X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=3e067247ddeff3edf66eea29b0f4d73b6c80727a;hb=91d45e7c90753d8061883f351da796c50f467ef5;hp=e37627dceb8dc5047919e1181c9eecc2b501f6bf;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index e37627d..3e06724 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; @@ -34,6 +35,7 @@ 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; @@ -83,18 +85,18 @@ 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; @@ -102,9 +104,9 @@ 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; @@ -113,12 +115,20 @@ 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; + + /** * Default constructor */ public StructureViewerBase() { super(); } + /** * * @param ap2 @@ -169,7 +179,7 @@ public abstract class StructureViewerBase extends GStructureViewer { if (_alignwith == null) { - _alignwith = new Vector(); + _alignwith = new Vector<>(); } if (_alignwith.size() == 0 && ap != null) { @@ -309,6 +319,8 @@ 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. @@ -355,7 +367,8 @@ 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; @@ -377,7 +390,8 @@ public abstract class StructureViewerBase extends GStructureViewer { int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage("label.add_pdbentry_to_view", - new Object[] { pdbId, view.getTitle() }), + new Object[] + { pdbId, view.getTitle() }), MessageManager .getString("label.align_to_existing_structure_view"), JvOptionPane.YES_NO_CANCEL_OPTION); @@ -389,8 +403,15 @@ public abstract class StructureViewerBase extends GStructureViewer return getBinding().hasPdbId(pdbId); } - protected abstract List getViewersFor( - AlignmentPanel alp); + /** + * 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 List getViewersFor(AlignmentPanel alp) + { + return Desktop.instance.getStructureViewers(alp, this.getClass()); + } + /** * Check for any existing views involving this alignment and give user the @@ -403,41 +424,23 @@ public abstract class StructureViewerBase extends GStructureViewer * @param pdbId * @return true if user adds to a view, or cancels entirely, else false */ - protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, - String[] chains, final AlignmentPanel apanel, String pdbId) + @Override + public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, + String[] chains, final AlignmentViewPanel apanel, String pdbId) { - 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 - } - } - /* - * 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) */ - return false; + if (hasPdbId(pdbId)) + { + return false; + } + AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this + // cast fails + useAlignmentPanelForSuperposition(ap); + addStructure(pdbentry, seq, chains, true, ap.alignFrame); + return true; } /** @@ -449,15 +452,18 @@ 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 @@ -465,7 +471,9 @@ 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); } /* @@ -488,8 +496,8 @@ public abstract class StructureViewerBase extends GStructureViewer */ viewer.useAlignmentPanelForColourbyseq(apanel); viewer.buildActionMenu(); - apanel.getStructureSelectionManager().sequenceColoursChanged( - apanel); + apanel.getStructureSelectionManager() + .sequenceColoursChanged(apanel); break; } } @@ -506,8 +514,9 @@ public abstract class StructureViewerBase extends GStructureViewer * @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() @@ -518,23 +527,8 @@ public abstract class StructureViewerBase extends GStructureViewer /* * 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; - } + addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); + finished = true; } return finished; } @@ -596,8 +590,8 @@ 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, al, null); getBinding().setJalviewColourScheme(cs); } @@ -714,11 +708,11 @@ 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( @@ -780,7 +774,8 @@ public abstract class StructureViewerBase extends GStructureViewer } @Override - public void setJalviewColourScheme(ColourSchemeI cs) { + public void setJalviewColourScheme(ColourSchemeI cs) + { getBinding().setJalviewColourScheme(cs); } @@ -790,8 +785,7 @@ public abstract class StructureViewerBase extends GStructureViewer * the operation. */ @Override - protected String alignStructs_actionPerformed( - ActionEvent actionEvent) + protected String alignStructs_actionPerformed(ActionEvent actionEvent) { return alignStructs_withAllAlignPanels(); } @@ -802,12 +796,12 @@ public abstract class StructureViewerBase extends GStructureViewer { return null; } - + if (_alignwith.size() == 0) { _alignwith.add(getAlignmentPanel()); } - + String reply = null; try { @@ -815,7 +809,7 @@ public abstract class StructureViewerBase extends GStructureViewer HiddenColumns[] alc = new HiddenColumns[_alignwith.size()]; int[] alm = new int[_alignwith.size()]; int a = 0; - + for (AlignmentPanel ap : _alignwith) { als[a] = ap.av.getAlignment(); @@ -825,8 +819,8 @@ public abstract class StructureViewerBase extends GStructureViewer reply = getBinding().superposeStructures(als, alm, alc); if (reply != null) { - String text = MessageManager.formatMessage( - "error.superposition_failed", reply); + String text = MessageManager + .formatMessage("error.superposition_failed", reply); statusBar.setText(text); } } catch (Exception e) @@ -853,6 +847,7 @@ public abstract class StructureViewerBase extends GStructureViewer getBinding().setBackgroundColour(col); } } + @Override public void viewerColour_actionPerformed(ActionEvent actionEvent) { @@ -862,18 +857,21 @@ 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) { @@ -881,7 +879,7 @@ public abstract class StructureViewerBase extends GStructureViewer binding.setColourBySequence(seqColour.isSelected()); if (_colourwith == null) { - _colourwith = new Vector(); + _colourwith = new Vector<>(); } if (binding.isColourBySequence()) { @@ -898,20 +896,22 @@ public abstract class StructureViewerBase extends GStructureViewer { binding.colourBySequence(ap); } + 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; @@ -919,9 +919,9 @@ 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) @@ -950,6 +950,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { @@ -975,6 +976,7 @@ public abstract class StructureViewerBase extends GStructureViewer /** * Configures the title and menu items of the viewer panel. */ + @Override public void updateTitleAndMenus() { AAStructureBindingModel binding = getBinding(); @@ -984,14 +986,14 @@ public abstract class StructureViewerBase extends GStructureViewer return; } setChainMenuItems(binding.getChainNames()); - + this.setTitle(binding.getViewerTitle(getViewerName(), true)); /* * enable 'Superpose with' if more than one mapped structure */ viewSelectionMenu.setEnabled(false); - if (getBinding().getPdbFile().length > 1 + if (getBinding().getStructureFiles().length > 1 && getBinding().getSequence().length > 1) { viewSelectionMenu.setEnabled(true); @@ -1015,4 +1017,42 @@ public abstract class StructureViewerBase extends GStructureViewer seqColour_actionPerformed(null); } } + + @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; + } + }