package jalview.workers;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import java.awt.Color;
/**
* Factory class with methods which allow clients (including external scripts
* such as Groovy) to 'register and forget' an alignment annotation calculator.
* Currently supports two flavours of calculator:
*
* - a simple 'feature counter' which counts any desired score derivable from
* residue value and any sequence features at each position of the alignment
* - a 'general purpose' calculator which computes one or more complete
* AlignmentAnnotation objects
*
*/
public class AlignmentAnnotationFactory
{
/**
* Constructs and registers a new alignment annotation worker
*
* @param counter
* provider of feature counts per alignment position
*/
public static void newCalculator(FeatureCounterI counter)
{
// TODO need an interface for AlignFrame by which to access
// its AlignViewportI and AlignmentViewPanel
AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
if (currentAlignFrame != null)
{
newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
.getAlignPanels().get(0), counter);
}
else
{
System.err
.println("Can't register calculator as no alignment window has focus");
}
}
/**
* Constructs and registers a new alignment annotation worker
*
* @param viewport
* @param panel
* @param counter
* provider of feature counts per alignment position
*/
public static void newCalculator(AlignViewportI viewport,
AlignmentViewPanel panel, FeatureCounterI counter)
{
new ColumnCounterWorker(viewport, panel, counter);
}
/**
* Constructs and registers a new alignment annotation worker
*
* @param calculator
* provider of AlignmentAnnotation for the alignment
*/
public static void newCalculator(AnnotationProviderI calculator)
{
// TODO need an interface for AlignFrame by which to access
// its AlignViewportI and AlignmentViewPanel
AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
if (currentAlignFrame != null)
{
newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
.getAlignPanels().get(0), calculator);
}
else
{
System.err
.println("Can't register calculator as no alignment window has focus");
}
}
/**
* Constructs and registers a new alignment annotation worker
*
* @param viewport
* @param panel
* @param calculator
* provider of AlignmentAnnotation for the alignment
*/
public static void newCalculator(AlignViewportI viewport,
AlignmentViewPanel panel,
AnnotationProviderI calculator)
{
new AnnotationWorker(viewport, panel, calculator);
}
/**
* Factory method to construct an Annotation object
*
* @param displayChar
* @param desc
* @param secondaryStructure
* @param val
* @param color
* @return
*/
public static Annotation newAnnotation(String displayChar, String desc,
char secondaryStructure, float val, Color color)
{
return new Annotation(displayChar, desc, secondaryStructure, val, color);
}
/**
* Factory method to construct an AlignmentAnnotation object
*
* @param name
* @param desc
* @param anns
* @return
*/
public static AlignmentAnnotation newAlignmentAnnotation(String name,
String desc, Annotation[] anns)
{
return new AlignmentAnnotation(name, desc, anns);
}
}