*/
package jalview.ext.jmol;
-import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureCommandsI.SuperposeData;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
-import java.awt.Color;
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import java.net.URL;
import java.util.ArrayList;
import java.util.BitSet;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
-import org.jmol.script.T;
import org.jmol.viewer.Viewer;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
{
private String lastMessage;
- boolean allChainsSelected = false;
-
/*
* when true, try to search the associated datamodel for sequences that are
* associated with any unknown structures in the Jmol view.
*/
private boolean associateNewStructs = false;
- Vector<String> atomsPicked = new Vector<>();
-
- private List<String> chainNames;
-
- Hashtable<String, String> chainFile;
+ private Vector<String> atomsPicked = new Vector<>();
- /*
- * the default or current model displayed if the model cannot be identified
- * from the selection message
- */
- int frameNo = 0;
+ private String lastCommand;
- // protected JmolGenericPopup jmolpopup; // not used - remove?
+ private boolean loadedInline;
- String lastCommand;
+ private StringBuffer resetLastRes = new StringBuffer();
- boolean loadedInline;
-
- StringBuffer resetLastRes = new StringBuffer();
-
- public Viewer viewer;
+ public Viewer jmolViewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
+ setStructureCommands(new JmolCommands());
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
{
super(ssm, seqs);
- viewer = theViewer;
- viewer.setJmolStatusListener(this);
- viewer.addSelectionListener(this);
+ jmolViewer = theViewer;
+ jmolViewer.setJmolStatusListener(this);
+ jmolViewer.addSelectionListener(this);
+ setStructureCommands(new JmolCommands());
}
/**
return getViewerTitle("Jmol", true);
}
- /**
- * prepare the view for a given set of models/chains. chainList contains
- * strings of the form 'pdbfilename:Chaincode'
- *
- * @param chainList
- * list of chains to make visible
- */
- public void centerViewer(Vector<String> chainList)
- {
- StringBuilder cmd = new StringBuilder(128);
- int mlength, p;
- for (String lbl : chainList)
- {
- mlength = 0;
- do
- {
- 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) + " /"
- + (1 + getModelNum(chainFile.get(lbl))) + " or ");
- }
- if (cmd.length() > 0)
- {
- cmd.setLength(cmd.length() - 4);
- }
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
- }
-
public void closeViewer()
{
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
- viewer.dispose();
+ jmolViewer.dispose();
lastCommand = null;
- viewer = null;
+ jmolViewer = null;
releaseUIResources();
}
- @Override
- public void colourByChain()
- {
- colourBySequence = false;
- // 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");
- }
-
- @Override
- public void colourByCharge()
- {
- colourBySequence = false;
- evalStateCommand("select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
- }
-
/**
* superpose the structures associated with sequences in the alignment
* according to their corresponding positions.
+ *
+ * @deprecated not used - remove?
*/
+ @Deprecated
public void superposeStructures(AlignmentI alignment)
{
superposeStructures(alignment, -1, null);
* @param refStructure
* - select which pdb file to use as reference (default is -1 - the
* first structure in the alignment)
+ * @deprecated not used - remove?
*/
+ @Deprecated
public void superposeStructures(AlignmentI alignment, int refStructure)
{
superposeStructures(alignment, refStructure, null);
* first structure in the alignment)
* @param hiddenCols
* TODO
+ * @deprecated not used - remove?
*/
+ @Deprecated
public void superposeStructures(AlignmentI alignment, int refStructure,
HiddenColumns hiddenCols)
{
/**
* {@inheritDoc}
*/
- @Override
public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
- while (viewer.isScriptExecuting())
+ while (jmolViewer.isScriptExecuting())
{
try
{
SuperposeData[] structures = new SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
- structures[f] = new SuperposeData(alignment.getWidth());
+ structures[f] = new SuperposeData(alignment.getWidth(), f);
}
/*
}
if (selectioncom.length() > 0)
{
- // TODO is performing selectioncom redundant here? is done later on
- // System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("
- + selectioncom.toString() + "); cartoons; ");
- // selcom.append("; ribbons; ");
String cmdString = command.toString();
- // System.out.println("Superimpose command(s):\n" + cmdString);
-
- evalStateCommand(cmdString);
+ executeCommand(cmdString, false);
}
}
if (selectioncom.length() > 0)
- {// finally, mark all regions that were superposed.
- if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
+ {
+ /*
+ * finally, highlight with cartoons the residues that were superposed
+ */
+ if (selectioncom.charAt(selectioncom.length() - 1) == '|')
{
selectioncom.setLength(selectioncom.length() - 1);
}
- // System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("
- + selectioncom.toString() + "); cartoons; ");
- // evalStateCommand("select *; backbone; select "+selcom.toString()+";
- // cartoons; center "+selcom.toString());
+ executeCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ", false);
}
return null;
}
- public void evalStateCommand(String command)
+ @Override
+ public List<String> executeCommand(String command, boolean getReply)
{
+ if (command == null)
+ {
+ return null;
+ }
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
- viewer.evalStringQuiet(command + "\n");
+ jmolViewer.evalStringQuiet(command + "\n");
}
jmolHistory(true);
lastCommand = command;
- }
-
- Thread colourby = null;
- /**
- * Sends a set of colour commands to the structure viewer
- *
- * @param colourBySequenceCommands
- */
- @Override
- protected void colourBySequence(
- final StructureMappingcommandSet[] colourBySequenceCommands)
- {
- if (colourby != null)
- {
- colourby.interrupt();
- colourby = null;
- }
- colourby = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
- {
- for (String cbyseq : cpdbbyseq.commands)
- {
- executeWhenReady(cbyseq);
- }
- }
- }
- });
- colourby.start();
- }
-
- /**
- * @param files
- * @param sr
- * @param viewPanel
- * @return
- */
- @Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
- {
- return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel);
- }
-
- /**
- * @param command
- */
- protected void executeWhenReady(String command)
- {
- evalStateCommand(command);
+ return null;
}
public void createImage(String file, String type, int quality)
return null;
}
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (getModelNum(pdbfile) < 0)
- {
- return null;
- }
- // TODO: verify atomIndex is selecting correct model.
- // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
- int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
- return new Color(colour);
- }
-
- /**
- * instruct the Jalview binding to update the pdbentries vector if necessary
- * prior to matching the jmol view's contents to the list of structure files
- * Jalview knows about.
- */
- public abstract void refreshPdbEntries();
-
- private int getModelNum(String modelFileName)
- {
- String[] mfn = getStructureFiles();
- if (mfn == null)
- {
- return -1;
- }
- for (int i = 0; i < mfn.length; i++)
- {
- if (mfn[i].equalsIgnoreCase(modelFileName))
- {
- return i;
- }
- }
- 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 -
public synchronized String[] getStructureFiles()
{
List<String> mset = new ArrayList<>();
- if (viewer == null)
+ if (jmolViewer == null)
{
return new String[0];
}
if (modelFileNames == null)
{
- int modelCount = viewer.ms.mc;
+ int modelCount = jmolViewer.ms.mc;
String filePath = null;
for (int i = 0; i < modelCount; ++i)
{
- filePath = viewer.ms.getModelFileName(i);
+ filePath = jmolViewer.ms.getModelFileName(i);
if (!mset.contains(filePath))
{
mset.add(filePath);
{
if (resetLastRes.length() > 0)
{
- viewer.evalStringQuiet(resetLastRes.toString());
+ jmolViewer.evalStringQuiet(resetLastRes.toString());
resetLastRes.setLength(0);
}
for (AtomSpec atom : atoms)
jmolHistory(false);
StringBuilder cmd = new StringBuilder(64);
- cmd.append("select " + pdbResNum); // +modelNum
+ cmd.append("select ").append(String.valueOf(pdbResNum)); // +modelNum
- resetLastRes.append("select " + pdbResNum); // +modelNum
+ resetLastRes.append("select ").append(String.valueOf(pdbResNum)); // +modelNum
cmd.append(":");
resetLastRes.append(":");
resetLastRes.append(chain);
}
{
- cmd.append(" /" + (mdlNum + 1));
- resetLastRes.append("/" + (mdlNum + 1));
+ cmd.append(" /").append(String.valueOf(mdlNum + 1));
+ resetLastRes.append("/").append(String.valueOf(mdlNum + 1));
}
cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
cmd.append("spacefill 200;select none");
- viewer.evalStringQuiet(cmd.toString());
+ jmolViewer.evalStringQuiet(cmd.toString());
jmolHistory(true);
}
- boolean debug = true;
+ private boolean debug = true;
private void jmolHistory(boolean enable)
{
- viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+ jmolViewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)
// 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);
+ jmolViewer.openStringInline(string);
}
protected void mouseOverStructure(int atomIndex, final String strInfo)
chainId = " ";
}
- String pdbfilename = modelFileNames[frameNo]; // default is first or current
- // model
+ String pdbfilename = modelFileNames[0]; // default is first model
if (mdlSep > -1)
{
if (chainSeparator1 == -1)
if (pdbfilename == null)
{
- pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
+ pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
}
pdbfilename);
if (label != null)
{
+ // change comma to pipe separator (newline token for Jmol)
+ label = label.replace(',', '|');
StringTokenizer toks = new StringTokenizer(strInfo, " ");
StringBuilder sb = new StringBuilder();
sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
.append(toks.nextToken());
sb.append("|").append(label).append("\"");
- evalStateCommand(sb.toString());
+ executeCommand(sb.toString(), false);
}
}
if (!atomsPicked.contains(picked))
{
- viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+ jmolViewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
{
- viewer.evalString("select " + picked + ";label off");
+ jmolViewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
jmolHistory(true);
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new ArrayList<>();
- chainFile = new Hashtable<>();
boolean notifyLoaded = false;
String[] modelfilenames = getStructureFiles();
// first check if we've lost any structures
// 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(
+ pdbfile = jmolViewer.getData(
"" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
// add an entry for every chain in the model
for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(
- pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
- chainFile.put(chid, fileName);
- chainNames.add(chid);
+ String chid = pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id;
+ addChainFile(chid, fileName);
+ getChainNames().add(chid);
}
notifyLoaded = true;
}
// 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",
+ String pdbcontent = jmolViewer.getData("/" + (modelnum + 1) + ".1",
"PDB");
// parse pdb file into a chain, etc.
// locate best match for pdb in associated views and add mapping to
// }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet(
+ jmolViewer.evalStringQuiet(
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
setLoadingFromArchive(false);
}
- @Override
- public List<String> getChainNames()
- {
- return chainNames;
- }
-
protected IProgressIndicator getIProgressIndicator()
{
return null;
}
- @Override
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
-
- if (cs == null)
- {
- return;
- }
-
- jmolHistory(false);
- StringBuilder command = new StringBuilder(128);
- command.append("select *;color white;");
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
- for (String resName : residueSet)
- {
- char res = resName.length() == 3
- ? ResidueProperties.getSingleCharacterCode(resName)
- : resName.charAt(0);
- Color col = cs.findColour(res, 0, null, null, 0f);
- command.append("select " + resName + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- evalStateCommand(command.toString());
- jmolHistory(true);
- }
-
public void showHelp()
{
showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
public abstract void showUrl(String url, String target);
/**
- * called when the binding thinks the UI needs to be refreshed after a Jmol
- * state change. this could be because structures were loaded, or because an
- * error has occured.
- */
- public abstract void refreshGUI();
-
- /**
* called to show or hide the associated console window container.
*
* @param show
{
commandOptions = "";
}
- viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
+ jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null),
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+ jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)
protected org.jmol.api.JmolAppConsoleInterface console = null;
@Override
- public void setBackgroundColour(java.awt.Color col)
- {
- jmolHistory(false);
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- jmolHistory(true);
- }
-
- @Override
public int[] resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
{
showConsole(false);
}
+
+ @Override
+ protected int getModelNoForFile(String pdbFile)
+ {
+ if (modelFileNames == null)
+ {
+ return -1;
+ }
+ for (int i = 0; i < modelFileNames.length; i++)
+ {
+ if (modelFileNames[i].equalsIgnoreCase(pdbFile))
+ {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ @Override
+ protected ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
}