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Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
[jalview.git]
/
src
/
jalview
/
ext
/
rbvi
/
chimera
/
JalviewChimeraBinding.java
diff --git
a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index
fad3137
..
00446f2
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@
-25,7
+25,7
@@
import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
@@
-79,7
+79,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
private List<String> chainNames = new ArrayList<String>();
private Hashtable<String, String> chainFile = new Hashtable<String, String>();
private List<String> chainNames = new ArrayList<String>();
private Hashtable<String, String> chainFile = new Hashtable<String, String>();
-
+
/*
* Object through which we talk to Chimera
*/
/*
* Object through which we talk to Chimera
*/
@@
-172,8
+172,6
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- refreshGUI();
}
return true;
} catch (Exception q)
}
return true;
} catch (Exception q)
@@
-194,7
+192,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
* @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));
{
super(ssm, pdbentry, sequenceIs, protocol);
viewer = new ChimeraManager(new StructureManager(true));
@@
-243,8
+242,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
viewer.startListening(chimeraListener.getUri());
} catch (BindException e)
{
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());
}
}
}
}
@@
-265,8
+264,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
for (String chain : toshow)
{
int modelNumber = getModelNoForChain(chain);
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(",");
if (!first)
{
cmd.append(",");
@@
-291,7
+290,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
*/
public void closeViewer(boolean closeChimera)
{
*/
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
if (closeChimera)
{
viewer.exitChimera();
if (closeChimera)
{
viewer.exitChimera();
@@
-339,10
+338,10
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
*/
@Override
public String superposeStructures(AlignmentI[] _alignment,
*/
@Override
public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ int[] _refStructure, HiddenColumns[] _hiddenCols)
{
StringBuilder allComs = new StringBuilder(128);
{
StringBuilder allComs = new StringBuilder(128);
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (!waitForFileLoad(files))
{
if (!waitForFileLoad(files))
{
@@
-355,7
+354,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
int refStructure = _refStructure[a];
AlignmentI alignment = _alignment[a];
{
int refStructure = _refStructure[a];
AlignmentI alignment = _alignment[a];
- ColumnSelection hiddenCols = _hiddenCols[a];
+ HiddenColumns hiddenCols = _hiddenCols[a];
if (refStructure >= files.length)
{
if (refStructure >= files.length)
{
@@
-517,8
+516,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
if (debug)
{
System.out.println("Select regions:\n" + selectioncom.toString());
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())
}
allComs.append("~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString())
@@
-579,7
+578,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
* to the Chimera command 'list models type molecule', see
* ChimeraManager.getModelList().
*/
* 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" : "");
}
boolean hasSubModels = maps != null && maps.size() > 1;
return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
}
@@
-598,8
+597,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
return true;
}
return true;
}
- boolean launched = viewer.launchChimera(StructureManager
- .getChimeraPaths());
+ boolean launched = viewer
+ .launchChimera(StructureManager.getChimeraPaths());
if (launched)
{
startChimeraProcessMonitor();
if (launched)
{
startChimeraProcessMonitor();
@@
-743,19
+742,18
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
*/
private int _modelFileNameMap[];
*/
private int _modelFileNameMap[];
-
// ////////////////////////////////
// /StructureListener
@Override
// ////////////////////////////////
// /StructureListener
@Override
- public synchronized String[] getPdbFile()
+ public synchronized String[] getStructureFiles()
{
if (viewer == null)
{
return new String[0];
}
{
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()]);
}
/**
}
/**
@@
-839,7
+837,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
* Parse model number, residue and chain for each selected position,
* formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
*/
* 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
/*
* Broadcast the selection (which may be empty, if the user just cleared all
@@
-934,12
+933,13
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
false);
for (String resName : residueSet)
{
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 + ","
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);
}
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
@@
-985,7
+985,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
/**
* Send the Chimera 'background solid <color>" command.
*
/**
* Send the Chimera 'background solid <color>" command.
*
- * @see https
+ * @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
@@
-996,8
+996,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
viewerCommandHistory(false);
double normalise = 255D;
final String command = "background solid " + col.getRed() / normalise
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);
}
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
@@
-1102,7
+1102,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
// TODO refactor as required to pull up to an interface
AlignmentI alignment = avp.getAlignment();
// 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;
if (files == null)
{
return 0;
@@
-1150,9
+1150,8
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
sendAsynchronousCommand("open cmd:" + path, null);
} catch (IOException e)
{
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());
}
}
}
}
@@
-1290,7
+1289,6
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
return CHIMERA_FEATURE_GROUP;
}
return CHIMERA_FEATURE_GROUP;
}
-
public Hashtable<String, String> getChainFile()
{
return chainFile;
public Hashtable<String, String> getChainFile()
{
return chainFile;