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Merge branch 'codereviews/JAL-1990_IProgressIndicator_jalview.structure' into patch...
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JalviewJmolBinding.java
diff --git
a/src/jalview/ext/jmol/JalviewJmolBinding.java
b/src/jalview/ext/jmol/JalviewJmolBinding.java
index
96dfcfe
..
51f2708
100644
(file)
--- a/
src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/
src/jalview/ext/jmol/JalviewJmolBinding.java
@@
-27,6
+27,7
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
@@
-72,7
+73,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
*/
private boolean associateNewStructs = false;
*/
private boolean associateNewStructs = false;
- Vector<String> atomsPicked = new Vector<String>();
+ Vector<String> atomsPicked = new Vector<>();
private List<String> chainNames;
private List<String> chainNames;
@@
-610,7
+611,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
}
if (modelFileNames == null)
{
}
if (modelFileNames == null)
{
- List<String> mset = new ArrayList<String>();
+ List<String> mset = new ArrayList<>();
_modelFileNameMap = new int[viewer.ms.mc];
String m = viewer.ms.getModelFileName(0);
if (m != null)
_modelFileNameMap = new int[viewer.ms.mc];
String m = viewer.ms.getModelFileName(0);
if (m != null)
@@
-670,7
+671,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
@Override
public synchronized String[] getStructureFiles()
{
@Override
public synchronized String[] getStructureFiles()
{
- List<String> mset = new ArrayList<String>();
+ List<String> mset = new ArrayList<>();
if (viewer == null)
{
return new String[0];
if (viewer == null)
{
return new String[0];
@@
-1059,8
+1060,8
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new ArrayList<String>();
- chainFile = new Hashtable<String, String>();
+ chainNames = new ArrayList<>();
+ chainFile = new Hashtable<>();
boolean notifyLoaded = false;
String[] modelfilenames = getStructureFiles();
// first check if we've lost any structures
boolean notifyLoaded = false;
String[] modelfilenames = getStructureFiles();
// first check if we've lost any structures
@@
-1126,7
+1127,8
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE);
+ pdbfile, DataSourceType.PASTE,
+ getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
@@
-1158,7
+1160,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
// pdbentry[pe].getFile(), protocol);
}
@@
-1226,6
+1228,8
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
return chainNames;
}
return chainNames;
}
+ protected abstract IProgressIndicator getIProgressIndicator();
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);