @@ -121,6 +133,26 @@ 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 @@ -130,13 +162,14 @@ 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); } @@ -186,6 +219,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } + @Override public AlignmentPanel getAlignmentPanel() { return ap; @@ -238,7 +272,8 @@ public abstract class StructureViewerBase extends GStructureViewer * * @param nap */ - public void removeAlignmentPanel(AlignmentPanel nap) + @Override + public void removeAlignmentPanel(AlignmentViewPanel nap) { try { @@ -310,8 +345,6 @@ 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. @@ -326,7 +359,7 @@ 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) { @@ -350,7 +383,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } // and call ourselves again. - addStructure(pdbentry, seqs, chains, align, alignFrame); + addStructure(pdbentry, seqs, chains, alignFrame); } }).start(); return; @@ -362,87 +395,42 @@ 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); } - protected abstract List getViewersFor( - AlignmentPanel alp); - /** - * 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 + * Returns a list of any viewer of the instantiated type. The list is + * restricted to those linked to the given alignment panel if it is not null. */ - protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, - String[] chains, final AlignmentPanel apanel, String pdbId) + protected List getViewersFor(AlignmentPanel alp) { - for (StructureViewerBase view : getViewersFor(apanel)) - { - // TODO: highlight the view somehow - /* - * JAL-1742 exclude view with this structure already mapped (don't offer - * to align chain B to chain A of the same structure) - */ - if (view.hasPdbId(pdbId)) - { - continue; - } - int option = chooseAlignStructureToViewer(pdbId, view); - if (option == JvOptionPane.CANCEL_OPTION) - { - return true; - } - else if (option == JvOptionPane.YES_OPTION) - { - view.useAlignmentPanelForSuperposition(apanel); - view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame); - return true; - } - else - { - // NO_OPTION - offer the next viewer if any - } - } + return Desktop.instance.getStructureViewers(alp, this.getClass()); + } + @Override + public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, + String[] chains, final AlignmentViewPanel apanel, String pdbId) + { /* - * nothing offered and selected + * JAL-1742 exclude view with this structure already mapped (don't offer + * to align chain B to chain A of the same structure); code may defend + * against this possibility before we reach here */ - return false; + if (hasPdbId(pdbId)) + { + return; + } + AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this + // cast fails + useAlignmentPanelForSuperposition(alignPanel); + addStructure(pdbentry, seq, chains, alignPanel.alignFrame); } /** @@ -454,15 +442,18 @@ public abstract class StructureViewerBase extends GStructureViewer * @param apanel * @param pdbFilename */ - protected void addSequenceMappingsToStructure(SequenceI[] seq, - String[] chains, final AlignmentPanel apanel, String pdbFilename) + public void addSequenceMappingsToStructure(SequenceI[] seq, + String[] chains, final AlignmentViewPanel alpanel, + String pdbFilename) { + AlignmentPanel apanel = (AlignmentPanel) alpanel; + // TODO : Fix multiple seq to one chain issue here. /* * 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 @@ -503,47 +494,20 @@ 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 - */ - protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains, - final AlignmentPanel apanel, String pdbId) + @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 - */ - int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.pdb_entry_is_already_displayed", new Object[] - { pdbId }), - MessageManager.formatMessage( - "label.map_sequences_to_visible_window", new Object[] - { pdbId }), - JvOptionPane.YES_NO_CANCEL_OPTION); - if (option == JvOptionPane.CANCEL_OPTION) - { - finished = true; - } - else if (option == JvOptionPane.YES_OPTION) - { - addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); - finished = true; - } + return false; } - return finished; + + addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); + return true; } void setChainMenuItems(List chainNames) @@ -594,8 +558,6 @@ public abstract class StructureViewerBase extends GStructureViewer } } - abstract void showSelectedChains(); - /** * Action on selecting one of Jalview's registered colour schemes */ @@ -604,8 +566,9 @@ 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); } /** @@ -639,7 +602,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - viewerColour_actionPerformed(actionEvent); + viewerColour_actionPerformed(); } }); colourMenu.add(viewerColour); @@ -655,7 +618,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - background_actionPerformed(actionEvent); + background_actionPerformed(); } }); colourMenu.add(backGround); @@ -686,7 +649,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - seqColour_actionPerformed(actionEvent); + seqColour_actionPerformed(); } }); @@ -698,7 +661,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - chainColour_actionPerformed(actionEvent); + chainColour_actionPerformed(); } }); @@ -710,7 +673,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void actionPerformed(ActionEvent actionEvent) { - chargeColour_actionPerformed(actionEvent); + chargeColour_actionPerformed(); } }); @@ -742,7 +705,7 @@ public abstract class StructureViewerBase extends GStructureViewer else { // update the Chimera display now. - seqColour_actionPerformed(null); + seqColour_actionPerformed(); } } }); @@ -786,24 +749,13 @@ 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) { @@ -818,19 +770,8 @@ 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); @@ -839,9 +780,9 @@ 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); @@ -850,7 +791,7 @@ 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"), @@ -862,7 +803,7 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) + public void viewerColour_actionPerformed() { if (viewerColour.isSelected()) { @@ -872,21 +813,21 @@ 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()); @@ -905,15 +846,16 @@ 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")); @@ -964,7 +906,7 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void viewMapping_actionPerformed(ActionEvent actionEvent) + public void viewMapping_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -988,6 +930,7 @@ public abstract class StructureViewerBase extends GStructureViewer /** * Configures the title and menu items of the viewer panel. */ + @Override public void updateTitleAndMenus() { AAStructureBindingModel binding = getBinding(); @@ -1025,7 +968,123 @@ 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)) + { + return false; + } + if (getBinding() == null) + { + if (_aps == null || _aps.size() == 0) + { + // viewer has been closed, but we did at some point run. + return true; + } + return false; + } + String[] pdbids = getBinding().getStructureFiles(); + if (pdbids == null) + { + return false; + } + int p=0; + for (String pdbid:pdbids) { + StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid); + if (sm!=null && sm.length>0 && sm[0]!=null) { + p++; + } + } + // only return true if there is a mapping for every structure file we have loaded + if (p == 0 || p != pdbids.length) + { + return false; + } + // and that coloring has been applied + 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); + } + }