private List<String> chainNames = new ArrayList<String>();
private Hashtable<String, String> chainFile = new Hashtable<String, String>();
-
+
/*
* Object through which we talk to Chimera
*/
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
viewer = new ChimeraManager(new StructureManager(true));
viewer.startListening(chimeraListener.getUri());
} catch (BindException e)
{
- System.err.println("Failed to start Chimera listener: "
- + e.getMessage());
+ System.err.println(
+ "Failed to start Chimera listener: " + e.getMessage());
}
}
for (String chain : toshow)
{
int modelNumber = getModelNoForChain(chain);
- String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
- + chain.split(":")[1];
+ String showChainCmd = modelNumber == -1 ? ""
+ : modelNumber + ":." + chain.split(":")[1];
if (!first)
{
cmd.append(",");
*/
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (closeChimera)
{
viewer.exitChimera();
int[] _refStructure, HiddenColumns[] _hiddenCols)
{
StringBuilder allComs = new StringBuilder(128);
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (!waitForFileLoad(files))
{
if (debug)
{
System.out.println("Select regions:\n" + selectioncom.toString());
- System.out.println("Superimpose command(s):\n"
- + command.toString());
+ System.out.println(
+ "Superimpose command(s):\n" + command.toString());
}
allComs.append("~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString())
* to the Chimera command 'list models type molecule', see
* ChimeraManager.getModelList().
*/
- List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+ List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
boolean hasSubModels = maps != null && maps.size() > 1;
return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
}
return true;
}
- boolean launched = viewer.launchChimera(StructureManager
- .getChimeraPaths());
+ boolean launched = viewer
+ .launchChimera(StructureManager.getChimeraPaths());
if (launched)
{
startChimeraProcessMonitor();
*/
private int _modelFileNameMap[];
-
// ////////////////////////////////
// /StructureListener
@Override
- public synchronized String[] getPdbFile()
+ public synchronized String[] getStructureFiles()
{
if (viewer == null)
{
return new String[0];
}
- return chimeraMaps.keySet().toArray(
- modelFileNames = new String[chimeraMaps.size()]);
+ return chimeraMaps.keySet()
+ .toArray(modelFileNames = new String[chimeraMaps.size()]);
}
/**
* Parse model number, residue and chain for each selected position,
* formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
*/
- List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
+ List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+ selection);
/*
* Broadcast the selection (which may be empty, if the user just cleared all
false);
for (String resName : residueSet)
{
- char res = resName.length() == 3 ? ResidueProperties
- .getSingleCharacterCode(resName) : resName.charAt(0);
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
Color col = cs.findColour(res, 0, null, null, 0f);
command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + resName + ";");
+ + col.getGreen() / normalise + "," + col.getBlue() / normalise
+ + " ::" + resName + ";");
}
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
/**
* Send the Chimera 'background solid <color>" command.
*
- * @see https
+ * @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
viewerCommandHistory(false);
double normalise = 255D;
final String command = "background solid " + col.getRed() / normalise
- + "," + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + ";";
+ + "," + col.getGreen() / normalise + ","
+ + col.getBlue() / normalise + ";";
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
// TODO refactor as required to pull up to an interface
AlignmentI alignment = avp.getAlignment();
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (files == null)
{
return 0;
sendAsynchronousCommand("open cmd:" + path, null);
} catch (IOException e)
{
- System.err
- .println("Sending commands to Chimera via file failed with "
- + e.getMessage());
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
}
}
return CHIMERA_FEATURE_GROUP;
}
-
public Hashtable<String, String> getChainFile()
{
return chainFile;