*/
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
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
protected boolean allChainsSelected = false;
/**
+ * Default constructor
+ */
+ public StructureViewerBase()
+ {
+ super();
+ }
+ /**
*
* @param ap2
* @return true if this Jmol instance is linked with the given alignPanel
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.
}
}
// 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;
return option;
}
- protected abstract boolean hasPdbId(String pdbId);
+ protected boolean hasPdbId(String pdbId)
+ {
+ return getBinding().hasPdbId(pdbId);
+ }
protected abstract List<StructureViewerBase> getViewersFor(
AlignmentPanel alp);
// 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))
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<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ 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<AlignmentPanel>();
+ }
+ 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("<PRE>") > -1 || data.indexOf("</PRE>") > -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);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff