From f831ddf7f52d6c4a1918e87d94877b22bd322648 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 22 Dec 2016 13:12:33 +0000 Subject: [PATCH] JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods and fields removed, more methods pulled up --- src/jalview/appletgui/AppletJmol.java | 2 +- src/jalview/ext/jmol/JalviewJmolBinding.java | 63 +-- .../ext/rbvi/chimera/JalviewChimeraBinding.java | 92 +---- src/jalview/gui/AlignFrame.java | 4 +- src/jalview/gui/AppJmol.java | 434 +------------------- src/jalview/gui/ChimeraViewFrame.java | 432 +------------------ src/jalview/gui/ColourMenuHelper.java | 75 ++-- src/jalview/gui/JalviewChimeraBindingModel.java | 2 +- src/jalview/gui/PopupMenu.java | 9 +- src/jalview/gui/StructureViewerBase.java | 432 ++++++++++++++++++- src/jalview/jbgui/GStructureViewer.java | 327 +-------------- src/jalview/schemes/AnnotationColourGradient.java | 6 + src/jalview/schemes/Blosum62ColourScheme.java | 6 + src/jalview/schemes/ClustalxColourScheme.java | 6 + src/jalview/schemes/ColourSchemeI.java | 11 + src/jalview/schemes/CovariationColourScheme.java | 6 + src/jalview/schemes/PIDColourScheme.java | 6 + src/jalview/schemes/RNAHelicesColour.java | 6 + src/jalview/schemes/ResidueColourScheme.java | 10 + src/jalview/schemes/TCoffeeColourScheme.java | 6 + .../structures/models/AAStructureBindingModel.java | 85 ++++ .../models/AAStructureBindingModelTest.java | 70 ++++ 22 files changed, 766 insertions(+), 1324 deletions(-) diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 8196c2b..c0b4ff0 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -586,7 +586,7 @@ public class AppletJmol extends EmbmenuFrame implements public void updateTitleAndMenus() { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) + if (jmb.hasFileLoadingError()) { repaint(); return; diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 38ce476..b4586ca 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -20,7 +20,6 @@ */ package jalview.ext.jmol; -import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; @@ -76,8 +75,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel Hashtable chainFile; - public String fileLoadingError; - /* * the default or current model displayed if the model cannot be identified * from the selection message @@ -241,6 +238,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * @param _hiddenCols * an array of corresponding hidden columns for each alignment */ + @Override public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { @@ -487,35 +485,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands */ - public void colourBySequence(AlignmentViewPanel alignmentv) + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) { - boolean showFeatures = alignmentv.getAlignViewport() - .isShowSequenceFeatures(); - if (!colourBySequence || !isLoadingFinished()) - { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( - files, sr, fr, alignment)) + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { for (String cbyseq : cpdbbyseq.commands) { @@ -531,6 +509,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * @param alignment * @return */ + @Override protected StructureMappingcommandSet[] getColourBySequenceCommands( String[] files, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) @@ -598,17 +577,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - - /** * instruct the Jalview binding to update the pdbentries vector if necessary * prior to matching the jmol view's contents to the list of structure files * Jalview knows about. @@ -717,16 +685,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return null; } - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); + // /////////////////////////////// // JmolStatusListener @@ -1286,6 +1245,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -1402,6 +1362,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel protected org.jmol.api.JmolAppConsoleInterface console = null; + @Override public void setBackgroundColour(java.awt.Color col) { jmolHistory(false); diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 8354410..2171815 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -93,8 +93,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean loadingFinished = true; - public String fileLoadingError; - /* * Map of ChimeraModel objects keyed by PDB full local file name */ @@ -254,18 +252,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return - */ - public String getViewerTitle(boolean verbose) - { - return getViewerTitle("Chimera", verbose); - } - - /** * Tells Chimera to display only the specified chains * * @param toshow @@ -328,6 +314,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel releaseUIResources(); } + @Override public void colourByChain() { colourBySequence = false; @@ -343,6 +330,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel *
  • all others - white
    • * */ + @Override public void colourByCharge() { colourBySequence = false; @@ -364,6 +352,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param _hiddenCols * an array of corresponding hidden columns for each alignment */ + @Override public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { @@ -680,34 +669,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String progressMsg); /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) { - if (!colourBySequence || !loadingFinished) - { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( - files, sr, fr, alignment)) + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { for (String command : cpdbbyseq.commands) { @@ -723,6 +693,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param alignment * @return */ + @Override protected StructureMappingcommandSet[] getColourBySequenceCommands( String[] files, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) @@ -758,40 +729,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // ////////////////////////// /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - - /** * instruct the Jalview binding to update the pdbentries vector if necessary * prior to matching the viewer's contents to the list of structure files * Jalview knows about. */ public abstract void refreshPdbEntries(); - private int getModelNum(String modelFileName) - { - String[] mfn = getPdbFile(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) - { - if (mfn[i].equalsIgnoreCase(modelFileName)) - { - return i; - } - } - return -1; - } - /** * map between index of model filename returned from getPdbFile and the first * index of models from this file in the viewer. Note - this is not trimmed - @@ -814,17 +757,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - /** * Construct and send a command to highlight zero, one or more atoms. We do * this by sending an "rlabel" command to show the residue label at that * position. @@ -976,6 +908,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return loadNotifiesHandled; } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -1050,6 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * .html * @param col */ + @Override public void setBackgroundColour(Color col) { viewerCommandHistory(false); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 29a160c..3c0569e 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -5689,8 +5689,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper - .addMenuItems(colourMenu, this, viewport.getAlignment()); + ColourMenuHelper.addMenuItems(colourMenu, this, + viewport.getAlignment(), false); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index aaa2397..ffb9639 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -21,25 +21,12 @@ package jalview.gui; import jalview.bin.Cache; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.StructureViewer.ViewerType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.dbsources.Pdb; @@ -51,20 +38,12 @@ import java.awt.Font; import java.awt.Graphics; import java.awt.Rectangle; import java.awt.event.ActionEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.io.BufferedReader; import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.IOException; -import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JPanel; @@ -72,8 +51,6 @@ import javax.swing.JSplitPane; import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; public class AppJmol extends StructureViewerBase { @@ -92,8 +69,6 @@ public class AppJmol extends StructureViewerBase RenderPanel renderPanel; - ViewSelectionMenu seqColourBy; - /** * * @param files @@ -137,6 +112,7 @@ public class AppJmol extends StructureViewerBase { useAlignmentPanelForSuperposition(ap); } + initMenus(); if (leaveColouringToJmol || !usetoColour) { jmb.setColourBySequence(false); @@ -151,7 +127,6 @@ public class AppJmol extends StructureViewerBase viewerColour.setSelected(false); } this.setBounds(bounds); - initMenus(); setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -165,84 +140,19 @@ public class AppJmol extends StructureViewerBase } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! - } - private void initMenus() + @Override + protected void initMenus() { - seqColour.setSelected(jmb.isColourBySequence()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - seqColourBy = new ViewSelectionMenu( - MessageManager.getString("label.colour_by"), this, _colourwith, - new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - if (!seqColour.isSelected()) - { - seqColour.doClick(); - } - else - { - // update the jmol display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu( - MessageManager.getString("label.superpose_with"), this, - _alignwith, handler = new ItemListener() - { + super.initMenus(); - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText(MessageManager - .formatMessage( - "label.align_structures_using_linked_alignment_views", - new String[] { new Integer(_alignwith - .size()).toString() })); - } - }); - handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); - viewerActionMenu.addMenuListener(new MenuListener() - { + viewerActionMenu = new JMenu(MessageManager.getString("label.jmol")); - @Override - public void menuSelected(MenuEvent e) - { - handler.itemStateChanged(null); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - - } - }); + viewerColour + .setText(MessageManager.getString("label.colour_with_jmol")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_jmol_manage_structure_colours")); } IProgressIndicator progressBar = null; @@ -285,15 +195,6 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); } - /** - * Answers true if this viewer already involves the given PDB ID - */ - @Override - protected boolean hasPdbId(String pdbId) - { - return jmb.hasPdbId(pdbId); - } - private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { @@ -302,6 +203,7 @@ public class AppJmol extends StructureViewerBase pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { alignAddedStructures = true; @@ -685,76 +587,6 @@ public class AppJmol extends StructureViewerBase } @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.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; - try - { - // TODO: cope with multiple PDB files in view - in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("
    ") > -1 || data.indexOf("
    ") > -1)) - { - out.println(data); - } - } - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - // ignore - } - } - } - } - } - - @Override - public void viewMapping_actionPerformed(ActionEvent actionEvent) - { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - try - { - cap.appendText(jmb.printMappings()); - } catch (OutOfMemoryError e) - { - new OOMWarning( - "composing sequence-structure alignments for display in text box.", - e); - cap.dispose(); - return; - } - jalview.gui.Desktop.addInternalFrame(cap, - MessageManager.getString("label.pdb_sequence_mapping"), 550, - 600); - } - - @Override public void eps_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.TYPE.EPS); @@ -801,148 +633,11 @@ public class AppJmol extends StructureViewerBase } @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) - { - if (viewerColour.isSelected()) - { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - - @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) - { - if (!jmb.isLoadingFromArchive()) - { - if (_colourwith.size() == 0 && getAlignmentPanel() != null) - { - // Make the currently displayed alignment panel the associated view - _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); - } - } - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) - { - jmb.colourBySequence(ap); - } - } - } - - @Override - public void chainColour_actionPerformed(ActionEvent actionEvent) - { - chainColour.setSelected(true); - jmb.colourByChain(); - } - - @Override - public void chargeColour_actionPerformed(ActionEvent actionEvent) - { - chargeColour.setSelected(true); - jmb.colourByCharge(); - } - - @Override - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - zappoColour.setSelected(true); - jmb.setJalviewColourScheme(new ZappoColourScheme()); - } - - @Override - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - taylorColour.setSelected(true); - jmb.setJalviewColourScheme(new TaylorColourScheme()); - } - - @Override - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - hydroColour.setSelected(true); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); - } - - @Override - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - helixColour.setSelected(true); - jmb.setJalviewColourScheme(new HelixColourScheme()); - } - - @Override - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - strandColour.setSelected(true); - jmb.setJalviewColourScheme(new StrandColourScheme()); - } - - @Override - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - turnColour.setSelected(true); - jmb.setJalviewColourScheme(new TurnColourScheme()); - } - - @Override - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - buriedColour.setSelected(true); - jmb.setJalviewColourScheme(new BuriedColourScheme()); - } - - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new PurinePyrimidineColourScheme()); - } - - /** - * Action on either selecting a user-defined colour, or 'User Defined...' - */ - @Override - public void userColour_actionPerformed(ActionEvent e) - { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) - { - userColour.setSelected(true); - new UserDefinedColours(this, null); - } - else - { - UserColourScheme udc = UserDefinedColours.getUserColourSchemes().get( - e.getActionCommand()); - jmb.setJalviewColourScheme(udc); - } - } - - @Override - public void backGround_actionPerformed(ActionEvent actionEvent) - { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_background_colour"), - null); - if (col != null) - { - jmb.setBackgroundColour(col); - } - } - - @Override public void showHelp_actionPerformed(ActionEvent actionEvent) { try { - jalview.util.BrowserLauncher + BrowserLauncher .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { @@ -991,7 +686,7 @@ public class AppJmol extends StructureViewerBase { getSize(currentSize); - if (jmb != null && jmb.fileLoadingError != null) + if (jmb != null && jmb.hasFileLoadingError()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1034,104 +729,6 @@ public class AppJmol extends StructureViewerBase } } - public void updateTitleAndMenus() - { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.getChainNames()); - - this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) - { - viewerActionMenu.setVisible(true); - } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ - @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) - { - alignStructs_withAllAlignPanels(); - } - - private void alignStructs_withAllAlignPanels() - { - if (getAlignmentPanel() == null) - { - return; - } - ; - if (_alignwith.size() == 0) - { - _alignwith.add(getAlignmentPanel()); - } - ; - try - { - AlignmentI[] als = new Alignment[_alignwith.size()]; - ColumnSelection[] alc = new ColumnSelection[_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.getColumnSelection(); - } - jmb.superposeStructures(als, alm, alc); - } catch (Exception e) - { - StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) - { - sp.append("'" + ap.alignFrame.getTitle() + "' "); - } - Cache.log.info("Couldn't align structures with the " + sp.toString() - + "associated alignment panels.", e); - - } - - } - - @Override - public void setJalviewColourScheme(ColourSchemeI ucs) - { - jmb.setJalviewColourScheme(ucs); - - } - - /** - * - * @param alignment - * @return first alignment panel displaying given alignment, or the default - * alignment panel - */ - public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) - { - for (AlignmentPanel ap : getAllAlignmentPanels()) - { - if (ap.av.getAlignment() == alignment) - { - return ap; - } - } - return getAlignmentPanel(); - } - @Override public AAStructureBindingModel getBinding() { @@ -1151,9 +748,8 @@ public class AppJmol extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Jmol"; } - } diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 048f441..530f4fe 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -21,57 +21,32 @@ package jalview.gui; import jalview.bin.Cache; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.JalviewChimeraBinding; import jalview.gui.StructureViewer.ViewerType; import jalview.io.DataSourceType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; import jalview.io.StructureFile; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.dbsources.Pdb; -import java.awt.Color; import java.awt.event.ActionEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.FileReader; import java.io.IOException; import java.io.InputStream; -import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; import java.util.Random; -import java.util.Vector; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JInternalFrame; -import javax.swing.JMenu; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; /** * GUI elements for handling an external chimera display @@ -99,88 +74,21 @@ public class ChimeraViewFrame extends StructureViewerBase /** * Initialise menu options. */ - private void initMenus() + @Override + protected void initMenus() { + super.initMenus(); + viewerActionMenu.setText(MessageManager.getString("label.chimera")); + viewerColour.setText(MessageManager .getString("label.colour_with_chimera")); viewerColour.setToolTipText(MessageManager .getString("label.let_chimera_manage_structure_colours")); - helpItem.setText(MessageManager.getString("label.chimera_help")); - seqColour.setSelected(jmb.isColourBySequence()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - // save As not yet implemented - savemenu.setVisible(false); - ViewSelectionMenu seqColourBy = new ViewSelectionMenu( - MessageManager.getString("label.colour_by"), this, _colourwith, - new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent e) - { - if (!seqColour.isSelected()) - { - seqColour.doClick(); - } - else - { - // update the Chimera display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); + helpItem.setText(MessageManager.getString("label.chimera_help")); + savemenu.setVisible(false); // not yet implemented viewMenu.add(fitToWindow); - - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu( - MessageManager.getString("label.superpose_with"), this, - _alignwith, handler = new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText(MessageManager - .formatMessage( - "label.align_structures_using_linked_alignment_views", - new Object[] { new Integer(_alignwith - .size()).toString() })); - } - }); - handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); - viewerActionMenu.addMenuListener(new MenuListener() - { - - @Override - public void menuSelected(MenuEvent e) - { - handler.itemStateChanged(null); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - } - }); } /** @@ -234,15 +142,6 @@ public class ChimeraViewFrame extends StructureViewerBase } } - /** - * Answers true if this viewer already involves the given PDB ID - */ - @Override - protected boolean hasPdbId(String pdbId) - { - return jmb.hasPdbId(pdbId); - } - private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { @@ -252,6 +151,7 @@ public class ChimeraViewFrame extends StructureViewerBase ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { alignAddedStructures = true; @@ -276,8 +176,6 @@ public class ChimeraViewFrame extends StructureViewerBase } - - /** * Create a new viewer from saved session state data including Chimera session * file @@ -373,7 +271,7 @@ public class ChimeraViewFrame extends StructureViewerBase { jmb.setFinishedInit(false); jalview.gui.Desktop.addInternalFrame(this, - jmb.getViewerTitle("Chimera", true), getBounds().width, + jmb.getViewerTitle(getViewerName(), true), getBounds().width, getBounds().height); if (!jmb.launchChimera()) @@ -440,7 +338,8 @@ public class ChimeraViewFrame extends StructureViewerBase { String prompt = MessageManager.formatMessage( "label.confirm_close_chimera", - new Object[] { jmb.getViewerTitle("Chimera", false) }); + new Object[] { jmb.getViewerTitle(getViewerName(), + false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); int confirm = JvOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), @@ -570,7 +469,7 @@ public class ChimeraViewFrame extends StructureViewerBase try { int pos = filePDBpos.get(num).intValue(); - long startTime = startProgressBar("Chimera " + long startTime = startProgressBar(getViewerName() + " " + MessageManager.getString("status.opening_file_for") + " " + pe.getId()); jmb.openFile(pe); @@ -735,76 +634,6 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.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; - try - { - // TODO: cope with multiple PDB files in view - in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("
    ") > -1 || data.indexOf("
    ") > -1)) - { - out.println(data); - } - } - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - e.printStackTrace(); - } - } - } - } - } - - @Override - public void viewMapping_actionPerformed(ActionEvent actionEvent) - { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - try - { - cap.appendText(jmb.printMappings()); - } catch (OutOfMemoryError e) - { - new OOMWarning( - "composing sequence-structure alignments for display in text box.", - e); - cap.dispose(); - return; - } - jalview.gui.Desktop.addInternalFrame(cap, - MessageManager.getString("label.pdb_sequence_mapping"), 550, - 600); - } - - @Override public void eps_actionPerformed(ActionEvent e) { throw new Error( @@ -821,246 +650,17 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) - { - if (viewerColour.isSelected()) - { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - - @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) - { - if (!jmb.isLoadingFromArchive()) - { - if (_colourwith.size() == 0 && getAlignmentPanel() != null) - { - // Make the currently displayed alignment panel the associated view - _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); - } - } - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) - { - jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap); - } - } - } - - @Override - public void chainColour_actionPerformed(ActionEvent actionEvent) - { - chainColour.setSelected(true); - jmb.colourByChain(); - } - - @Override - public void chargeColour_actionPerformed(ActionEvent actionEvent) - { - chargeColour.setSelected(true); - jmb.colourByCharge(); - } - - @Override - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - zappoColour.setSelected(true); - jmb.setJalviewColourScheme(new ZappoColourScheme()); - } - - @Override - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - taylorColour.setSelected(true); - jmb.setJalviewColourScheme(new TaylorColourScheme()); - } - - @Override - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - hydroColour.setSelected(true); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); - } - - @Override - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - helixColour.setSelected(true); - jmb.setJalviewColourScheme(new HelixColourScheme()); - } - - @Override - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - strandColour.setSelected(true); - jmb.setJalviewColourScheme(new StrandColourScheme()); - } - - @Override - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - turnColour.setSelected(true); - jmb.setJalviewColourScheme(new TurnColourScheme()); - } - - @Override - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - buriedColour.setSelected(true); - jmb.setJalviewColourScheme(new BuriedColourScheme()); - } - - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new PurinePyrimidineColourScheme()); - } - - @Override - public void userColour_actionPerformed(ActionEvent e) - { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) - { - new UserDefinedColours(this, null); - } - else - { - UserColourScheme udc = UserDefinedColours.getUserColourSchemes().get( - e.getActionCommand()); - jmb.setJalviewColourScheme(udc); - } - } - - @Override - public void backGround_actionPerformed(ActionEvent actionEvent) - { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_background_colour"), - null); - if (col != null) - { - jmb.setBackgroundColour(col); - } - } - - @Override public void showHelp_actionPerformed(ActionEvent actionEvent) { try { - jalview.util.BrowserLauncher + BrowserLauncher .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); } catch (Exception ex) { } } - public void updateTitleAndMenus() - { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.getChainNames()); - - this.setTitle(jmb.getViewerTitle("Chimera", true)); - if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) - { - viewerActionMenu.setVisible(true); - } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ - @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) - { - alignStructs_withAllAlignPanels(); - } - - private void alignStructs_withAllAlignPanels() - { - if (getAlignmentPanel() == null) - { - return; - } - - if (_alignwith.size() == 0) - { - _alignwith.add(getAlignmentPanel()); - } - - try - { - AlignmentI[] als = new Alignment[_alignwith.size()]; - ColumnSelection[] alc = new ColumnSelection[_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.getColumnSelection(); - } - jmb.superposeStructures(als, alm, alc); - } catch (Exception e) - { - StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) - { - sp.append("'" + ap.alignFrame.getTitle() + "' "); - } - Cache.log.info("Couldn't align structures with the " + sp.toString() - + "associated alignment panels.", e); - } - } - - @Override - public void setJalviewColourScheme(ColourSchemeI ucs) - { - jmb.setJalviewColourScheme(ucs); - - } - - /** - * - * @param alignment - * @return first alignment panel displaying given alignment, or the default - * alignment panel - */ - public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) - { - for (AlignmentPanel ap : getAllAlignmentPanels()) - { - if (ap.av.getAlignment() == alignment) - { - return ap; - } - } - return getAlignmentPanel(); - } - @Override public AAStructureBindingModel getBinding() { @@ -1150,8 +750,8 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Chimera"; } } diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java index a5f4355..8e0765b 100644 --- a/src/jalview/gui/ColourMenuHelper.java +++ b/src/jalview/gui/ColourMenuHelper.java @@ -27,8 +27,9 @@ public class ColourMenuHelper /** * Adds items to the colour menu, as mutually exclusive members of a button * group. The callback handler is responsible for the action on selecting any - * of these options. It is returned the name of the selected colour, or "None" - * or "User Defined". + * of these options. The callback method receives the name of the selected + * colour, or "None" or "User Defined". This method returns the ButtonGroup to + * which items were added. *
      *
    • None
      • *
    • Clustal
      • @@ -43,28 +44,35 @@ public class ColourMenuHelper * a callback to handle menu selection * @param coll * the data the menu is being built for + * @param simpleOnly + * if true, only simple per-residue colour schemes are included */ - public static void addMenuItems(final JMenu colourMenu, - final ColourChangeListener client, AnnotatedCollectionI coll) + public static ButtonGroup addMenuItems(final JMenu colourMenu, + final ColourChangeListener client, AnnotatedCollectionI coll, + boolean simpleOnly) { /* * ButtonGroup groups those items whose * selection is mutually exclusive */ ButtonGroup colours = new ButtonGroup(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem( - MessageManager.getString("label.none")); - noColourmenuItem.setName(ResidueColourScheme.NONE); - noColourmenuItem.addActionListener(new ActionListener() + + if (!simpleOnly) { - @Override - public void actionPerformed(ActionEvent e) + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem( + MessageManager.getString("label.none")); + noColourmenuItem.setName(ResidueColourScheme.NONE); + noColourmenuItem.addActionListener(new ActionListener() { - client.changeColour_actionPerformed(ResidueColourScheme.NONE); - } - }); - colourMenu.add(noColourmenuItem); - colours.add(noColourmenuItem); + @Override + public void actionPerformed(ActionEvent e) + { + client.changeColour_actionPerformed(ResidueColourScheme.NONE); + } + }); + colourMenu.add(noColourmenuItem); + colours.add(noColourmenuItem); + } /* * scan registered colour schemes (built-in or user-defined @@ -74,9 +82,14 @@ public class ColourMenuHelper .getColourSchemes(); for (ColourSchemeI scheme : colourSchemes) { + if (simpleOnly && !scheme.isSimple()) + { + continue; + } + /* * button text is i18n'd but the name is the canonical name of - * the colour scheme (inspected in changeColour_actionPerformed) + * the colour scheme (inspected in setColourSelected()) */ final String name = scheme.getSchemeName(); String label = MessageManager.getStringOrReturn("label.colourScheme_" @@ -148,18 +161,28 @@ public class ColourMenuHelper colours.add(radioItem); } - final String label = MessageManager.getString("action.user_defined"); - JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(label); - userDefinedColour.addActionListener(new ActionListener() + /* + * only add the option to load/configure a user-defined colour + * to the AlignFrame colour menu + */ + if (client instanceof AlignFrame) { - @Override - public void actionPerformed(ActionEvent e) + final String label = MessageManager.getString("action.user_defined"); + JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem( + label); + userDefinedColour.addActionListener(new ActionListener() { - client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED); - } - }); - colourMenu.add(userDefinedColour); - colours.add(userDefinedColour); + @Override + public void actionPerformed(ActionEvent e) + { + client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED); + } + }); + colourMenu.add(userDefinedColour); + colours.add(userDefinedColour); + } + + return colours; } /** diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java index 801b285..a797872 100644 --- a/src/jalview/gui/JalviewChimeraBindingModel.java +++ b/src/jalview/gui/JalviewChimeraBindingModel.java @@ -95,7 +95,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding } if (!isLoadingFromArchive()) { - colourBySequence(ap.av.isShowSequenceFeatures(), ap); + colourBySequence(ap); } } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index b6fd5fc..c660ab5 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1271,11 +1271,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected void buildColourMenu() { SequenceGroup sg = getGroup(); + if (sg == null) + { + /* + * popup menu with no sequence group scope + */ + return; + } colourMenu.removeAll(); colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, sg); + ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 91d7130..34ad659 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -20,27 +20,47 @@ */ package jalview.gui; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; 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.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; +import java.awt.Color; import java.awt.Component; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileOutputStream; +import java.io.FileReader; +import java.io.IOException; +import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; import java.util.Vector; +import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; /** * Base class with common functionality for JMol, Chimera or other structure @@ -52,6 +72,13 @@ import javax.swing.JOptionPane; public abstract class StructureViewerBase extends GStructureViewer implements Runnable, ViewSetProvider { + /* + * names for colour options (additional to Jalview colour schemes) + */ + enum ViewerColour + { + BySequence, ByChain, ChargeCysteine, ByViewer + } /** * list of sequenceSet ids associated with the view @@ -84,6 +111,13 @@ public abstract class StructureViewerBase extends GStructureViewer protected boolean allChainsSelected = false; /** + * Default constructor + */ + public StructureViewerBase() + { + super(); + } + /** * * @param ap2 * @return true if this Jmol instance is linked with the given alignPanel @@ -273,8 +307,6 @@ public abstract class StructureViewerBase extends GStructureViewer public abstract ViewerType getViewerType(); - protected abstract AAStructureBindingModel getBindingModel(); - /** * add a new structure (with associated sequences and chains) to this viewer, * retrieving it if necessary first. @@ -320,7 +352,7 @@ public abstract class StructureViewerBase extends GStructureViewer } } // otherwise, start adding the structure. - getBindingModel().addSequenceAndChain(new PDBEntry[] { pdbentry }, + getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry }, new SequenceI[][] { seqs }, new String[][] { chains }); addingStructures = true; _started = false; @@ -350,7 +382,10 @@ public abstract class StructureViewerBase extends GStructureViewer return option; } - protected abstract boolean hasPdbId(String pdbId); + protected boolean hasPdbId(String pdbId) + { + return getBinding().hasPdbId(pdbId); + } protected abstract List getViewersFor( AlignmentPanel alp); @@ -438,7 +473,7 @@ public abstract class StructureViewerBase extends GStructureViewer // JBPNOTE: this looks like a binding routine, rather than a gui routine for (StructureViewerBase viewer : getViewersFor(null)) { - AAStructureBindingModel bindingModel = viewer.getBindingModel(); + AAStructureBindingModel bindingModel = viewer.getBinding(); for (int pe = 0; pe < bindingModel.getPdbCount(); pe++) { if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename)) @@ -552,4 +587,389 @@ public abstract class StructureViewerBase extends GStructureViewer abstract void showSelectedChains(); + /** + * Action on selecting one of Jalview's registered colour schemes + */ + @Override + public void changeColour_actionPerformed(String colourSchemeName) + { + AlignmentI al = getAlignmentPanel().av.getAlignment(); + ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme( + colourSchemeName, al, null); + getBinding().setJalviewColourScheme(cs); + } + + /** + * Builds the colour menu + */ + protected void buildColourMenu() + { + colourMenu.removeAll(); + AlignmentI al = getAlignmentPanel().av.getAlignment(); + + /* + * add colour by sequence, by chain, by charge and cysteine + */ + colourMenu.add(seqColour); + colourMenu.add(chainColour); + colourMenu.add(chargeColour); + chargeColour.setEnabled(!al.isNucleotide()); + + /* + * add all 'simple' (per-residue) colour schemes registered to Jalview + */ + ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this, + al, true); + + /* + * add 'colour by viewer' (menu item text is set in subclasses) + */ + viewerColour.setSelected(false); + viewerColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + viewerColour_actionPerformed(actionEvent); + } + }); + colourMenu.add(viewerColour); + + /* + * add 'set background colour' + */ + JMenuItem backGround = new JMenuItem(); + backGround + .setText(MessageManager.getString("action.background_colour")); + backGround.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + background_actionPerformed(actionEvent); + } + }); + colourMenu.add(backGround); + + /* + * add colour buttons to a group so their selection is + * mutually exclusive (background colour is a separate option) + */ + itemGroup.add(seqColour); + itemGroup.add(chainColour); + itemGroup.add(chargeColour); + itemGroup.add(viewerColour); + } + + /** + * Construct menu items + */ + protected void initMenus() + { + AAStructureBindingModel binding = getBinding(); + + seqColour = new JRadioButtonMenuItem(); + seqColour.setText(MessageManager.getString("action.by_sequence")); + seqColour.setName(ViewerColour.BySequence.name()); + seqColour.setSelected(binding.isColourBySequence()); + seqColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + seqColour_actionPerformed(actionEvent); + } + }); + + chainColour = new JRadioButtonMenuItem(); + chainColour.setText(MessageManager.getString("action.by_chain")); + chainColour.setName(ViewerColour.ByChain.name()); + chainColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + chainColour_actionPerformed(actionEvent); + } + }); + + chargeColour = new JRadioButtonMenuItem(); + chargeColour.setText(MessageManager.getString("label.charge_cysteine")); + chargeColour.setName(ViewerColour.ChargeCysteine.name()); + chargeColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + chargeColour_actionPerformed(actionEvent); + } + }); + + viewerColour = new JRadioButtonMenuItem(); + // text is set in overrides of this method + viewerColour.setName(ViewerColour.ByViewer.name()); + viewerColour.setSelected(!binding.isColourBySequence()); + + if (_colourwith == null) + { + _colourwith = new Vector(); + } + if (_alignwith == null) + { + _alignwith = new Vector(); + } + + ViewSelectionMenu seqColourBy = new ViewSelectionMenu( + MessageManager.getString("label.colour_by"), this, _colourwith, + new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + if (!seqColour.isSelected()) + { + seqColour.doClick(); + } + else + { + // update the Chimera display now. + seqColour_actionPerformed(null); + } + } + }); + viewMenu.add(seqColourBy); + + final ItemListener handler = new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + alignStructs.setEnabled(_alignwith.size() > 0); + alignStructs.setToolTipText(MessageManager.formatMessage( + "label.align_structures_using_linked_alignment_views", + new String[] { String.valueOf(_alignwith.size()) })); + } + }; + JMenu alpanels = new ViewSelectionMenu( + MessageManager.getString("label.superpose_with"), this, + _alignwith, handler); + handler.itemStateChanged(null); + viewerActionMenu.add(alpanels); + viewerActionMenu.addMenuListener(new MenuListener() + { + @Override + public void menuSelected(MenuEvent e) + { + handler.itemStateChanged(null); + } + + @Override + public void menuDeselected(MenuEvent e) + { + } + + @Override + public void menuCanceled(MenuEvent e) + { + } + }); + + buildColourMenu(); + } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) { + getBinding().setJalviewColourScheme(cs); + } + @Override + protected void alignStructs_actionPerformed(ActionEvent actionEvent) + { + alignStructs_withAllAlignPanels(); + } + protected void alignStructs_withAllAlignPanels() + { + if (getAlignmentPanel() == null) + { + return; + } + + if (_alignwith.size() == 0) + { + _alignwith.add(getAlignmentPanel()); + } + + try + { + AlignmentI[] als = new Alignment[_alignwith.size()]; + ColumnSelection[] alc = new ColumnSelection[_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.getColumnSelection(); + } + getBinding().superposeStructures(als, alm, alc); + } catch (Exception e) + { + StringBuffer sp = new StringBuffer(); + for (AlignmentPanel ap : _alignwith) + { + sp.append("'" + ap.alignFrame.getTitle() + "' "); + } + Cache.log.info("Couldn't align structures with the " + sp.toString() + + "associated alignment panels.", e); + } + } + @Override + public void background_actionPerformed(ActionEvent actionEvent) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_background_colour"), + null); + if (col != null) + { + getBinding().setBackgroundColour(col); + } + } + @Override + public void viewerColour_actionPerformed(ActionEvent actionEvent) + { + if (viewerColour.isSelected()) + { + // disable automatic sequence colouring. + 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) + { + AAStructureBindingModel binding = getBinding(); + binding.setColourBySequence(seqColour.isSelected()); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + if (binding.isColourBySequence()) + { + if (!binding.isLoadingFromArchive()) + { + if (_colourwith.size() == 0 && getAlignmentPanel() != null) + { + // Make the currently displayed alignment panel the associated view + _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); + } + } + // Set the colour using the current view for the associated alignframe + for (AlignmentPanel ap : _colourwith) + { + binding.colourBySequence(ap); + } + } + } + @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; + try + { + // TODO: cope with multiple PDB files in view + in = new BufferedReader( + new FileReader(getBinding().getPdbFile()[0])); + File outFile = chooser.getSelectedFile(); + + PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); + String data; + while ((data = in.readLine()) != null) + { + if (!(data.indexOf("
      ") > -1 || data.indexOf("
      ") > -1)) + { + out.println(data); + } + } + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); + } finally + { + if (in != null) + { + try + { + in.close(); + } catch (IOException e) + { + // ignore + } + } + } + } + } + @Override + public void viewMapping_actionPerformed(ActionEvent actionEvent) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + try + { + cap.appendText(getBinding().printMappings()); + } catch (OutOfMemoryError e) + { + new OOMWarning( + "composing sequence-structure alignments for display in text box.", + e); + cap.dispose(); + return; + } + Desktop.addInternalFrame(cap, + MessageManager.getString("label.pdb_sequence_mapping"), 550, + 600); + } + + protected abstract String getViewerName(); + public void updateTitleAndMenus() + { + AAStructureBindingModel binding = getBinding(); + if (binding.hasFileLoadingError()) + { + repaint(); + return; + } + setChainMenuItems(binding.getChainNames()); + + this.setTitle(binding.getViewerTitle(getViewerName(), true)); + if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1) + { + viewerActionMenu.setVisible(true); + } + if (!binding.isLoadingFromArchive()) + { + seqColour_actionPerformed(null); + } + } } diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java index 52f745d..6b89ab4 100644 --- a/src/jalview/jbgui/GStructureViewer.java +++ b/src/jalview/jbgui/GStructureViewer.java @@ -21,17 +21,14 @@ package jalview.jbgui; import jalview.api.structures.JalviewStructureDisplayI; -import jalview.gui.UserDefinedColours; -import jalview.schemes.UserColourScheme; +import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.util.MessageManager; import java.awt.BorderLayout; import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.Map; -import javax.swing.ButtonGroup; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenu; @@ -41,7 +38,7 @@ import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; public abstract class GStructureViewer extends JInternalFrame implements - JalviewStructureDisplayI + JalviewStructureDisplayI, ColourChangeListener { // private AAStructureBindingModel bindingModel; @@ -65,26 +62,6 @@ public abstract class GStructureViewer extends JInternalFrame implements protected JRadioButtonMenuItem chargeColour; - protected JRadioButtonMenuItem zappoColour; - - protected JRadioButtonMenuItem taylorColour; - - protected JRadioButtonMenuItem hydroColour; - - protected JRadioButtonMenuItem strandColour; - - protected JRadioButtonMenuItem helixColour; - - protected JRadioButtonMenuItem turnColour; - - protected JRadioButtonMenuItem buriedColour; - - protected JRadioButtonMenuItem nucleotideColour; - - protected JRadioButtonMenuItem purinePyrimidineColour; - - protected JRadioButtonMenuItem userColour; - protected JRadioButtonMenuItem viewerColour; protected JMenuItem helpItem; @@ -204,11 +181,11 @@ public abstract class GStructureViewer extends JInternalFrame implements } }); - viewerActionMenu = new JMenu(MessageManager.getString("label.jmol")); + viewerActionMenu = new JMenu(); viewerActionMenu.setVisible(false); viewerActionMenu.add(alignStructs); colourMenu = new JMenu(); - buildColourMenu(); + colourMenu.setText(MessageManager.getString("label.colours")); fileMenu.add(savemenu); fileMenu.add(viewMapping); savemenu.add(pdbFile); @@ -230,240 +207,6 @@ public abstract class GStructureViewer extends JInternalFrame implements statusPanel.add(statusBar, null); } - /** - * Builds the colour menu - */ - protected void buildColourMenu() - { - colourMenu.removeAll(); - colourMenu.setText(MessageManager.getString("label.colours")); - - JMenuItem backGround = new JMenuItem(); - backGround - .setText(MessageManager.getString("action.background_colour")); - backGround.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - backGround_actionPerformed(actionEvent); - } - }); - seqColour = new JRadioButtonMenuItem(); - seqColour.setSelected(false); - seqColour.setText(MessageManager.getString("action.by_sequence")); - seqColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - seqColour_actionPerformed(actionEvent); - } - }); - chainColour = new JRadioButtonMenuItem(); - chainColour.setText(MessageManager.getString("action.by_chain")); - chainColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - chainColour_actionPerformed(actionEvent); - } - }); - chargeColour = new JRadioButtonMenuItem(); - chargeColour.setText(MessageManager.getString("label.charge_cysteine")); - chargeColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - chargeColour_actionPerformed(actionEvent); - } - }); - zappoColour = new JRadioButtonMenuItem(); - zappoColour.setText(MessageManager - .getString("label.colourScheme_zappo")); - zappoColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - zappoColour_actionPerformed(actionEvent); - } - }); - taylorColour = new JRadioButtonMenuItem(); - taylorColour.setText(MessageManager - .getString("label.colourScheme_taylor")); - taylorColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - taylorColour_actionPerformed(actionEvent); - } - }); - hydroColour = new JRadioButtonMenuItem(); - hydroColour.setText(MessageManager - .getString("label.colourScheme_hydrophobic")); - hydroColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - hydroColour_actionPerformed(actionEvent); - } - }); - strandColour = new JRadioButtonMenuItem(); - strandColour.setText(MessageManager - .getString("label.colourScheme_strand_propensity")); - strandColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - strandColour_actionPerformed(actionEvent); - } - }); - helixColour = new JRadioButtonMenuItem(); - helixColour.setText(MessageManager - .getString("label.colourScheme_helix_propensity")); - helixColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - helixColour_actionPerformed(actionEvent); - } - }); - turnColour = new JRadioButtonMenuItem(); - turnColour.setText(MessageManager - .getString("label.colourScheme_turn_propensity")); - turnColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - turnColour_actionPerformed(actionEvent); - } - }); - buriedColour = new JRadioButtonMenuItem(); - buriedColour.setText(MessageManager - .getString("label.colourScheme_buried_index")); - buriedColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - buriedColour_actionPerformed(actionEvent); - } - }); - nucleotideColour = new JRadioButtonMenuItem(); - nucleotideColour.setText(MessageManager - .getString("label.colourScheme_nucleotide")); - nucleotideColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - nucleotideColour_actionPerformed(actionEvent); - } - }); - purinePyrimidineColour = new JRadioButtonMenuItem(); - purinePyrimidineColour.setText(MessageManager - .getString("label.colourScheme_purine/pyrimidine")); - purinePyrimidineColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - purinePyrimidineColour_actionPerformed(actionEvent); - } - }); - userColour = new JRadioButtonMenuItem(); - userColour.setText(MessageManager.getString("action.user_defined")); - userColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - userColour_actionPerformed(actionEvent); - } - }); - viewerColour = new JRadioButtonMenuItem(); - viewerColour.setSelected(false); - viewerColour - .setText(MessageManager.getString("label.colour_with_jmol")); - viewerColour.setToolTipText(MessageManager - .getString("label.let_jmol_manage_structure_colours")); - viewerColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - viewerColour_actionPerformed(actionEvent); - } - }); - - /* - * add colour buttons to a group so their selection - * is mutually exclusive - */ - ButtonGroup colourButtons = new ButtonGroup(); - - colourMenu.add(seqColour); - colourMenu.add(chainColour); - colourMenu.add(chargeColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydroColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(purinePyrimidineColour); - - /* - * add any user-defined colours that are loaded - */ - Map userColourSchemes = UserDefinedColours - .getUserColourSchemes(); - if (userColourSchemes != null) - { - for (String schemeName : userColourSchemes.keySet()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - schemeName); - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userColour_actionPerformed(evt); - } - }); - colourMenu.add(radioItem); - colourButtons.add(radioItem); - } - } - colourMenu.add(userColour); - colourMenu.add(viewerColour); - colourMenu.add(backGround); - - colourButtons.add(seqColour); - colourButtons.add(chainColour); - colourButtons.add(chargeColour); - colourButtons.add(zappoColour); - colourButtons.add(taylorColour); - colourButtons.add(hydroColour); - colourButtons.add(helixColour); - colourButtons.add(strandColour); - colourButtons.add(turnColour); - colourButtons.add(buriedColour); - colourButtons.add(purinePyrimidineColour); - colourButtons.add(userColour); - colourButtons.add(viewerColour); - } - protected void fitToWindow_actionPerformed() { } @@ -515,57 +258,7 @@ public abstract class GStructureViewer extends JInternalFrame implements } - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void nucleotideColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void userColour_actionPerformed(ActionEvent actionEvent) - { - - } - - public void backGround_actionPerformed(ActionEvent actionEvent) + public void background_actionPerformed(ActionEvent actionEvent) { } @@ -574,14 +267,4 @@ public abstract class GStructureViewer extends JInternalFrame implements { } - - // { - // return bindingModel; - // } - - // public void setBindingModel(AAStructureBindingModel bindingModel) - // { - // this.bindingModel = bindingModel; - // } - } diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index e3ef391..fb1443d 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -426,4 +426,10 @@ public class AnnotationColourGradient extends FollowerColourScheme { return "Annotation"; } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index d68791c..be77e00 100755 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -122,4 +122,10 @@ public class Blosum62ColourScheme extends ResidueColourScheme { return JalviewColourScheme.Blosum62.toString(); } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index 2bb64fc..9c0b953 100755 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -361,4 +361,10 @@ public class ClustalxColourScheme extends ResidueColourScheme { return JalviewColourScheme.Clustal.toString(); } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java index be8793b..372b569 100755 --- a/src/jalview/schemes/ColourSchemeI.java +++ b/src/jalview/schemes/ColourSchemeI.java @@ -159,4 +159,15 @@ public interface ColourSchemeI * @return */ String getSchemeName(); + + /** + * Answers true if the colour scheme depends only on the sequence symbol, and + * not on other information such as alignment consensus or annotation. (Note + * that simple colour schemes may have a fading by percentage identity or + * conservation overlaid.) Simple colour schemes can be propagated to + * structure viewers. + * + * @return + */ + boolean isSimple(); } diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java index 3637ce3..6cb095b 100644 --- a/src/jalview/schemes/CovariationColourScheme.java +++ b/src/jalview/schemes/CovariationColourScheme.java @@ -149,4 +149,10 @@ public class CovariationColourScheme extends ResidueColourScheme { return "Covariation"; } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java index 5628fcd..389655c 100755 --- a/src/jalview/schemes/PIDColourScheme.java +++ b/src/jalview/schemes/PIDColourScheme.java @@ -114,4 +114,10 @@ public class PIDColourScheme extends ResidueColourScheme { return new PIDColourScheme(); } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java index 7a1d8d3..056a167 100644 --- a/src/jalview/schemes/RNAHelicesColour.java +++ b/src/jalview/schemes/RNAHelicesColour.java @@ -240,4 +240,10 @@ public class RNAHelicesColour extends ResidueColourScheme { return JalviewColourScheme.RNAHelices.toString(); } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 92de7ac..57f7d57 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -409,4 +409,14 @@ public abstract class ResidueColourScheme implements ColourSchemeI { return false; } + + /** + * Default method returns true. Override this to return false in colour + * schemes that are not determined solely by the sequence symbol. + */ + @Override + public boolean isSimple() + { + return true; + } } diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java index 6f55204..13d1d55 100644 --- a/src/jalview/schemes/TCoffeeColourScheme.java +++ b/src/jalview/schemes/TCoffeeColourScheme.java @@ -170,4 +170,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme { return JalviewColourScheme.TCoffee.toString(); } + + @Override + public boolean isSimple() + { + return false; + } } diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 063eacf..fda08fd 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,19 +20,26 @@ */ package jalview.structures.models; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; +import jalview.schemes.ColourSchemeI; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; +import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -85,6 +92,8 @@ public abstract class AAStructureBindingModel extends */ protected String[] modelFileNames = null; + public String fileLoadingError; + /** * Data bean class to simplify parameterisation in superposeStructures */ @@ -688,4 +697,80 @@ public abstract class AAStructureBindingModel extends { return null; } + + public abstract void setJalviewColourScheme(ColourSchemeI cs); + + public abstract void superposeStructures(AlignmentI[] als, int[] alm, + ColumnSelection[] alc); + + public abstract void setBackgroundColour(Color col); + + protected abstract StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, FeatureRenderer fr, + AlignmentI alignment); + + /** + * returns the current featureRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment); + + /** + * returns the current sequenceRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment); + + protected abstract void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands); + + public abstract void colourByChain(); + + public abstract void colourByCharge(); + + /** + * colour any structures associated with sequences in the given alignment + * using the getFeatureRenderer() and getSequenceRenderer() renderers but only + * if colourBySequence is enabled. + */ + public void colourBySequence(AlignmentViewPanel alignmentv) + { + boolean showFeatures = alignmentv.getAlignViewport() + .isShowSequenceFeatures(); + if (!colourBySequence || !isLoadingFinished()) + { + return; + } + if (getSsm() == null) + { + return; + } + String[] files = getPdbFile(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); + + FeatureRenderer fr = null; + if (showFeatures) + { + fr = getFeatureRenderer(alignmentv); + } + AlignmentI alignment = alignmentv.getAlignment(); + + StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands( + files, sr, fr, alignment); + colourBySequence(colourBySequenceCommands); + } + + public boolean hasFileLoadingError() + { + return fileLoadingError != null && fileLoadingError.length() > 0; + } } diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index b74a089..0422537 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -24,18 +24,25 @@ import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; +import jalview.schemes.ColourSchemeI; import jalview.structure.AtomSpec; +import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel.SuperposeData; +import java.awt.Color; import java.util.Arrays; import java.util.List; @@ -155,6 +162,59 @@ public class AAStructureBindingModelTest { return null; } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) + { + } + + @Override + public void superposeStructures(AlignmentI[] als, int[] alm, + ColumnSelection[] alc) + { + } + + @Override + public void setBackgroundColour(Color col) + { + } + + @Override + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, FeatureRenderer fr, + AlignmentI alignment) + { + return null; + } + + @Override + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) + { + return null; + } + + @Override + public SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) + { + return null; + } + + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) + { + } + + @Override + public void colourByChain() + { + } + + @Override + public void colourByCharge() + { + } }; } @@ -239,4 +299,14 @@ public class AAStructureBindingModelTest assertFalse(matched[4]); // superposable, but hidden, column assertTrue(matched[5]); } + + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) + { + return null; + } + + public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) + { + return null; + } } -- 1.7.10.2