X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=853ecc1c71d5dd8ce2ceaaca9c688ca18f0d9ca4;hb=8f0f304ea24d01bc052089dde29a22934c73b326;hp=34ad659402361ea2c50394a9356a3117003b6e67;hpb=f831ddf7f52d6c4a1918e87d94877b22bd322648;p=jalview.git diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 34ad659..853ecc1 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -20,10 +20,12 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.StructureViewer.ViewerType; @@ -34,6 +36,7 @@ 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; @@ -50,6 +53,7 @@ import java.io.FileReader; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; +import java.util.Collections; import java.util.List; import java.util.Vector; @@ -83,18 +87,18 @@ public abstract class StructureViewerBase extends GStructureViewer /** * list of sequenceSet ids associated with the view */ - protected List _aps = new ArrayList(); + protected List _aps = new ArrayList<>(); /** * 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; @@ -102,14 +106,23 @@ 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; protected boolean allChainsSelected = false; + 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; + /** * Default constructor */ @@ -117,6 +130,27 @@ public abstract class StructureViewerBase extends GStructureViewer { super(); } + + /** + * @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 @@ -133,9 +167,10 @@ public abstract class StructureViewerBase extends GStructureViewer return (_alignwith != null) && _alignwith.contains(ap2); } - public boolean isUsedforcolourby(AlignmentPanel ap2) + @Override + public boolean isUsedforcolourby(AlignmentViewPanel avp) { - return (_colourwith != null) && _colourwith.contains(ap2); + return (_colourwith != null) && _colourwith.contains(avp); } /** @@ -167,7 +202,7 @@ public abstract class StructureViewerBase extends GStructureViewer { if (_alignwith == null) { - _alignwith = new Vector(); + _alignwith = new Vector<>(); } if (_alignwith.size() == 0 && ap != null) { @@ -307,6 +342,8 @@ 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. @@ -321,7 +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) { @@ -345,7 +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; @@ -353,89 +390,46 @@ public abstract class StructureViewerBase extends GStructureViewer } // otherwise, start adding the structure. getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry }, - new SequenceI[][] { seqs }, new String[][] { chains }); + new SequenceI[][] + { 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); } /** @@ -447,15 +441,18 @@ 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); + pdbFilename, DataSourceType.FILE, getIProgressIndicator()); /* * alert the FeatureRenderer to show new (PDB RESNUM) features @@ -463,7 +460,9 @@ public abstract class StructureViewerBase extends GStructureViewer if (apanel.getSeqPanel().seqCanvas.fr != null) { apanel.getSeqPanel().seqCanvas.fr.featuresAdded(); - apanel.paintAlignment(true); + // note - we don't do a refresh for structure here because we do it + // explicitly for all panels later on + apanel.paintAlignment(true, false); } /* @@ -486,55 +485,28 @@ public abstract class StructureViewerBase extends GStructureViewer */ viewer.useAlignmentPanelForColourbyseq(apanel); viewer.buildActionMenu(); - apanel.getStructureSelectionManager().sequenceColoursChanged( - apanel); + apanel.getStructureSelectionManager() + .sequenceColoursChanged(apanel); break; } } } } - /** - * 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) - { - /* - * 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; - } + if (alreadyMapped == null) + { + return false; } - return finished; + + addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); + return true; } void setChainMenuItems(List chainNames) @@ -544,6 +516,10 @@ public abstract class StructureViewerBase extends GStructureViewer { return; } + + /* + * add the 'All' menu item + */ JMenuItem menuItem = new JMenuItem( MessageManager.getString("label.all")); menuItem.addActionListener(new ActionListener() @@ -563,12 +539,29 @@ public abstract class StructureViewerBase extends GStructureViewer allChainsSelected = false; } }); - chainMenu.add(menuItem); + /* + * add a menu item for each structure and chain + */ + Collections.sort(chainNames); + String lastSeqName = ""; for (String chain : chainNames) { - menuItem = new JCheckBoxMenuItem(chain, true); + String seqName = getSequenceNameForChain(chain); + int nameLength = seqName.length(); + if (nameLength > 16) + { + seqName = seqName.substring(0, 8) + "..." + + seqName.substring(nameLength - 8, nameLength); + } + String text = chain; + if (!lastSeqName.equals(seqName)) + { + text = text + " " + seqName; + } + lastSeqName = seqName; + menuItem = new JCheckBoxMenuItem(text, true); menuItem.addItemListener(new ItemListener() { @Override @@ -585,7 +578,25 @@ public abstract class StructureViewerBase extends GStructureViewer } } - abstract void showSelectedChains(); + /** + * Answers the name of the sequence mapped to the given chain (formatted as + * pdbId:chainId, e.g. 1A70:A). Answers null if no mapped sequence is found. If + * more than one sequence is matched, just answers the name of the first one + * found. + * + * @param chain + * @return + */ + private String getSequenceNameForChain(String chain) + { + String[] tokens = chain.split(":"); + String pdbId = tokens[0]; + String chainId = tokens[1]; + List mappings = getBinding().getSsm() + .getMappingForChain(pdbId, chainId); + return mappings.isEmpty() ? null + : mappings.get(0).getSequence().getName(); + } /** * Action on selecting one of Jalview's registered colour schemes @@ -594,8 +605,9 @@ public abstract class StructureViewerBase extends GStructureViewer public void changeColour_actionPerformed(String colourSchemeName) { AlignmentI al = getAlignmentPanel().av.getAlignment(); - ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme( - colourSchemeName, al, null); + ColourSchemeI cs = ColourSchemes.getInstance() + .getColourScheme(colourSchemeName, getAlignmentPanel().av, al, + null); getBinding().setJalviewColourScheme(cs); } @@ -712,11 +724,11 @@ public abstract class StructureViewerBase extends GStructureViewer if (_colourwith == null) { - _colourwith = new Vector(); + _colourwith = new Vector<>(); } if (_alignwith == null) { - _alignwith = new Vector(); + _alignwith = new Vector<>(); } ViewSelectionMenu seqColourBy = new ViewSelectionMenu( @@ -739,22 +751,52 @@ public abstract class StructureViewerBase extends GStructureViewer }); viewMenu.add(seqColourBy); + showAlignmentOnly = new JCheckBoxMenuItem( + MessageManager.getString("label.show_alignment_only")); + showAlignmentOnly.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideHiddenRegions.setEnabled(showAlignmentOnly.isSelected()); + getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected()); + getBinding().showStructures(getAlignmentPanel().getAlignViewport(), + true); + } + }); + viewMenu.add(showAlignmentOnly); + + hideHiddenRegions = new JCheckBoxMenuItem( + MessageManager.getString("label.hide_hidden_regions")); + hideHiddenRegions.setEnabled(false); + hideHiddenRegions.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + getBinding().setHideHiddenRegions(hideHiddenRegions.isSelected()); + getBinding().showStructures(getAlignmentPanel().getAlignViewport(), + false); + } + }); + viewMenu.add(hideHiddenRegions); + final ItemListener handler = new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { - alignStructs.setEnabled(_alignwith.size() > 0); + alignStructs.setEnabled(!_alignwith.isEmpty()); alignStructs.setToolTipText(MessageManager.formatMessage( "label.align_structures_using_linked_alignment_views", - new String[] { String.valueOf(_alignwith.size()) })); + _alignwith.size())); } }; - JMenu alpanels = new ViewSelectionMenu( + viewSelectionMenu = new ViewSelectionMenu( MessageManager.getString("label.superpose_with"), this, _alignwith, handler); handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); + viewerActionMenu.add(viewSelectionMenu, 0); viewerActionMenu.addMenuListener(new MenuListener() { @Override @@ -777,52 +819,65 @@ public abstract class StructureViewerBase extends GStructureViewer buildColourMenu(); } + /** + * Sends commands to the structure viewer to superimpose structures based on + * currently associated alignments. May optionally return an error message for + * the operation. + */ @Override - public void setJalviewColourScheme(ColourSchemeI cs) { - getBinding().setJalviewColourScheme(cs); - } - @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) + protected String alignStructs_actionPerformed(ActionEvent actionEvent) { - alignStructs_withAllAlignPanels(); + return alignStructs_withAllAlignPanels(); } - protected void alignStructs_withAllAlignPanels() + + protected String alignStructs_withAllAlignPanels() { if (getAlignmentPanel() == null) { - return; + return null; } - + if (_alignwith.size() == 0) { _alignwith.add(getAlignmentPanel()); } - + + String reply = null; try { AlignmentI[] als = new Alignment[_alignwith.size()]; - ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; + HiddenColumns[] alc = new HiddenColumns[_alignwith.size()]; int[] alm = new int[_alignwith.size()]; int a = 0; - - for (AlignmentPanel ap : _alignwith) + + for (AlignmentViewPanel alignPanel : _alignwith) { - als[a] = ap.av.getAlignment(); + AlignViewportI av = alignPanel.getAlignViewport(); + als[a] = av.getAlignment(); alm[a] = -1; - alc[a++] = ap.av.getColumnSelection(); + alc[a++] = av.getAlignment().getHiddenColumns(); + } + reply = getBinding().superposeStructures(als, alm, alc); + if (reply != null) + { + String text = MessageManager + .formatMessage("error.superposition_failed", reply); + statusBar.setText(text); } - getBinding().superposeStructures(als, alm, alc); } catch (Exception e) { StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) + for (AlignmentViewPanel avp : _alignwith) { - sp.append("'" + ap.alignFrame.getTitle() + "' "); + sp.append( + "'" + ((AlignmentPanel) avp).alignFrame.getTitle() + "' "); } Cache.log.info("Couldn't align structures with the " + sp.toString() + "associated alignment panels.", e); } + return reply; } + @Override public void background_actionPerformed(ActionEvent actionEvent) { @@ -834,6 +889,7 @@ public abstract class StructureViewerBase extends GStructureViewer getBinding().setBackgroundColour(col); } } + @Override public void viewerColour_actionPerformed(ActionEvent actionEvent) { @@ -843,18 +899,21 @@ public abstract class StructureViewerBase extends GStructureViewer getBinding().setColourBySequence(false); } } + @Override public void chainColour_actionPerformed(ActionEvent actionEvent) { chainColour.setSelected(true); getBinding().colourByChain(); } + @Override public void chargeColour_actionPerformed(ActionEvent actionEvent) { chargeColour.setSelected(true); getBinding().colourByCharge(); } + @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { @@ -862,7 +921,7 @@ public abstract class StructureViewerBase extends GStructureViewer binding.setColourBySequence(seqColour.isSelected()); if (_colourwith == null) { - _colourwith = new Vector(); + _colourwith = new Vector<>(); } if (binding.isColourBySequence()) { @@ -875,24 +934,26 @@ public abstract class StructureViewerBase extends GStructureViewer } } // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) + for (AlignmentViewPanel avp : _colourwith) { - binding.colourBySequence(ap); + binding.updateStructureColours(avp); } + seqColoursApplied = true; } } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( 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; @@ -900,9 +961,9 @@ public abstract class StructureViewerBase extends GStructureViewer { // TODO: cope with multiple PDB files in view in = new BufferedReader( - new FileReader(getBinding().getPdbFile()[0])); + new FileReader(getBinding().getStructureFiles()[0])); File outFile = chooser.getSelectedFile(); - + PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); String data; while ((data = in.readLine()) != null) @@ -931,6 +992,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { @@ -952,6 +1014,11 @@ public abstract class StructureViewerBase extends GStructureViewer } protected abstract String getViewerName(); + + /** + * Configures the title and menu items of the viewer panel. + */ + @Override public void updateTitleAndMenus() { AAStructureBindingModel binding = getBinding(); @@ -961,15 +1028,102 @@ public abstract class StructureViewerBase extends GStructureViewer return; } setChainMenuItems(binding.getChainNames()); - + this.setTitle(binding.getViewerTitle(getViewerName(), true)); - if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1) + + /* + * enable 'Superpose with' if more than one mapped structure + */ + viewSelectionMenu.setEnabled(false); + if (getBinding().getStructureFiles().length > 1 + && getBinding().getSequence().length > 1) { - viewerActionMenu.setVisible(true); + viewSelectionMenu.setEnabled(true); } + + /* + * Show action menu if it has any enabled items + */ + viewerActionMenu.setVisible(false); + for (int i = 0; i < viewerActionMenu.getItemCount(); i++) + { + if (viewerActionMenu.getItem(i).isEnabled()) + { + viewerActionMenu.setVisible(true); + break; + } + } + if (!binding.isLoadingFromArchive()) { seqColour_actionPerformed(null); } } + + @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 abstract AAStructureBindingModel getBinding(); + + /** + * Show only the selected chain(s) in the viewer + */ + protected void showSelectedChains() + { + setSelectedChains(); + + /* + * refresh display without resizing - easier to see what changed + */ + getBinding().showStructures(getAlignmentPanel().getAlignViewport(), + false); + } + }