*/
package jalview.gui;
+import jalview.api.FeatureRenderer;
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.ChimeraCommands;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
-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.ZappoColourScheme;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
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.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
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.Collections;
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.JMenuItem;
-import javax.swing.JOptionPane;
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
{
private JalviewChimeraBinding jmb;
- private boolean allChainsSelected = false;
-
private IProgressIndicator progressBar = null;
/*
private Random random = new Random();
+ private int myWidth = 500;
+
+ private int myHeight = 150;
+
/**
* 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
+ .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<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- // 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()
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_chimera_attributes_tip"));
+ writeFeatures.addActionListener(new ActionListener()
{
-
@Override
- public void menuSelected(MenuEvent e)
+ public void actionPerformed(ActionEvent e)
{
- handler.itemStateChanged(null);
+ sendFeaturesToChimera();
}
+ });
+ viewerActionMenu.add(writeFeatures);
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
- }
+ final JMenu fetchAttributes = new JMenu(
+ MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes.setToolTipText(
+ MessageManager.getString("label.fetch_chimera_attributes_tip"));
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
@Override
- public void menuCanceled(MenuEvent e)
+ public void mouseEntered(MouseEvent e)
{
- // TODO Auto-generated method stub
+ buildAttributesMenu(fetchAttributes);
}
});
- JMenuItem writeFeatures = new JMenuItem("Write Jalview features");
- writeFeatures
- .setToolTipText("Create attributes in Chimera for features in Jalview");
- writeFeatures.addActionListener(new ActionListener()
+ viewerActionMenu.add(fetchAttributes);
+ }
+
+ /**
+ * Query Chimera for its residue attribute names and add them as items off the
+ * attributes menu
+ *
+ * @param attributesMenu
+ */
+ protected void buildAttributesMenu(JMenu attributesMenu)
+ {
+ List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+ if (atts == null)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ return;
+ }
+ attributesMenu.removeAll();
+ Collections.sort(atts);
+ for (String att : atts)
+ {
+ final String attName = att.split(" ")[1];
+
+ /*
+ * ignore 'jv_*' attributes, as these are Jalview features that have
+ * been transferred to residue attributes in Chimera!
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
{
- sendFeaturesToChimera();
+ JMenuItem menuItem = new JMenuItem(attName);
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getChimeraAttributes(attName);
+ }
+ });
+ attributesMenu.add(menuItem);
}
- });
- viewerActionMenu.add(writeFeatures);
+ }
}
- protected void sendFeaturesToChimera()
+ /**
+ * Read residues in Chimera with the given attribute name, and set as features
+ * on the corresponding sequence positions (if any)
+ *
+ * @param attName
+ */
+ protected void getChimeraAttributes(String attName)
{
- // TODO Auto-generated method stub
+ jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
+ }
+ /**
+ * Send a command to Chimera to create residue attributes for Jalview features
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ */
+ protected void sendFeaturesToChimera()
+ {
+ int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
+ statusBar.setText(
+ MessageManager.formatMessage("label.attributes_set", count));
}
/**
- * add a single PDB structure to a new or existing Chimera view
+ * open a single PDB structure in a new Chimera view
*
* @param pdbentry
* @param seq
String[] chains, final AlignmentPanel ap)
{
this();
- String pdbId = pdbentry.getId();
-
- /*
- * If the PDB file is already loaded, the user may just choose to add to an
- * existing viewer (or cancel)
- */
- if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
- {
- return;
- }
-
- /*
- * Check if there are other Chimera views involving this alignment and give
- * user the option to add and align this molecule to one of them (or cancel)
- */
- if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
- {
- return;
- }
- /*
- * If the options above are declined or do not apply, show the structure in
- * a new viewer
- */
openNewChimera(ap, new PDBEntry[] { pdbentry },
- new SequenceI[][] { seq });
+ 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 openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
createProgressBar();
- // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
- String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
- null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
- alignAddedStructures = true;
useAlignmentPanelForSuperposition(ap);
}
jmb.setColourBySequence(true);
- setSize(400, 400); // probably should be a configurable/dynamic default here
+ setSize(myWidth, myHeight);
initMenus();
addingStructures = false;
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
}
/**
- * Retrieve chains for sequences by inspecting their PDB refs. The hope is
- * that the first will be to the sequence's own chain. Really need a more
- * managed way of doing this.
- *
- * @param seqs
- * @return
- */
- protected String[][] extractChains(SequenceI[][] seqs)
- {
- String[][] chains = new String[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
- {
- chains[i] = new String[seqs[i].length];
- int seqno = 0;
- for (SequenceI seq : seqs[i])
- {
- String chain = null;
- if (seq.getDatasetSequence() != null)
- {
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
- .getAllPDBEntries();
- if (pdbrefs != null && pdbrefs.size() > 0)
- {
- // FIXME: SequenceI.PDBEntry[0] chain mapping used for
- // ChimeraViewFrame. Is this even used ???
-
- chain = pdbrefs.get(0).getChainCode();
- }
- }
- chains[i][seqno++] = chain;
- }
- }
- return chains;
- }
-
- /**
* Create a new viewer from saved session state data including Chimera session
* file
*
}
/**
- * create a new viewer containing several structures superimposed using the
- * given alignPanel.
+ * create a new viewer containing several structures, optionally superimposed
+ * using the given alignPanel.
*
* @param pe
* @param seqs
* @param ap
*/
- public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+ public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded,
+ SequenceI[][] seqs,
AlignmentPanel ap)
{
this();
+ setAlignAddedStructures(alignAdded);
openNewChimera(ap, pe, seqs);
}
}
/**
- * Returns a list of any Chimera viewers in the desktop. The list is
- * restricted to those linked to the given alignment panel if it is not null.
- */
- @Override
- protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
- {
- List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof ChimeraViewFrame)
- {
- if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
- {
- result.add((StructureViewerBase) frame);
- }
- }
- }
- return result;
- }
-
- /**
* Launch Chimera. If we have a chimera session file name, send Chimera the
* command to open its saved session file.
*/
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this,
- jmb.getViewerTitle("Chimera", true), getBounds().width,
+ Desktop.addInternalFrame(this,
+ jmb.getViewerTitle(getViewerName(), true), getBounds().width,
getBounds().height);
if (!jmb.launchChimera())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
this.dispose();
return;
}
boolean opened = jmb.openSession(chimeraSessionFile);
if (!opened)
{
- System.err
- .println("An error occurred opening Chimera session file "
- + chimeraSessionFile);
+ System.err.println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
}
}
- jmb.setFinishedInit(true);
-
- jmb.startChimeraListener();
- }
- /**
- * If the list is not empty, add menu items for 'All' and each individual
- * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
- *
- * @param chainNames
- */
- void setChainMenuItems(List<String> chainNames)
- {
- chainMenu.removeAll();
- if (chainNames == null || chainNames.isEmpty())
+ if (!Platform.isJS())
{
- return;
- }
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.all"));
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- }
- showSelectedChains();
- allChainsSelected = false;
- }
- });
-
- chainMenu.add(menuItem);
-
- for (String chainName : chainNames)
- {
- menuItem = new JCheckBoxMenuItem(chainName, true);
- menuItem.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- showSelectedChains();
- }
- }
- });
-
- chainMenu.add(menuItem);
+ jmb.startChimeraListener();
}
}
/**
* Show only the selected chain(s) in the viewer
*/
+ @Override
void showSelectedChains()
{
- List<String> toshow = new ArrayList<String>();
+ List<String> toshow = new ArrayList<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
if (!closeChimera)
{
- String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera",
- new Object[] { jmb.getViewerTitle("Chimera", false) });
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_chimera", new Object[]
+ { jmb.getViewerTitle(getViewerName(), false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_CANCEL_OPTION);
+ JvOptionPane.YES_NO_CANCEL_OPTION);
/*
* abort closure if user hits escape or Cancel
*/
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
{
return;
}
- closeChimera = confirm == JOptionPane.YES_OPTION;
+ closeChimera = confirm == JvOptionPane.YES_OPTION;
}
jmb.closeViewer(closeChimera);
}
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder(128);
StringBuilder files = new StringBuilder(128);
- List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
- List<Integer> filePDBpos = new ArrayList<Integer>();
+ List<PDBEntry> filePDB = new ArrayList<>();
+ List<Integer> filePDBpos = new ArrayList<>();
PDBEntry thePdbEntry = null;
+ StructureFile pdb = null;
try
{
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ String[] curfiles = jmb.getStructureFiles(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles for '"
- + thePdbEntry.getId() + "'");
+ errormsgs.append(
+ "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'");
}
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[] { errormsgs.toString() }),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new Object[]
+ { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
if (files.length() > 0)
{
+ jmb.setFinishedInit(false);
if (!addingStructures)
{
try
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);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
- String protocol = AppletFormatAdapter.URL;
+ DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
} catch (Throwable e)
{
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos], pe.getFile(), protocol);
+
+ pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ jmb.getChains()[pos], pe.getFile(), protocol,
+ progressBar);
+ stashFoundChains(pdb, pe.getFile());
+
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
oomerror);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open " + pe.getFile()
- + " in Chimera viewer!", ex);
+ Cache.log.error(
+ "Couldn't open " + pe.getFile() + " in Chimera viewer!",
+ ex);
} finally
{
Cache.log.debug("File locations are " + files);
}
}
}
+
+ jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
+ /*
+ * ensure that any newly discovered features (e.g. RESNUM)
+ * are added to any open feature settings dialog
+ */
+ FeatureRenderer fr = getBinding().getFeatureRenderer(null);
+ if (fr != null)
+ {
+ fr.featuresAdded();
+ }
+
// refresh the sequence colours for the new structure(s)
for (AlignmentPanel ap : _colourwith)
{
jmb.updateColours(ap);
}
// do superposition if asked to
- if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ if (alignAddedStructures)
{
new Thread(new Runnable()
{
alignStructs_withAllAlignPanels();
}
}).start();
- alignAddedStructures = false;
}
addingStructures = false;
}
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails.
+ * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
*
* @param processingEntry
* @return
* @throws Exception
*/
+
+ private void stashFoundChains(StructureFile pdb, String file)
+ {
+ for (int i = 0; i < pdb.getChains().size(); i++)
+ {
+ String chid = new String(
+ pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
+ jmb.getChainNames().add(chid);
+ jmb.getChainFile().put(chid, file);
+ }
+ }
+
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
- // FIXME: this is duplicated code with Jmol frame ?
String filePath = null;
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[] { pdbid });
+ new Object[]
+ { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
}
@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("<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)
- {
- 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(
- MessageManager
- .getString("error.eps_generation_not_implemented"));
- }
-
- @Override
- public void png_actionPerformed(ActionEvent e)
- {
- throw new Error(
- MessageManager
- .getString("error.png_generation_not_implemented"));
- }
-
- @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<AlignmentPanel>();
- }
- 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)
+ public void makePDBImage(TYPE imageType)
{
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
+ throw new UnsupportedOperationException(
+ "Image export for Chimera is not implemented");
}
@Override
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
- } catch (Exception ex)
+ } catch (IOException 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()
{
}
@Override
- protected AAStructureBindingModel getBindingModel()
+ protected String getViewerName()
{
- return jmb;
+ return "Chimera";
+ }
+
+ /**
+ * Sends commands to align structures according to associated alignment(s).
+ *
+ * @return
+ */
+ @Override
+ protected String alignStructs_withAllAlignPanels()
+ {
+ String reply = super.alignStructs_withAllAlignPanels();
+ if (reply != null)
+ {
+ statusBar.setText("Superposition failed: " + reply);
+ }
+ return reply;
+ }
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
}
}
git://source.jalview.org / jalview.git / blobdiff