*/
package jalview.ext.jmol;
+import java.io.File;
+import java.net.URL;
import java.util.*;
+import java.applet.Applet;
import java.awt.*;
import java.awt.event.*;
import jalview.schemes.*;
public abstract class JalviewJmolBinding implements StructureListener,
- JmolStatusListener, SequenceStructureBinding
+ JmolStatusListener, SequenceStructureBinding, JmolSelectionListener
{
+ /**
+ * set if Jmol state is being restored from some source - instructs binding
+ * not to apply default display style when structure set is updated for first
+ * time.
+ */
+ private boolean loadingFromArchive = false;
+
+ /**
+ * state flag used to check if the Jmol viewer's paint method can be called
+ */
+ private boolean finishedInit = false;
+
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean finishedInit)
+ {
+ this.finishedInit = finishedInit;
+ }
boolean allChainsSelected = false;
Vector atomsPicked = new Vector();
- private Vector chainNames;
+ public Vector chainNames;
- String[] chains;
+ /**
+ * array of target chains for seuqences - tied to pdbentry and sequence[]
+ */
+ protected String[][] chains;
boolean colourBySequence = true;
StringBuffer eval = new StringBuffer();
- String fileLoadingError;
+ public String fileLoadingError;
/**
* the default or current model displayed if the model cannot be identified
*/
int frameNo = 0;
- JmolPopup jmolpopup;
+ protected JmolPopup jmolpopup;
String lastCommand;
*/
String[] modelFileNames = null;
- PDBEntry[] pdbentry;
+ public PDBEntry[] pdbentry;
/**
* datasource protocol for access to PDBEntry
StringBuffer resetLastRes = new StringBuffer();
- SequenceI[] sequence;
+ /**
+ * sequences mapped to each pdbentry
+ */
+ public SequenceI[][] sequence;
StructureSelectionManager ssm;
- JmolViewer viewer;
+ public JmolViewer viewer;
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
- String[] chains, String protocol)
+ public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ String[][] chains, String protocol)
{
+ this.sequence = sequenceIs;
+ this.chains = chains;
+ this.pdbentry = pdbentry;
+ this.protocol = protocol;
+ if (chains == null)
+ {
+ this.chains = new String[pdbentry.length][];
+ }
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
*/
}
+ public JalviewJmolBinding(JmolViewer viewer2)
+ {
+ viewer = viewer2;
+ viewer.setJmolStatusListener(this);
+ viewer.addSelectionListener(this);
+ }
+
+ /**
+ * construct a title string for the viewer window based on the data jalview
+ * knows about
+ *
+ * @return
+ */
+ public String getViewerTitle()
+ {
+ if (sequence == null || pdbentry == null || sequence.length < 1
+ || pdbentry.length < 1)
+ {
+ return ("Jalview Jmol Window");
+ }
+ StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
+ + pdbentry[0].getId());
+
+ if (pdbentry[0].getProperty() != null)
+ {
+ if (pdbentry[0].getProperty().get("method") != null)
+ {
+ title.append(" Method: ");
+ title.append(pdbentry[0].getProperty().get("method"));
+ }
+ if (pdbentry[0].getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdbentry[0].getProperty().get("chains"));
+ }
+ }
+ return title.toString();
+ }
+
/**
* 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
*/
- void centerViewer(Vector chainList)
+ public void centerViewer(Vector chainList)
{
StringBuffer cmd = new StringBuffer();
String lbl;
}
if (cmd.length() > 0)
cmd.setLength(cmd.length() - 4);
-
- jmolHistory(false);
- viewer
- .evalString("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
- jmolHistory(true);
+ evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
}
- void closeViewer()
+ public void closeViewer()
{
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
// remove listeners for all structures in viewer
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
-
+ lastCommand = null;
viewer = null;
}
public void colourByChain()
{
- jmolHistory(false);
colourBySequence = false;
- viewer.evalStringQuiet("select *;color chain");
- jmolHistory(true);
- }
+ evalStateCommand("select *;color chain");
+ }
public void colourByCharge()
{
- jmolHistory(false);
colourBySequence = false;
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
+ 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.
+ */
+ public void superposeStructures(AlignmentI alignment)
+ {
+ superposeStructures(alignment, -1, null);
+ }
+
+ /**
+ * 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)
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure)
+ {
+ superposeStructures(alignment, refStructure, null);
+ }
+
+ /**
+ * 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
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
+ {
+ String[] files = getPdbFile();
+ if (refStructure>=files.length)
+ {
+ System.err.println("Invalid reference structure value "+refStructure);
+ refStructure= -1;
+ }
+ if (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;
+ }
+
+ int commonrpositions[][] = new int[files.length][alignment.getWidth()];
+ String isel[] = new String[files.length];
+ // reference structure - all others are superposed in it
+ String[] targetC = new String[files.length];
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ continue;
+
+ int lastPos = -1;
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ if (refStructure == -1)
+ {
+ refStructure = pdbfnum;
+ }
+ SequenceI asp = alignment.getSequenceAt(sp);
+ for (int r = 0; r < matched.length; r++)
+ {
+ if (!matched[r])
+ {
+ continue;
+ }
+ matched[r] = false; // assume this is not a good site
+ if (r >= asp.getLength())
+ {
+ continue;
+ }
+
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ // no mapping to gaps in sequence
+ continue;
+ }
+ int t = asp.findPosition(r); // sequence position
+ int apos = mapping[m].getAtomNum(t);
+ int pos = mapping[m].getPDBResNum(t);
+
+ if (pos < 1 || pos == lastPos)
+ {
+ // can't align unmapped sequence
+ continue;
+ }
+ matched[r] = true; // this is a good ite
+ lastPos = pos;
+ // just record this residue position
+ commonrpositions[pdbfnum][r] = pos;
+ }
+ // create model selection suffix
+ isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+ if (mapping[m].getChain() == null
+ || mapping[m].getChain().trim().length() == 0)
+ {
+ targetC[pdbfnum] = "";
+ }
+ else
+ {
+ targetC[pdbfnum] = ":" + mapping[m].getChain();
+ }
+ // move on to next pdb file
+ s = sequence[pdbfnum].length;
+ break;
+ }
+ }
+ }
+ }
+ StringBuffer selcom[] = new StringBuffer[files.length];
+ // generate select statements to select regions to superimpose structures
+ {
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ String chainCd = targetC[pdbfnum];
+ int lpos = -1;
+ boolean run = false;
+ StringBuffer molsel = (selcom[pdbfnum] = new StringBuffer());
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
+ {
+ if (matched[r])
+ {
+
+ if (lpos != commonrpositions[pdbfnum][r] - 1)
+ {
+ // discontinuity
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ // molsel.append("} {");
+ molsel.append("|");
+ }
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
+ {
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
+ }
+ run = true;
+ }
+ lpos = commonrpositions[pdbfnum][r];
+ // molsel.append(lpos);
+ }
+ }
+ // add final selection phrase
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("}");
+ }
+ selectioncom.append("((");
+ selectioncom.append(molsel.subSequence(1, molsel.length()-1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum+1);
+ selectioncom.append(".1)");
+ if (pdbfnum<files.length-1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ }
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ if (pdbfnum == refStructure)
+ {
+ continue;
+ }
+ command.append("compare ");
+ command.append("{");
+ command.append(1 + pdbfnum);
+ command.append(".1} {");
+ command.append(1 + refStructure);
+ command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+
+ // form the matched pair strings
+ String sep = "";
+ for (int s = 0; s < 2; s++)
+ {
+ command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ }
+ command.append(" ROTATE TRANSLATE;\n");
+ }
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ 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());
+ }
+
+ public void evalStateCommand(String command)
+ {
+ jmolHistory(false);
+ if (lastCommand == null || !lastCommand.equals(command))
+ {
+ viewer.evalStringQuiet(command + "\n");
+ }
jmolHistory(true);
+ lastCommand = command;
}
/**
{
if (!colourBySequence)
return;
+ if (ssm == null)
+ {
+ return;
+ }
String[] files = getPdbFile();
SequenceRenderer sr = getSequenceRenderer();
continue;
int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
{
for (int sp, m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s]
- && (sp = alignment.findIndex(sequence[s])) > -1)
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
{
SequenceI asp = alignment.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
lastPos = pos;
- Color col = sr.getResidueBoxColour(sequence[s], r);
+ Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
}
}
}
+ evalStateCommand(command.toString());
+ }
- jmolHistory(false);
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- jmolHistory(true);
- lastCommand = command.toString();
+ public boolean isColourBySequence()
+ {
+ return colourBySequence;
+ }
+
+ public void setColourBySequence(boolean colourBySequence)
+ {
+ this.colourBySequence = colourBySequence;
}
StringBuffer condenseCommand(String command, int pos)
{
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
+ StringBuffer sb = new StringBuffer(command.substring(0,
+ command.lastIndexOf("select") + 7));
command = command.substring(sb.length());
public void createImage(String file, String type, int quality)
{
+ System.out.println("JMOL CREATE IMAGE");
}
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
- // TODO Auto-generated method stub
+ System.out.println("JMOL CREATE IMAGE");
return null;
}
*
* @return
*/
- abstract FeatureRenderer getFeatureRenderer();
+ public abstract FeatureRenderer getFeatureRenderer();
+
+ /**
+ * 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)
{
return modelFileNames;
}
- public Hashtable getRegistryInfo()
+ /**
+ * map from string to applet
+ */
+ public Map getRegistryInfo()
{
// TODO Auto-generated method stub
return null;
*
* @return
*/
- abstract SequenceRenderer getSequenceRenderer();
+ public abstract SequenceRenderer getSequenceRenderer();
// ///////////////////////////////
// JmolStatusListener
}
+ boolean debug = true;
+
private void jmolHistory(boolean enable)
{
- viewer.setBooleanProperty("history", enable);
+ viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)
String chainId;
if (strInfo.indexOf(":") > -1)
- chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+ strInfo.indexOf("."));
else
{
chainId = " ";
{
if (data != null)
{
- System.err.println("Ignoring additional hover info: " + data);
+ System.err.println("Ignoring additional hover info: " + data
+ + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
atomsPicked.removeElement(picked);
}
jmolHistory(true);
+ // TODO: in application this happens
+ //
+ // if (scriptWindow != null)
+ // {
+ // scriptWindow.sendConsoleMessage(strInfo);
+ // scriptWindow.sendConsoleMessage("\n");
+ // }
}
{
case JmolConstants.CALLBACK_LOADSTRUCT:
notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5])
- .intValue());
+ (String) data[3], (String) data[4],
+ ((Integer) data[5]).intValue());
break;
case JmolConstants.CALLBACK_PICK:
(String) data[0]);
break;
case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String) data[2], ((Integer) data[3])
- .intValue());
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
break;
case JmolConstants.CALLBACK_ECHO:
sendConsoleEcho((String) data[1]);
sendConsoleMessage((data == null) ? ((String) null)
: (String) data[1]);
break;
+ case JmolConstants.CALLBACK_ERROR:
+ // System.err.println("Ignoring error callback.");
+ break;
+ case JmolConstants.CALLBACK_SYNC:
+ case JmolConstants.CALLBACK_RESIZE:
+ refreshGUI();
+ break;
case JmolConstants.CALLBACK_MEASURE:
+
case JmolConstants.CALLBACK_CLICK:
+
default:
- System.err.println("Unhandled callback " + type + " " + data);
+ System.err.println("Unhandled callback " + type + " "
+ + data[1].toString());
break;
}
} catch (Exception e)
case JmolConstants.CALLBACK_HOVER:
case JmolConstants.CALLBACK_ERROR:
return true;
+ case JmolConstants.CALLBACK_RESIZE:
+ case JmolConstants.CALLBACK_SYNC:
case JmolConstants.CALLBACK_CLICK:
case JmolConstants.CALLBACK_ANIMFRAME:
case JmolConstants.CALLBACK_MINIMIZATION:
- case JmolConstants.CALLBACK_RESIZE:
- case JmolConstants.CALLBACK_SYNC:
}
return false;
}
if (errorMsg != null)
{
fileLoadingError = errorMsg;
- updateUI();
+ refreshGUI();
return;
}
+ // 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.
fileLoadingError = null;
+ String[] oldmodels = modelFileNames;
modelFileNames = null;
chainNames = new Vector();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
ssm = StructureSelectionManager.getStructureSelectionManager();
+ // first check if we've lost any structures
+ if (oldmodels != null && oldmodels.length > 0)
+ {
+ int oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
+ {
+ for (int n = 0; n < modelfilenames.length; n++)
+ {
+ if (modelfilenames[n] == oldmodels[i])
+ {
+ oldmodels[i] = null;
+ break;
+ }
+ }
+ if (oldmodels[i] != null)
+ {
+ oldm++;
+ }
+ }
+ if (oldm > 0)
+ {
+ String[] oldmfn = new String[oldm];
+ oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
+ {
+ if (oldmodels[i] != null)
+ {
+ oldmfn[oldm++] = oldmodels[i];
+ }
+ }
+ // deregister the Jmol instance for these structures - we'll add
+ // ourselves again at the end for the current structure set.
+ ssm.removeStructureViewerListener(this, oldmfn);
+ }
+ }
+ refreshPdbEntries();
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
if (fileName != null)
{
+ boolean foundEntry = false;
// search pdbentries and sequences to find correct pdbentry and
// sequence[] pair for this filename
if (pdbentry != null)
{
- boolean foundEntry = false;
for (int pe = 0; pe < pdbentry.length; pe++)
{
if (pdbentry[pe].getFile().equals(fileName))
if (loadedInline)
{
// TODO: replace with getData ?
- pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
- .getFile(), AppletFormatAdapter.PASTE);
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
+ pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
pdbentry[pe].setFile("INLINE" + pdb.id);
}
else
// needs
// to be tested. See mantis bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-
- pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
- .getFile(), AppletFormatAdapter.URL);
+ 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)
+ {
+ }
+ ;
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
+ pdbentry[pe].getFile(), protocol);
}
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
- jmolpopup.updateComputedMenus();
- viewer
- .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ if (jmolpopup != null)
+ {
+ jmolpopup.updateComputedMenus();
+ }
+ if (!isLoadingFromArchive())
+ {
+ viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ }
+ setLoadingFromArchive(false);
// register ourselves as a listener and notify the gui that it needs to
// update itself.
ssm.addStructureViewerListener(this);
if (notifyLoaded)
{
- updateUI();
+ FeatureRenderer fr = getFeatureRenderer();
+ if (fr != null)
+ {
+ fr.featuresAdded();
+ }
+ refreshGUI();
}
-
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
notifyAtomPicked(iatom, strMeasure, null);
}
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- }
+ public abstract void notifyScriptTermination(String strStatus,
+ int msWalltime);
/**
* display a message echoed from the jmol viewer
int index;
Color col;
jmolHistory(false);
-
+ // TODO: Switch between nucleotide or aa selection expressions
Enumeration en = ResidueProperties.aa3Hash.keys();
StringBuffer command = new StringBuffer("select *;color white;");
while (en.hasMoreElements())
+ col.getGreen() + "," + col.getBlue() + "];");
}
- viewer.evalStringQuiet(command.toString());
+ evalStateCommand(command.toString());
jmolHistory(true);
}
* state change. this could be because structures were loaded, or because an
* error has occured.
*/
- abstract void updateUI();
+ public abstract void refreshGUI();
+ /**
+ * @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
+ */
+ public void allocateViewer(Component renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions)
+ {
+ viewer = JmolViewer.allocateViewer(renderPanel,
+ (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ + ((Object) this).toString(), documentBase, codeBase,
+ commandOptions, this);
+ }
+
+ public void setLoadingFromArchive(boolean loadingFromArchive)
+ {
+ this.loadingFromArchive = loadingFromArchive;
+ }
+
+ public boolean isLoadingFromArchive()
+ {
+ return loadingFromArchive;
+ }
+
+ public void setBackgroundColour(java.awt.Color col)
+ {
+ jmolHistory(false);
+ viewer.evalStringQuiet("background [" + col.getRed() + ","
+ + col.getGreen() + "," + col.getBlue() + "];");
+ jmolHistory(true);
+ }
}
git://source.jalview.org / jalview.git / blobdiff