X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=2507bb58a9b0aee05356da7f2b371cca35f220ed;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=520b232f8102695f28af0636d03b96c02e58f79d;hpb=ea7b9666447dea727e9d607de3694cfe27bc811e;p=jalview.git
diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 520b232..2507bb5 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,5 +1,27 @@
+/*
+ * 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;
import jalview.datamodel.Annotation;
@@ -9,12 +31,14 @@ 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 'feature counter' which can count any desired property derivable from
- * residue value and any sequence features at each position of the alignment
- * - a 'general purpose' calculator which computes one more complete
+ *
- 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
*
*/
@@ -26,30 +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)
{
- if (Jalview.getCurrentAlignFrame() != null)
- {
- newCalculator(Jalview.getCurrentAlignFrame(), counter);
- }
- else
+ 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;
}
- }
-
- /**
- * Constructs and registers a new alignment annotation worker
- *
- * @param af
- * the AlignFrame for which the annotation is to be calculated
- * @param counter
- * provider of feature counts per alignment position
- */
- public static void newCalculator(AlignFrame af, FeatureCounterI counter)
- {
- new ColumnCounterWorker(af, counter);
+ new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
+ currentAlignFrame, counter);
}
/**
@@ -60,29 +72,33 @@ public class AlignmentAnnotationFactory
*/
public static void newCalculator(AnnotationProviderI calculator)
{
- if (Jalview.getCurrentAlignFrame() != null)
+ // TODO need an interface for AlignFrame by which to access
+ // its AlignViewportI and AlignmentViewPanel
+ AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
+ if (currentAlignFrame != null)
{
- newCalculator(Jalview.getCurrentAlignFrame(), calculator);
+ new AnnotationWorker(currentAlignFrame.getViewport(),
+ currentAlignFrame.getAlignPanels().get(0), calculator);
}
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 af
- * the AlignFrame for which the annotation is to be calculated
+ * @param viewport
+ * @param panel
* @param calculator
* provider of AlignmentAnnotation for the alignment
*/
- public static void newCalculator(AlignFrame af,
- AnnotationProviderI calculator)
+ public static void newCalculator(AlignViewportI viewport,
+ AlignmentViewPanel panel, AnnotationProviderI calculator)
{
- new AnnotationWorker(af, calculator);
+ new AnnotationWorker(viewport, panel, calculator);
}
/**
@@ -98,7 +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);
}
/**