package jalview.bin;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
* @param args
* open <em>filename</em>
*/
+ @SuppressWarnings("unused")
public static void main(String[] args)
{
- // Platform.startJavaLogging();
+ if (false)
+ {
+ Platform.startJavaLogging();
+ }
getInstance().doMain(args);
}
* .AlignFrame)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrameI alf)
+ public String getSelectedSequencesFrom(AlignFrame alf)
{
if (alf == null)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
if (alf == null)
{
}
@Override
- public void highlightIn(AlignFrameI alf, String sequenceId,
+ public void highlightIn(AlignFrame alf, String sequenceId,
String position, String alignedPosition)
{
if (alf == null)
}
@Override
- public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, null);
}
@Override
- public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns,
String sep)
{
if (alf == null)
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String sep)
{
if (alf == null)
}
@Override
- public String getAlignmentOrderFrom(AlignFrameI alf)
+ public String getAlignmentOrderFrom(AlignFrame alf)
{
return getAlignmentFrom(alf, null);
}
@Override
- public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
if (alf == null)
{
}
@Override
- public String orderAlignmentBy(AlignFrameI alf, String order,
+ public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
if (alf == null)
}
@Override
- public String getAlignmentFrom(AlignFrameI alf, String format)
+ public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, null);
}
}
@Override
- public String getAlignmentFrom(AlignFrameI alf, String format,
+ public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
return appLoader.getAlignmentFrom(alf, format, suffix);
}
@Override
- public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (alf == null)
{
}
@Override
- public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
if (alf == null)
}
@Override
- public String getFeaturesFrom(AlignFrameI alf, String format)
+ public String getFeaturesFrom(AlignFrame alf, String format)
{
if (alf == null)
{
}
@Override
- public String getAnnotationFrom(AlignFrameI alf)
+ public String getAnnotationFrom(AlignFrame alf)
{
if (alf == null)
{
return appLoader.getAnnotationFrom(alf);
}
- @Override
- public AlignFrameI newView()
- {
- return newViewFrom(null, null);
- }
-
- @Override
- public AlignFrameI newView(String name)
- {
- return newViewFrom(null, name);
- }
-
- @Override
- public AlignFrameI newViewFrom(AlignFrameI alf)
- {
- return newViewFrom(alf, null);
- }
+ // @Override
+ // public AlignFrame newView()
+ // {
+ // return newViewFrom(null, null);
+ // }
+ //
+ // @Override
+ // public AlignFrame newView(String name)
+ // {
+ // return newViewFrom(null, name);
+ // }
+ //
+ // @Override
+ // public AlignFrame newViewFrom(AlignFrame alf)
+ // {
+ // return newViewFrom(alf, null);
+ // }
- @Override
- public AlignFrameI newViewFrom(AlignFrameI alf, String name)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.newViewFrom(alf, name);
- }
+ // @Override
+ // public AlignFrame newViewFrom(AlignFrame alf, String name)
+ // {
+ // if (alf == null)
+ // {
+ // alf = getCurrentAlignFrame();
+ // }
+ // return appLoader.newViewFrom(alf, name);
+ // }
@Override
- public AlignFrameI loadAlignment(String text, String title)
+ public AlignFrame loadAlignment(String text, String title)
{
return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT, title);
}
@Override
- public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
if (alFrame == null)
}
@Override
- public void scrollViewToIn(AlignFrameI alf, String topRow,
+ public void scrollViewToIn(AlignFrame alf, String topRow,
String leftHandColumn)
{
if (alf == null)
}
@Override
- public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+ public void scrollViewToRowIn(AlignFrame alf, String topRow)
{
if (alf == null)
{
}
@Override
- public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+ public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
{
if (alf == null)
{
}
@Override
- public String getFeatureGroupsOn(AlignFrameI alf)
+ public String getFeatureGroupsOn(AlignFrame alf)
{
if (alf == null)
{
}
@Override
- public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
if (alf == null)
{
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups,
boolean state)
{
if (alf == null)
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, boolean suffix)
{
if (alf == null)
}
@Override
- public void setMouseoverListener(AlignFrameI af, String listener)
+ public void setMouseoverListener(AlignFrame af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public void setSelectionListener(AlignFrameI af, String listener)
+ public void setSelectionListener(AlignFrame af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public void removeJavascriptListener(AlignFrameI af, String listener)
+ public void removeJavascriptListener(AlignFrame af, String listener)
{
// TODO Auto-generated method stub