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Merge branch 'features/JAL-2376_add-horizontal-bar' into develop
[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
82e188f
..
00fd679
100644
(file)
--- a/
src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/
src/jalview/ext/jmol/JalviewJmolBinding.java
@@
-20,11
+20,11
@@
*/
package jalview.ext.jmol;
*/
package jalview.ext.jmol;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
@@
-222,11
+222,11
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
* TODO
*/
public void superposeStructures(AlignmentI alignment, int refStructure,
* TODO
*/
public void superposeStructures(AlignmentI alignment, int refStructure,
- ColumnSelection hiddenCols)
+ HiddenColumns hiddenCols)
{
superposeStructures(new AlignmentI[] { alignment },
new int[] { refStructure },
{
superposeStructures(new AlignmentI[] { alignment },
new int[] { refStructure },
- new ColumnSelection[] { hiddenCols });
+ new HiddenColumns[] { hiddenCols });
}
/**
}
/**
@@
-234,7
+234,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
*/
@Override
public String superposeStructures(AlignmentI[] _alignment,
*/
@Override
public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ int[] _refStructure, HiddenColumns[] _hiddenCols)
{
while (viewer.isScriptExecuting())
{
{
while (viewer.isScriptExecuting())
{
@@
-278,7
+278,7
@@
public abstract class JalviewJmolBinding 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 (a > 0
&& selectioncom.length() > 0
&& !selectioncom.substring(selectioncom.length() - 1).equals(
if (a > 0
&& selectioncom.length() > 0
&& !selectioncom.substring(selectioncom.length() - 1).equals(
@@
-499,17
+499,15
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
/**
* @param files
* @param sr
/**
* @param files
* @param sr
- * @param fr
- * @param viewport
+ * @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
return JmolCommands.getColourBySequenceCommand(getSsm(), files,
{
return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, viewport);
+ getSequence(), sr, viewPanel);
}
/**
}
/**