From 3429e8b2a3fceff4350d5554853403e903b4fc68 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 12 Feb 2016 15:03:51 +0000 Subject: [PATCH] JAL-2010 simple prototype of 'Highlight Selection' onto Chimera view --- resources/lang/Messages.properties | 3 +- .../ext/rbvi/chimera/JalviewChimeraBinding.java | 62 +++++++++++++++----- src/jalview/gui/ChimeraViewFrame.java | 14 +++++ src/jalview/jbgui/GStructureViewer.java | 38 ++++++++++++ .../structure/StructureSelectionManager.java | 37 ++++++------ 5 files changed, 122 insertions(+), 32 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index c4d1098..5ce5f46 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -133,6 +133,7 @@ action.using_jmol = Using Jmol action.link = Link action.group_link = Group Link action.show_chain = Show Chain +label.highlight_selection = Highlight Selection action.show_group = Show Group action.fetch_db_references = Fetch DB References action.view_flanking_regions = Show flanking regions @@ -1287,4 +1288,4 @@ label.mapping_method = Sequence \u27f7 Structure mapping method label.mapping_method = Sequence \u27f7 Structure mapping method status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file. status.cancelled_image_export_operation = Cancelled {0} export operation. -info.error_creating_file = Error creating {0} file. \ No newline at end of file +info.error_creating_file = Error creating {0} file. diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index eee8bca..af87e44 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -108,7 +108,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ String[] modelFileNames = null; - String lastMousedOverAtomSpec; + String lastHighlightCommand; private List lastReply; @@ -818,8 +818,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Construct and send a command to highlight zero, one or more atoms. * * 
-   * Done by generating a command like (to 'highlight' position 44)
-   *   show #0:44.C
+   * Done by generating a command like (to 'highlight' positions 44 and 46)
+   *   show #0:44,46.C
    *
*/ @Override @@ -829,8 +829,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { return; } - StringBuilder atomSpecs = new StringBuilder(); + StringBuilder cmd = new StringBuilder(128); boolean first = true; + boolean found = false; for (AtomSpec atom : atoms) { @@ -840,35 +841,42 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List cms = chimeraMaps.get(pdbfile); if (cms != null && !cms.isEmpty()) { - atomSpecs.append(first ? "" : ","); + if (first) + { + cmd.append("show #").append(cms.get(0).getModelNumber()) + .append(":"); + } + else + { + cmd.append(","); + } first = false; - atomSpecs.append(cms.get(0).getModelNumber()); - atomSpecs.append(":" + pdbResNum); + cmd.append(cms.get(0).getModelNumber()).append(":"); + cmd.append(pdbResNum); if (!chain.equals(" ")) { - atomSpecs.append("." + chain); + cmd.append(".").append(chain); } + found = true; } } - String atomSpec = atomSpecs.toString(); + String command = cmd.toString(); /* * Avoid repeated commands for the same residue */ - if (atomSpec.equals(lastMousedOverAtomSpec)) + if (command.equals(lastHighlightCommand)) { return; } - StringBuilder command = new StringBuilder(32); viewerCommandHistory(false); - if (atomSpec.length() > 0) + if (found) { - command.append("show #").append(atomSpec); viewer.sendChimeraCommand(command.toString(), false); } viewerCommandHistory(true); - this.lastMousedOverAtomSpec = atomSpec; + this.lastHighlightCommand = command; } /** @@ -1115,4 +1123,30 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { sendChimeraCommand("focus", false); } + + /** + * Send a 'show' command for all atoms in the currently selected columns + * + * @param vp + */ + public void highlightSelection(AlignmentViewPanel vp) + { + List cols = vp.getAlignViewport().getColumnSelection() + .getSelected(); + AlignmentI alignment = vp.getAlignment(); + StructureSelectionManager sm = getSsm(); + for (SequenceI seq : alignment.getSequences()) + { + /* + * convert selected columns into sequence positions + */ + int[] positions = new int[cols.size()]; + int i = 0; + for (Integer col : cols) + { + positions[i++] = seq.findPosition(col); + } + sm.highlightStructure(this, seq, positions); + } + } } diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 09451dc..f1c5097 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -143,6 +143,7 @@ public class ChimeraViewFrame extends StructureViewerBase }); viewMenu.add(seqColourBy); viewMenu.add(fitToWindow); + viewMenu.add(highlightSelection); final ItemListener handler; JMenu alpanels = new ViewSelectionMenu( @@ -270,6 +271,7 @@ public class ChimeraViewFrame extends StructureViewerBase this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { closeViewer(false); @@ -460,6 +462,7 @@ public class ChimeraViewFrame extends StructureViewerBase MessageManager.getString("label.all")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { allChainsSelected = true; @@ -482,6 +485,7 @@ public class ChimeraViewFrame extends StructureViewerBase menuItem = new JCheckBoxMenuItem(chainName, true); menuItem.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) @@ -523,6 +527,7 @@ public class ChimeraViewFrame extends StructureViewerBase * @param closeChimera * if true, close any linked Chimera process; if false, prompt first */ + @Override public void closeViewer(boolean closeChimera) { if (jmb != null && jmb.isChimeraRunning()) @@ -553,6 +558,7 @@ public class ChimeraViewFrame extends StructureViewerBase * Open any newly added PDB structures in Chimera, having first fetched data * from PDB (if not already saved). */ + @Override public void run() { _started = true; @@ -699,6 +705,7 @@ public class ChimeraViewFrame extends StructureViewerBase { new Thread(new Runnable() { + @Override public void run() { alignStructs_withAllAlignPanels(); @@ -1091,6 +1098,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } + @Override public void setJalviewColourScheme(ColourSchemeI ucs) { jmb.setJalviewColourScheme(ucs); @@ -1198,6 +1206,12 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override + protected void highlightSelection_actionPerformed() + { + jmb.highlightSelection(getAlignmentPanel()); + } + + @Override public ViewerType getViewerType() { return ViewerType.CHIMERA; diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java index 943aa8c..179607f 100644 --- a/src/jalview/jbgui/GStructureViewer.java +++ b/src/jalview/jbgui/GStructureViewer.java @@ -53,6 +53,8 @@ public abstract class GStructureViewer extends JInternalFrame implements protected JMenuItem fitToWindow = new JMenuItem(); + protected JMenuItem highlightSelection = new JMenuItem(); + protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem(); @@ -114,6 +116,7 @@ public abstract class GStructureViewer extends JInternalFrame implements pdbFile.setText(MessageManager.getString("label.pdb_file")); pdbFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { pdbFile_actionPerformed(actionEvent); @@ -124,6 +127,7 @@ public abstract class GStructureViewer extends JInternalFrame implements png.setText("PNG"); png.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { png_actionPerformed(actionEvent); @@ -134,6 +138,7 @@ public abstract class GStructureViewer extends JInternalFrame implements eps.setText("EPS"); eps.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { eps_actionPerformed(actionEvent); @@ -144,6 +149,7 @@ public abstract class GStructureViewer extends JInternalFrame implements viewMapping.setText(MessageManager.getString("label.view_mapping")); viewMapping.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { viewMapping_actionPerformed(actionEvent); @@ -156,12 +162,24 @@ public abstract class GStructureViewer extends JInternalFrame implements fitToWindow.setText(MessageManager.getString("label.fit_to_window")); fitToWindow.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { fitToWindow_actionPerformed(); } }); + highlightSelection.setText(MessageManager + .getString("label.highlight_selection")); + highlightSelection.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + highlightSelection_actionPerformed(); + } + }); + JMenu colourMenu = new JMenu(); colourMenu.setText(MessageManager.getString("label.colours")); @@ -170,6 +188,7 @@ public abstract class GStructureViewer extends JInternalFrame implements .setText(MessageManager.getString("action.background_colour")); backGround.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { backGround_actionPerformed(actionEvent); @@ -179,6 +198,7 @@ public abstract class GStructureViewer extends JInternalFrame implements seqColour.setText(MessageManager.getString("action.by_sequence")); seqColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { seqColour_actionPerformed(actionEvent); @@ -187,6 +207,7 @@ public abstract class GStructureViewer extends JInternalFrame implements chainColour.setText(MessageManager.getString("action.by_chain")); chainColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { chainColour_actionPerformed(actionEvent); @@ -195,6 +216,7 @@ public abstract class GStructureViewer extends JInternalFrame implements chargeColour.setText(MessageManager.getString("label.charge_cysteine")); chargeColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { chargeColour_actionPerformed(actionEvent); @@ -203,6 +225,7 @@ public abstract class GStructureViewer extends JInternalFrame implements zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { zappoColour_actionPerformed(actionEvent); @@ -211,6 +234,7 @@ public abstract class GStructureViewer extends JInternalFrame implements taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { taylorColour_actionPerformed(actionEvent); @@ -219,6 +243,7 @@ public abstract class GStructureViewer extends JInternalFrame implements hydroColour.setText(MessageManager.getString("label.hydrophobicity")); hydroColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { hydroColour_actionPerformed(actionEvent); @@ -228,6 +253,7 @@ public abstract class GStructureViewer extends JInternalFrame implements .getString("label.strand_propensity")); strandColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { strandColour_actionPerformed(actionEvent); @@ -236,6 +262,7 @@ public abstract class GStructureViewer extends JInternalFrame implements helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { helixColour_actionPerformed(actionEvent); @@ -244,6 +271,7 @@ public abstract class GStructureViewer extends JInternalFrame implements turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { turnColour_actionPerformed(actionEvent); @@ -252,6 +280,7 @@ public abstract class GStructureViewer extends JInternalFrame implements buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { buriedColour_actionPerformed(actionEvent); @@ -261,6 +290,7 @@ public abstract class GStructureViewer extends JInternalFrame implements .getString("label.purine_pyrimidine")); purinePyrimidineColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { purinePyrimidineColour_actionPerformed(actionEvent); @@ -270,6 +300,7 @@ public abstract class GStructureViewer extends JInternalFrame implements userColour.setText(MessageManager.getString("action.user_defined")); userColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { userColour_actionPerformed(actionEvent); @@ -282,6 +313,7 @@ public abstract class GStructureViewer extends JInternalFrame implements .getString("label.let_jmol_manage_structure_colours")); viewerColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { viewerColour_actionPerformed(actionEvent); @@ -293,6 +325,7 @@ public abstract class GStructureViewer extends JInternalFrame implements helpItem.setText(MessageManager.getString("label.jmol_help")); helpItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { showHelp_actionPerformed(actionEvent); @@ -302,6 +335,7 @@ public abstract class GStructureViewer extends JInternalFrame implements .setText(MessageManager.getString("label.align_structures")); alignStructs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { alignStructs_actionPerformed(actionEvent); @@ -364,6 +398,10 @@ public abstract class GStructureViewer extends JInternalFrame implements { } + protected void highlightSelection_actionPerformed() + { + } + protected void viewerColour_actionPerformed(ActionEvent actionEvent) { } diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 4da715e..b6bb70d 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -768,19 +768,19 @@ public class StructureSelectionManager * the sequence that the mouse over occurred on * @param indexpos * the absolute position being mouseovered in seq (0 to seq.length()) - * @param index + * @param seqPos * the sequence position (if -1, seq.findPosition is called to * resolve the residue number) */ - public void mouseOverSequence(SequenceI seq, int indexpos, int index, + public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos, VamsasSource source) { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); SearchResults results = null; - if (index == -1) + if (seqPos == -1) { - index = seq.findPosition(indexpos); + seqPos = seq.findPosition(indexpos); } for (int i = 0; i < listeners.size(); i++) { @@ -793,7 +793,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -807,12 +807,12 @@ public class StructureSelectionManager { if (results == null) { - results = MappingUtils.buildSearchResults(seq, index, + results = MappingUtils.buildSearchResults(seq, seqPos, seqmappings); } if (handlingVamsasMo) { - results.addResult(seq, index, index); + results.addResult(seq, seqPos, seqPos); } if (!results.isEmpty()) @@ -830,7 +830,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -838,14 +838,14 @@ public class StructureSelectionManager /** * Send suitable messages to a StructureListener to highlight atoms - * corresponding to the given sequence position. + * corresponding to the given sequence position(s) * * @param sl * @param seq - * @param index + * @param positions */ - protected void highlightStructure(StructureListener sl, SequenceI seq, - int index) + public void highlightStructure(StructureListener sl, SequenceI seq, + int... positions) { if (!sl.isListeningFor(seq)) { @@ -857,12 +857,15 @@ public class StructureSelectionManager { if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()) { - atomNo = sm.getAtomNum(index); - - if (atomNo > 0) + for (int index : positions) { - atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm - .getPDBResNum(index), atomNo)); + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm + .getPDBResNum(index), atomNo)); + } } } } -- 1.7.10.2