import java.awt.*;
import java.awt.event.*;
+import javax.swing.JPanel;
+
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.SequenceStructureBinding;
import org.jmol.popup.*;
import org.jmol.viewer.JmolConstants;
+import org.jmol.viewer.Viewer;
import jalview.schemes.*;
public abstract class JalviewJmolBinding implements StructureListener,
- JmolStatusListener, SequenceStructureBinding, JmolSelectionListener
+ JmolStatusListener, SequenceStructureBinding,
+ JmolSelectionListener, ComponentListener
{
/**
public Vector chainNames;
+ Hashtable chainFile;
+
/**
* array of target chains for seuqences - tied to pdbentry and sequence[]
*/
public String getViewerTitle()
{
if (sequence == null || pdbentry == null || sequence.length < 1
- || pdbentry.length < 1)
+ || pdbentry.length < 1 || sequence[0].length < 1)
{
return ("Jalview Jmol Window");
}
+ // TODO: give a more informative title when multiple structures are
+ // displayed.
StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
+ pdbentry[0].getId());
p = mlength;
mlength = lbl.indexOf(":", p);
} while (p < mlength && mlength < (lbl.length() - 2));
+ // TODO: lookup each pdb id and recover proper model number for it.
cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + getModelNum(lbl.substring(0, mlength)) + " or ");
+ + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
cmd.setLength(cmd.length() - 4);
viewer.setJmolStatusListener(null);
lastCommand = null;
viewer = null;
+ releaseUIResources();
}
+ /**
+ * called by JalviewJmolbinding after closeViewer is called - release any
+ * resources and references so they can be garbage collected.
+ */
+ protected abstract void releaseUIResources();
+
public void colourByChain()
{
colourBySequence = false;
- // TODO: colour by chain should colour each chain distinctly across all visible models
+ // TODO: colour by chain should colour each chain distinctly across all
+ // visible models
// TODO: http://issues.jalview.org/browse/JAL-628
evalStateCommand("select *;color chain");
}
/**
* superpose the structures associated with sequences in the alignment
* according to their corresponding positions. ded)
+ *
* @param refStructure
* - select which pdb file to use as reference (default is -1 - the
* first structure in the alignment)
- * @param hiddenCols TODO
+ * @param hiddenCols
+ * TODO
*/
- public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
+ public void superposeStructures(AlignmentI alignment, int refStructure,
+ ColumnSelection hiddenCols)
{
String[] files = getPdbFile();
- if (refStructure>=files.length)
+ if (refStructure >= files.length)
{
- System.err.println("Invalid reference structure value "+refStructure);
- refStructure= -1;
+ System.err.println("Invalid reference structure value "
+ + refStructure);
+ refStructure = -1;
}
- if (refStructure<-1)
+ if (refStructure < -1)
{
- refStructure=-1;
+ refStructure = -1;
}
StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
-
+
boolean matched[] = new boolean[alignment.getWidth()];
for (int m = 0; m < matched.length; m++)
{
-
- matched[m] = (hiddenCols!=null) ? hiddenCols.isVisible(m) : true;
+
+ matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
}
-
+
int commonrpositions[][] = new int[files.length][alignment.getWidth()];
String isel[] = new String[files.length];
// reference structure - all others are superposed in it
}
}
String[] selcom = new String[files.length];
+ int nmatched = 0;
// generate select statements to select regions to superimpose structures
{
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (matched[r])
{
-
+ if (pdbfnum == 0)
+ {
+ nmatched++;
+ }
if (lpos != commonrpositions[pdbfnum][r] - 1)
{
// discontinuity
molsel.append(chainCd);
molsel.append("}");
}
- selcom[pdbfnum] = molsel.toString();
+ selcom[pdbfnum] = molsel.toString();
selectioncom.append("((");
- selectioncom.append(selcom[pdbfnum].substring(1, selcom[pdbfnum].length()-1));
+ selectioncom.append(selcom[pdbfnum].substring(1,
+ selcom[pdbfnum].length() - 1));
selectioncom.append(" )& ");
- selectioncom.append(pdbfnum+1);
+ selectioncom.append(pdbfnum + 1);
selectioncom.append(".1)");
- if (pdbfnum<files.length-1)
+ if (pdbfnum < files.length - 1)
{
selectioncom.append("|");
}
}
}
-
+ // TODO: consider bailing if nmatched less than 4 because superposition not
+ // well defined.
+ // TODO: refactor superposable position search (above) from jmol selection
+ // construction (below)
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure)
command.append(" ROTATE TRANSLATE;\n");
}
System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("+selectioncom.toString()+"); cartoons; ");
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
System.out.println("Superimpose command(s):\n" + command.toString());
evalStateCommand(command.toString());
-
+
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
- if (showFeatures)
+ if (showFeatures && fr != null)
col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
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 -
+ * use getPdbFile to get number of unique models.
+ */
+ private int _modelFileNameMap[];
+
// ////////////////////////////////
// /StructureListener
public synchronized String[] getPdbFile()
{
+ if (viewer == null)
+ {
+ return new String[0];
+ }
if (modelFileNames == null)
{
+
String mset[] = new String[viewer.getModelCount()];
- int j=1;
+ _modelFileNameMap = new int[mset.length];
+ int j = 1;
mset[0] = viewer.getModelFileName(0);
for (int i = 1; i < mset.length; i++)
{
- // skip any additional models in the same file (NMR structures)
- if (!(mset[j] = viewer.getModelFileName(i)).equals(mset[j-1]))
+ mset[j] = viewer.getModelFileName(i);
+ _modelFileNameMap[j] = i; // record the model index for the filename
+ // skip any additional models in the same file (NMR structures)
+ if ((mset[j] == null ? mset[j] != mset[j - 1]
+ : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
{
j++;
}
public void loadInline(String string)
{
loadedInline = true;
+ // TODO: re JAL-623
+ // viewer.loadInline(strModel, isAppend);
+ // could do this:
+ // construct fake fullPathName and fileName so we can identify the file
+ // later.
+ // Then, construct pass a reader for the string to Jmol.
+ // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+ // fileName, null, reader, false, null, null, 0);
viewer.openStringInline(string);
}
case JmolConstants.CALLBACK_MEASURE:
case JmolConstants.CALLBACK_CLICK:
-
default:
System.err.println("Unhandled callback " + type + " "
+ data[1].toString());
return false;
}
+ // incremented every time a load notification is successfully handled -
+ // lightweight mechanism for other threads to detect when they can start
+ // referrring to new structures.
+ private long loadNotifiesHandled = 0;
+
+ public long getLoadNotifiesHandled()
+ {
+ return loadNotifiesHandled;
+ }
+
public void notifyFileLoaded(String fullPathName, String fileName2,
String modelName, String errorMsg, int modelParts)
{
refreshGUI();
return;
}
+ // TODO: deal sensibly with models loaded inLine:
+ // modelName will be null, as will fullPathName.
+
// the rest of this routine ignores the arguments, and simply interrogates
// the Jmol view to find out what structures it contains, and adds them to
// the structure selection manager.
String[] oldmodels = modelFileNames;
modelFileNames = null;
chainNames = new Vector();
+ chainFile = new Hashtable();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
ssm = StructureSelectionManager.getStructureSelectionManager();
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
- if (fileName != null)
+ boolean foundEntry = false;
+ MCview.PDBfile pdb = null;
+ String pdbfile = null, pdbfhash = null;
+ // model was probably loaded inline - so check the pdb file hashcode
+ if (loadedInline)
{
- boolean foundEntry = false;
- // search pdbentries and sequences to find correct pdbentry and
- // sequence[] pair for this filename
- if (pdbentry != null)
+ // calculate essential attributes for the pdb data imported inline.
+ // prolly need to resolve modelnumber properly - for now just use our
+ // 'best guess'
+ pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ + ".0", "PDB");
+ pdbfhash = "" + pdbfile.hashCode();
+ }
+ if (pdbentry != null)
+ {
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < pdbentry.length; pe++)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ boolean matches = false;
+ if (fileName == null)
{
- if (pdbentry[pe].getFile().equals(fileName))
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
{
+ pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
+ AppletFormatAdapter.PASTE);
+ pdbentry[modelnum].setFile("INLINE" + pdb.id);
+ matches = true;
foundEntry = true;
- MCview.PDBfile pdb;
- if (loadedInline)
- {
- // TODO: replace with getData ?
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
- pdbentry[pe].setFile("INLINE" + pdb.id);
- }
- else
+ }
+ }
+ else
+ {
+ if (matches = pdbentry[pe].getFile().equals(fileName))
+ {
+ foundEntry = true;
+ // TODO: Jmol can in principle retrieve from CLASSLOADER but
+ // this
+ // needs
+ // to be tested. See mantis bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ String protocol = AppletFormatAdapter.URL;
+ try
{
- // TODO: Jmol can in principle retrieve from CLASSLOADER but
- // this
- // needs
- // to be tested. See mantis bug
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- String protocol = AppletFormatAdapter.URL;
- try
- {
- File fl = new java.io.File(pdbentry[pe].getFile());
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
+ File fl = new java.io.File(pdbentry[pe].getFile());
+ if (fl.exists())
{
+ protocol = AppletFormatAdapter.FILE;
}
- ;
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), protocol);
-
- }
-
- pdbentry[pe].setId(pdb.id);
-
- for (int i = 0; i < pdb.chains.size(); i++)
+ } catch (Exception e)
+ {
+ } catch (Error e)
{
- chainNames.addElement(new String(pdb.id + ":"
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
}
- notifyLoaded = true;
+ ;
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
+ pdbentry[pe].getFile(), protocol);
+
+ }
+ }
+ if (matches)
+ {
+ pdbentry[pe].setId(pdb.id);
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.chains.size(); i++)
+ {
+ String chid = new String(pdb.id + ":"
+ + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+ chainFile.put(chid, pdbentry[pe].getFile());
+ chainNames.addElement(chid);
}
+ notifyLoaded = true;
}
}
- if (!foundEntry && associateNewStructs)
- {
- // this is a foreign pdb file that jalview doesn't know about - add
- // it to the dataset and try to find a home - either on a matching
- // sequence or as a new sequence.
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
- "PDB");
- // parse pdb file into a chain, etc.
- // locate best match for pdb in associated views and add mapping to
- // ssm
- // if properly registered then
- notifyLoaded = true;
+ }
+ if (!foundEntry && associateNewStructs)
+ {
+ // this is a foreign pdb file that jalview doesn't know about - add
+ // it to the dataset and try to find a home - either on a matching
+ // sequence or as a new sequence.
+ String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+ "PDB");
+ // parse pdb file into a chain, etc.
+ // locate best match for pdb in associated views and add mapping to
+ // ssm
+ // if properly registered then
+ notifyLoaded = true;
- }
}
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
if (jmolpopup != null)
{
- jmolpopup.updateComputedMenus();
+ // potential for deadlock here:
+ // jmolpopup.updateComputedMenus();
}
if (!isLoadingFromArchive())
{
fr.featuresAdded();
}
refreshGUI();
+ loadNotifiesHandled++;
}
}
public abstract void refreshGUI();
/**
+ * called to show or hide the associated console window container.
+ *
+ * @param show
+ */
+ public abstract void showConsole(boolean show);
+
+ /**
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* @param codeBase
* @param commandOptions
*/
- public void allocateViewer(Component renderPanel, boolean jmolfileio,
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions)
{
+ allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+ codeBase, commandOptions, null, null);
+ }
+
+ /**
+ *
+ * @param renderPanel
+ * @param jmolfileio
+ * - when true will initialise jmol's file IO system (should be false
+ * in applet context)
+ * @param htmlName
+ * @param documentBase
+ * @param codeBase
+ * @param commandOptions
+ * @param consolePanel
+ * - panel to contain Jmol console
+ * @param buttonsToShow
+ * - buttons to show on the console, in ordr
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions, final Container consolePanel,
+ String buttonsToShow)
+ {
viewer = JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
+
+ console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+ if (consolePanel != null)
+ {
+ consolePanel.addComponentListener(this);
+
+ }
+
+ }
+
+ protected abstract JmolAppConsoleInterface createJmolConsole(
+ JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+
+ protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+ @Override
+ public void componentResized(ComponentEvent e)
+ {
+
+ }
+
+ @Override
+ public void componentMoved(ComponentEvent e)
+ {
+
+ }
+
+ @Override
+ public void componentShown(ComponentEvent e)
+ {
+ showConsole(true);
+ }
+
+ @Override
+ public void componentHidden(ComponentEvent e)
+ {
+ showConsole(false);
}
public void setLoadingFromArchive(boolean loadingFromArchive)
*
* @returns the pdb entries added to the current set.
*/
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
- String[][] chns)
+ public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
{
int pe = -1;
Vector v = new Vector();
git://source.jalview.org / jalview.git / blobdiff