X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=2507bb58a9b0aee05356da7f2b371cca35f220ed;hb=6d03a7bc7ca503f0e845dcbc568e44a39c842612;hp=68c229581db3af2b68751e240b5347026a3c6c76;hpb=e811386cfe6d7ab7d73db56a31ac83732e185861;p=jalview.git
diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 68c2295..2507bb5 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.workers;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
@@ -10,11 +31,13 @@ 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
*
@@ -29,11 +52,12 @@ public class AlignmentAnnotationFactory
*/
public static void newCalculator(FeatureSetCounterI counter)
{
- AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
+ AlignmentViewPanel currentAlignFrame = Jalview
+ .getCurrentAlignFrame().alignPanel;
if (currentAlignFrame == null)
{
- System.err
- .println("Can't register calculator as no alignment window has focus");
+ System.err.println(
+ "Can't register calculator as no alignment window has focus");
return;
}
new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
@@ -48,6 +72,8 @@ public class AlignmentAnnotationFactory
*/
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)
{
@@ -56,12 +82,26 @@ public class AlignmentAnnotationFactory
}
else
{
- System.err
- .println("Can't register calculator as no alignment window has focus");
+ 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
@@ -74,7 +114,8 @@ 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);
}
/**