import java.io.*;
import jalview.jbgui.GStructureViewer;
+import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.popup.*;
import org.jmol.viewer.JmolConstants;
+import org.openscience.jmol.app.jmolpanel.AppConsole;
-public class AppJmol extends GStructureViewer implements StructureListener,
- JmolStatusListener, Runnable
+public class AppJmol extends GStructureViewer implements Runnable,
+ SequenceStructureBinding
{
- JmolViewer viewer;
-
- JmolPopup jmolpopup;
-
- ScriptWindow scriptWindow;
-
- PDBEntry pdbentry;
-
- SequenceI[] sequence;
-
- String[] chains;
-
- StructureSelectionManager ssm;
+ AppJmolBinding jmb;
+ JPanel scriptWindow;
+
JSplitPane splitPane;
RenderPanel renderPanel;
AlignmentPanel ap;
- String fileLoadingError;
-
- boolean colourBySequence = true;
-
- boolean loadingFromArchive = false;
-
Vector atomsPicked = new Vector();
+ private boolean addingStructures = false;
+
+ /**
+ *
+ * @param file
+ * @param id
+ * @param seq
+ * @param ap
+ * @param loadStatus
+ * @param bounds
+ * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+ */
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds)
{
this(file, id, seq, ap, loadStatus, bounds, null);
}
+ /**
+ * @deprecated
+ */
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds,
String viewid)
{
- loadingFromArchive = true;
- pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
- this.sequence = seq;
+ this(new String[]
+ { file }, new String[]
+ { id }, new SequenceI[][]
+ { seq }, ap, loadStatus, bounds, viewid);
+ }
+
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ */
+ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds,
+ String viewid)
+ {
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];
+ for (int i = 0; i < pdbentrys.length; i++)
+ {
+ PDBEntry pdbentry = new PDBEntry();
+ pdbentry.setFile(files[i]);
+ pdbentry.setId(ids[i]);
+ pdbentrys[i] = pdbentry;
+ }
+ // / TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+
+ jmb.setLoadingFromArchive(true);
this.ap = ap;
this.setBounds(bounds);
- colourBySequence = false;
+ jmb.setColourBySequence(false);
seqColour.setSelected(false);
viewId = viewid;
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
- initJmol(loadStatus);
-
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
closeViewer();
}
});
- }
-
- public synchronized void addSequence(SequenceI[] seq)
- {
- Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
-
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
}
+ IProgressIndicator progressBar = null;
+
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap)
{
+ progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
String alreadyMapped = StructureSelectionManager
if (alreadyMapped != null)
{
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " is already displayed."
- + "\nDo you want to map sequences to the visible structure?",
- "Map Sequences to Visible Window: "
- + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ pdbentry.getId() + " is already displayed."
+ + "\nDo you want to re-use this viewer ?",
+ "Map Sequences to Visible Window: " + pdbentry.getId(),
+ JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
if (frames[i] instanceof AppJmol)
{
AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.pdbentry.getFile().equals(alreadyMapped))
+ // JBPNOTE: this looks like a binding routine, rather than a gui
+ // routine
+ for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
{
- topJmol.addSequence(seq);
- break;
+ if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+ {
+ topJmol.jmb.addSequence(pe, seq);
+ break;
+ }
}
}
}
}
}
// /////////////////////////////////
+ // Check if there are other Jmol views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ Vector existingViews = getJmolsFor(ap);
+ if (existingViews.size() > 0)
+ {
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements())
+ {
+ AppJmol topJmol = (AppJmol) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "Do you want to add " + pdbentry.getId()
+ + " to the view called\n'" + topJmol.getTitle()
+ + "'\n", "Align to existing structure view",
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
+ }
+ // /////////////////////////////////
+ jmb = new AppJmolBinding(this, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, null, null);
this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
- this.setSize(400, 400);
- // jalview.gui.Desktop.addInternalFrame(this, "Jmol
- // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
- // : ""), 400, 400);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
if (pdbentry.getFile() != null)
{
}
else
{
- Thread worker = new Thread(this);
+ addingStructures = false;
+ worker = new Thread(this);
worker.start();
}
closeViewer();
}
});
+
}
- void initJmol(String command)
+ /**
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param alignFrame
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
+ final String[] chains, final boolean b, final IProgressIndicator alignFrame)
{
- renderPanel = new RenderPanel();
+ if (pdbentry.getFile() == null)
+ {
+ if (worker != null && worker.isAlive())
+ {
+ // a retrieval is in progress, wait around and add ourselves to the
+ // queue.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ while (worker != null && worker.isAlive() && _started)
+ {
+ try
+ {
+ Thread.sleep(100 + ((int) Math.random() * 100));
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ } catch (Exception e)
+ {
+ }
+
+ }
+ // and call ourselves again.
+ addStructure(pdbentry, seq, chains, b, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ jmb.addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = b;
+ progressBar = alignFrame; // visual indication happens on caller frame.
+ (worker = new Thread(this)).start();
+ return;
+ }
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
+ private Vector getJmolsFor(AlignmentPanel ap2)
+ {
+ Vector otherJmols = new Vector();
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
- if (pdbentry.getProperty() != null)
+ for (int i = 0; i < frames.length; i++)
{
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
+ if (frames[i] instanceof AppJmol)
{
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
+ AppJmol topJmol = ((AppJmol) frames[i]);
+ if (topJmol.ap == ap2)
+ {
+ otherJmols.addElement(topJmol);
+ }
}
}
+ return otherJmols;
+ }
- this.setTitle(title.toString());
- jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+ void initJmol(String command)
+ {
+ jmb.setFinishedInit(false);
+ renderPanel = new RenderPanel();
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
getBounds().width, getBounds().height);
- // * OK, but safer to assign htmlName, URL bases, comandOptions, and
- // statusListener now.
-
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter(), "", null, null, "", this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
-
- viewer.evalStringQuiet(command);
+ if (scriptWindow == null)
+ {
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ };
+
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null);
+ jmb.newJmolPopup(true, "Jmol", true);
+ jmb.evalStateCommand(command);
+ jmb.setFinishedInit(true);
}
void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
-
+ if (chains == null)
+ {
+ return;
+ }
JMenuItem menuItem = new JMenuItem("All");
menuItem.addActionListener(new ActionListener()
{
boolean allChainsSelected = false;
+ private boolean alignAddedStructures = false;
+
void centerViewer()
{
- StringBuffer cmd = new StringBuffer();
+ Vector toshow = new Vector();
+ String lbl;
+ int mlength, p, mnum;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
- cmd.append(":" + item.getText() + " or ");
+ {
+ toshow.addElement(item.getText());
+ }
}
}
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
-
- viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
+ jmb.centerViewer(toshow);
}
void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
-
- // We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getFile());
+ jmb.closeViewer();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ jmb = null;
}
+ /**
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
+
public void run()
{
+ _started = true;
+ String pdbid = "";
+ // todo - record which pdbids were successfuly imported.
+ StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- AlignmentI pdbseq;
- if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
- {
- // just transfer the file name from the first seuqence's first PDBEntry
- pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile());
- initJmol("load " + pdbentry.getFile());
- }
- else
+ for (int pi = 0; pi < jmb.pdbentry.length; pi++)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " could not be retrieved. Please try downloading the file manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
+ String file = jmb.pdbentry[pi].getFile();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.pdbentry[pi].getId();
+ long hdl=pdbid.hashCode()-System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Fetching PDB " + pdbid,
+ hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+ .getId());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'" + pdbid + "'");
+ }
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar("Finished.", hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
+ .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+ files.append(" \"" + file + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
+ }
+ else
+ {
+ if (curfiles != null && curfiles.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < curfiles.length; c++)
+ {
+ if (curfiles[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.append(" \"" + file + "\"");
+ }
+ }
}
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
- oomerror);
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
+ }
+ if (errormsgs.length() > 0)
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "The following pdb entries could not be retrieved from the PDB:\n"
+ + errormsgs.toString()
+ + "\nPlease try downloading them manually.",
+ "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
}
+ if (files.length() > 0)
+ {
+ if (!addingStructures)
+ {
+
+ try
+ {
+ initJmol("load FILES " + files.toString());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuffer cmd = new StringBuffer();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(files.toString());
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ cmd = null;
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ long lastnotify=jmb.getLoadNotifiesHandled();
+ // need to wait around until script has finished
+ while (lastnotify>=jmb.getLoadNotifiesHandled());
+ {
+ try
+ {
+ Thread.sleep(35);
+ } catch (Exception e)
+ {
+ }
+ }
+ // refresh the sequence colours for the new structure(s)
+ jmb.updateColours(ap);
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ }
+ });
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+ }
+ }
+ _started = false;
+ worker = null;
}
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
{
try
{
- BufferedReader in = new BufferedReader(new FileReader(pdbentry
- .getFile()));
+ // TODO: cope with multiple PDB files in view
+ BufferedReader in = new BufferedReader(new FileReader(
+ jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try
+ {
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ {
+ cap.appendText(StructureSelectionManager
+ .getStructureSelectionManager().printMapping(
+ jmb.pdbentry[pdbe].getFile()));
+ cap.appendText("\n");
+ }
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
550, 600);
- cap.setText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(pdbentry.getFile()));
}
/**
else
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
}
if (im.getGraphics() != null)
{
Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+ jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
im.writeImage();
}
}
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
+ jmb.setColourBySequence(seqColour.isSelected());
+ // Set the colour using the current view for the associated alignframe
+ jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures,
+ ap.alignFrame.viewport.alignment);
}
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color chain");
+ chainColour.setSelected(true);
+ jmb.colourByChain();
}
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
}
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new ZappoColourScheme());
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
}
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new TaylorColourScheme());
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
}
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new HydrophobicColourScheme());
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new HelixColourScheme());
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
}
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new StrandColourScheme());
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
}
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new TurnColourScheme());
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
}
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new BuriedColourScheme());
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
-
- if (cs == null)
- return;
-
- String res;
- int index;
- Color col;
-
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select " + res + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- viewer.evalStringQuiet(command.toString());
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
}
public void userColour_actionPerformed(ActionEvent actionEvent)
{
+ userColour.setSelected(true);
new UserDefinedColours(this, null);
}
{
java.awt.Color col = JColorChooser.showDialog(this,
"Select Background Colour", null);
-
if (col != null)
{
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
+ jmb.setBackgroundColour(col);
}
}
{
}
}
-
- // ////////////////////////////////
- // /StructureListener
- public String getPdbFile()
- {
- return pdbentry.getFile();
- }
-
- Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
- matcher.group(1);
- int pdbResNum = Integer.parseInt(matcher.group(2));
- String chainId = matcher.group(3);
-
- if (chainId != null)
- chainId = chainId.substring(1, chainId.length());
- else
- {
- chainId = " ";
- }
-
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
- }
- lastMessage = strInfo;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- // TODO: rna: remove CA dependency in select string
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
-
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
-
- eval.append(":");
- resetLastRes.append(":");
- if (!chain.equals(" "))
- {
- eval.append(chain);
- resetLastRes.append(chain);
- }
-
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); // ".*;");
-
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- // + ".*;spacefill 0;");
- + " and not hetero;spacefill 0;");
-
- eval.append("spacefill 200;select none");
- // System.out.println("jmol:\n"+eval+"\n");
- viewer.evalStringQuiet(eval.toString());
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
-
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- public void updateColours(Object source)
- {
- colourBySequence((AlignmentPanel) source);
- }
-
- // End StructureListener
- // //////////////////////////
-
- String lastCommand;
-
- FeatureRenderer fr = null;
-
- public void colourBySequence(AlignmentPanel sourceap)
- {
- this.ap = sourceap;
-
- if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
- {
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
-
- int lastPos = -1;
- for (int sp, s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
- {
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // No mapping to gaps in sequence.
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(asp, r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, asp, r);
-
- if (command.toString().endsWith(
- ":" + mapping[m].getChain() + ";color[" + col.getRed()
- + "," + col.getGreen() + "," + col.getBlue()
- + "]"))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color[" + col.getRed() + "," + col.getGreen()
- + "," + col.getBlue() + "]");
-
- }
- break;
- }
- }
- }
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- lastCommand = command.toString();
- }
-
- StringBuffer condenseCommand(StringBuffer command, int pos)
- {
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
-
- command.delete(0, sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
- // ///////////////////////////////
- // JmolStatusListener
-
- public String eval(String strEval)
- {
- // System.out.println(strEval);
- // "# 'eval' is implemented only for the applet.";
- return null;
- }
-
- public void createImage(String file, String type, int quality)
- {
- System.out.println("JMOL CREATE IMAGE");
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, String errorMsg, int modelParts)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
-
- fileLoadingError = null;
-
- if (fileName != null)
- {
- // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains
- // FILE LOADED OK
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
- .getFile(), AppletFormatAdapter.FILE);
- ssm.addStructureViewerListener(this);
- Vector chains = new Vector();
- for (int i = 0; i < pdbFile.chains.size(); i++)
- {
- chains
- .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
-
- jmolpopup.updateComputedMenus();
-
- if (!loadingFromArchive)
- {
- viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
- }
- if (fr != null)
- fr.featuresAdded();
-
- loadingFromArchive = false;
- }
- else
- return;
- }
-
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
- }
-
- public void sendConsoleMessage(String strStatus)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
- }
-
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure, null);
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
- {
- if (strData!=null)
- {
- Cache.log.info("Non null pick data string: "+strData+" (other info: '"+strInfo+"' pos "+atomIndex+")");
- }
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
-
- matcher.group(1);
- String resnum = new String(matcher.group(2));
- String chainId = matcher.group(3);
-
- String picked = resnum;
-
- if (chainId != null)
- picked += (":" + chainId.substring(1, chainId.length()));
-
- picked = "(("+picked+".CA" + ")|("+picked+".P"+"))";
-
- if (!atomsPicked.contains(picked))
- {
- if (chainId != null)
- viewer.evalString("select " + picked + ";label %n %r:%c");
- else
- viewer.evalString("select " + picked + ";label %n %r");
- atomsPicked.addElement(picked);
- }
- else
- {
- viewer.evalString("select " + picked + ";label off");
- atomsPicked.removeElement(picked);
- }
-
- if (scriptWindow != null)
- {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo, String data)
- {
- if (data!=null)
- {
- Cache.log.info("Non null hover data string: "+data+" (other info: '"+strInfo+"' pos "+atomIndex+")");
- }
- mouseOverStructure(atomIndex, strInfo);
- }
-
- @Override
- public void showUrl(String url)
- {
- try {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (IOException e)
- {
- Cache.log.error("Failed to launch Jmol-associated url "+url,e);
- // TODO: 2.6 : warn user if browser was not configured.
- }
- }
-
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
if (showConsole)
{
splitPane.setTopComponent(renderPanel);
splitPane.setBottomComponent(scriptWindow);
this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
}
- splitPane.setDividerLocation(getHeight() - 200);
- splitPane.validate();
}
else
{
if (splitPane != null)
- splitPane.setVisible(false);
+ {
+ splitPane.setVisible(false);
+ }
splitPane = null;
validate();
}
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
-
- // /End JmolStatusListener
- // /////////////////////////////
-
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
getSize(currentSize);
g.getClipBounds(rectClip);
- if (viewer == null)
+ if (jmb.fileLoadingError != null)
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ g.drawString("Error loading file...", 20, currentSize.height / 2);
+ StringBuffer sb = new StringBuffer();
+ int lines = 0;
+ for (int e = 0; e < jmb.pdbentry.length; e++)
+ {
+ sb.append(jmb.pdbentry[e].getId());
+ if (e < jmb.pdbentry.length - 1)
+ {
+ sb.append(",");
+ }
+
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
+ }
+ }
}
- else if (fileLoadingError != null)
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file..." + pdbentry.getId(), 20,
- currentSize.height / 2);
+ g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
}
else
{
- viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize, rectClip);
}
}
}
return viewId;
}
- @Override
- public String createImage(String fileName, String type,
- Object textOrBytes, int quality)
+ public void updateTitleAndMenus()
{
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Hashtable getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void notifyCallback(int type, Object[] data)
- {
- try {
- switch (type)
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
{
- case JmolConstants.CALLBACK_LOADSTRUCT:
- notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5]).intValue());
-
- break;
- case JmolConstants.CALLBACK_PICK:
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
- // also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
- break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue());
- break;
- case JmolConstants.CALLBACK_ECHO:
- sendConsoleEcho((String)data[1]);
- break;
- case JmolConstants.CALLBACK_MESSAGE:
- sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]);
- break;
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_CLICK:
- default:
- System.err.println("Unhandled callback "+type+" "+data);
- break;
- }
+ repaint();
+ return;
}
- catch (Exception e)
+ setChainMenuItems(jmb.chainNames);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
- Cache.log.warn("Squashed Jmol callback handler error: ",e);
+ jmolActionMenu.setVisible(true);
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
@Override
- public boolean notifyEnabled(int callbackPick)
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
- switch (callbackPick)
+
+ try
{
- case JmolConstants.CALLBACK_ECHO:
- case JmolConstants.CALLBACK_LOADSTRUCT:
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_MESSAGE:
- case JmolConstants.CALLBACK_PICK:
- case JmolConstants.CALLBACK_SCRIPT:
- case JmolConstants.CALLBACK_HOVER:
- case JmolConstants.CALLBACK_ERROR:
- return true;
- case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
- case JmolConstants.CALLBACK_MINIMIZATION:
- case JmolConstants.CALLBACK_RESIZE:
- case JmolConstants.CALLBACK_SYNC:
+ jmb.superposeStructures(ap.av.getAlignment(), -1,
+ ap.av.getColumnSelection());
+ } catch (Exception e)
+ {
+ Cache.log.info("Couldn't align structures in alignframe "
+ + ap.alignFrame.getTitle(), e);
+
}
- return false;
}
- @Override
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
+ public void setJalviewColourScheme(ColourSchemeI ucs)
{
- Cache.log.debug("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction);
-
+ jmb.setJalviewColourScheme(ucs);
+
}
}
git://source.jalview.org / jalview.git / blobdiff