@Override
public String getSelectedSequencesFrom(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return getSelectedSequencesFrom(alf, null);
}
@Override
public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesFrom(alf, sep);
}
public void highlight(String sequenceId, String position,
String alignedPosition)
{
- highlightIn(getCurrentAlignFrame(), sequenceId, position,
+ highlightIn(null, sequenceId, position,
alignedPosition);
}
public void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
}
@Override
public void select(String sequenceIds, String columns, String sep)
{
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
+ selectIn(null, sequenceIds, columns, sep);
}
@Override
public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.selectIn(alf, sequenceIds, columns, sep);
}
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ return getSelectedSequencesAsAlignmentFrom(null,
format, suffix);
}
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
}
@Override
public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAlignmentOrderFrom(alf, sep);
}
public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.orderAlignmentBy(alf, order, undoName, sep);
}
@Override
public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.loadAnnotationFrom(alf, annotation);
}
public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
}
@Override
public String getFeatures(String format)
{
- return getFeaturesFrom(getCurrentAlignFrame(), format);
+ return getFeaturesFrom(null, format);
}
@Override
public String getFeaturesFrom(AlignFrameI alf, String format)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeaturesFrom(alf, format);
}
@Override
public String getAnnotation()
{
- return getAnnotationFrom(getCurrentAlignFrame());
+ return getAnnotationFrom(null);
}
@Override
public String getAnnotationFrom(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAnnotationFrom(alf);
}
@Override
public AlignFrameI newView()
{
- return newViewFrom(getCurrentAlignFrame(), null);
+ return newViewFrom(null, null);
}
@Override
public AlignFrameI newView(String name)
{
- return newViewFrom(getCurrentAlignFrame(), name);
+ return newViewFrom(null, name);
}
@Override
@Override
public AlignFrameI newViewFrom(AlignFrameI alf, String name)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.newViewFrom(alf, name);
}
public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
pdbFile);
}
public void scrollViewToIn(AlignFrameI alf, String topRow,
String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
public void scrollViewToRowIn(AlignFrameI alf, String topRow)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToColumnIn(alf, leftHandColumn);
}
@Override
public String getFeatureGroups()
{
- return getFeatureGroupsOn(getCurrentAlignFrame());
+ return getFeatureGroupsOn(null);
}
@Override
public String getFeatureGroupsOn(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeatureGroupsOn(alf);
}
@Override
public String getFeatureGroupsOfState(boolean visible)
{
- return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
+ return getFeatureGroupsOfStateOn(null, visible);
}
@Override
public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeatureGroupsOfStateOn(alf, visible);
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
- boolean state)
- {
- setFeatureGroupStateOn(alf, groups, state);
+ public void setFeatureGroupState(String groups, boolean state)
+ { // JalviewLite API
+ setFeatureGroupStateOn(null, groups, state);
}
@Override
- public void setFeatureGroupState(String groups, boolean state)
+ public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ boolean state)
{
- appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.setFeatureGroupStateOn(alf, groups, state);
}
@Override
@Override
public Object openTreePanel(AlignFrame af, String treeType,
String modelName)
- {
+ { // JalviewJS api
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
return CalculationChooser.openTreePanel(af, treeType, modelName, null);
}
@Override
public Object openPcaPanel(AlignFrame af, String modelName)
{
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
return CalculationChooser.openPcaPanel(af, modelName, null);
}
public String getSelectedSequencesAsAlignment(String format,
boolean suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ return getSelectedSequencesAsAlignmentFrom(null,
format, suffix);
}
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, boolean suffix)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
"" + suffix);
}