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spike branch updated from latest features/JAL-2446
[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
..
b954677
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;
@@
-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)
@@
-291,7
+289,7
@@
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
+337,10
@@
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
+353,7
@@
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)
{
@@
-579,7
+577,7
@@
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" : "");
}
@@
-747,7
+745,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
// ////////////////////////////////
// /StructureListener
@Override
// ////////////////////////////////
// /StructureListener
@Override
- public synchronized String[] getPdbFile()
+ public synchronized String[] getStructureFiles()
{
if (viewer == null)
{
{
if (viewer == null)
{
@@
-1102,7
+1100,7
@@
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;