X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=8b5240ca5fbf56edf9693a086cafedccb92b858a;hb=f6d1305378fa256a42caf7d284b13d5a084bc471;hp=beee1eb9b86a00bb8d87c55e6a7bcf379d3b8834;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git
diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index beee1eb..8b5240c 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -20,6 +20,8 @@
*/
package jalview.workers;
+import java.awt.Color;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Jalview;
@@ -27,15 +29,15 @@ 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.
+ * 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
+ * residue value and any sequence features at each position of the
+ * alignment
* - a 'general purpose' calculator which computes one or more complete
* AlignmentAnnotation objects
*
@@ -48,35 +50,18 @@ public class AlignmentAnnotationFactory
* @param counter
* provider of feature counts per alignment position
*/
- public static void newCalculator(FeatureCounterI counter)
+ public static void newCalculator(FeatureSetCounterI counter)
{
- // TODO need an interface for AlignFrame by which to access
- // its AlignViewportI and AlignmentViewPanel
- AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
- if (currentAlignFrame != null)
+ AlignmentViewPanel currentAlignFrame = Jalview.getInstance()
+ .getCurrentAlignFrame().alignPanel;
+ if (currentAlignFrame == null)
{
- newCalculator(currentAlignFrame.getAlignViewport(),
- currentAlignFrame, counter);
+ jalview.bin.Console.errPrintln(
+ "Can't register calculator as no alignment window has focus");
+ return;
}
- 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);
+ new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
+ currentAlignFrame, counter);
}
/**
@@ -89,16 +74,17 @@ public class AlignmentAnnotationFactory
{
// TODO need an interface for AlignFrame by which to access
// its AlignViewportI and AlignmentViewPanel
- AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
+ AlignFrame currentAlignFrame = Jalview.getInstance()
+ .getCurrentAlignFrame();
if (currentAlignFrame != null)
{
- newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
- .getAlignPanels().get(0), calculator);
+ new AnnotationWorker(currentAlignFrame.getViewport(),
+ currentAlignFrame.getAlignPanels().get(0), calculator);
}
else
{
- System.err
- .println("Can't register calculator as no alignment window has focus");
+ jalview.bin.Console.errPrintln(
+ "Can't register calculator as no alignment window has focus");
}
}
@@ -129,7 +115,8 @@ public class AlignmentAnnotationFactory
public static Annotation newAnnotation(String displayChar, String desc,
char secondaryStructure, float val, Color color)
{
- return new Annotation(displayChar, desc, secondaryStructure, val, color);
+ return new Annotation(displayChar, desc, secondaryStructure, val,
+ color);
}
/**