X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=34ad659402361ea2c50394a9356a3117003b6e67;hb=f831ddf7f52d6c4a1918e87d94877b22bd322648;hp=91d71309c7c57ff198eb650efd0310aed15ab70a;hpb=94751f42fae76e075240eeac0c708abbc8cf9253;p=jalview.git 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); + } + } }