X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignmentAnnotationFactory.java;h=2507bb58a9b0aee05356da7f2b371cca35f220ed;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=4e11c7066db6f6821566d911d9104b741b68ecff;hpb=c41d746aef7cc3fda8d4fcee41a19443b2bf0281;p=jalview.git
diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 4e11c70..2507bb5 100644
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -8,15 +28,16 @@ import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import java.awt.Color;
-import java.lang.reflect.Method;
/**
* 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
*
@@ -29,83 +50,18 @@ public class AlignmentAnnotationFactory
* @param counter
* provider of feature counts per alignment position
*/
- public static void newCalculator(ColumnCounterI 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)
- {
- Method newCalcMethod = null;
- try
- {
- for (Method m : AlignmentAnnotationFactory.class.getMethods())
- {
- if (m.getName().equals("newCalculator"))
- {
- if (m.getParameterTypes().length == 3
- && m.getParameterTypes()[2].isInstance(counter))
- {
- newCalcMethod = m;
- break;
- }
- }
- }
- } catch (Exception q)
- {
- }
- if (newCalcMethod == null)
- {
-
- System.err
- .println("Couldn't find a newCalculator method for ColumnCounterI type "
- + counter.getClass().getName());
- }
- try
- {
- newCalcMethod.invoke(null, currentAlignFrame.getAlignViewport(),
- currentAlignFrame, counter);
- } catch (Exception ie)
- {
- System.err
- .println("Exception when reporting newCalculator method for ColumnCounterI type "
- + counter.getClass().getName());
- }
- }
- 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 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 for a set of
- * column counters
- *
- * @param viewport
- * @param panel
- * @param counter
- * provider of feature counts per alignment position
- */
- public static void newCalculator(AlignViewportI viewport,
- AlignmentViewPanel panel, FeatureSetCounterI counter)
- {
- new ColumnCounterSetWorker(viewport, panel, counter);
+ new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
+ currentAlignFrame, counter);
}
/**
@@ -121,13 +77,13 @@ public class AlignmentAnnotationFactory
AlignFrame currentAlignFrame = Jalview.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");
+ System.err.println(
+ "Can't register calculator as no alignment window has focus");
}
}
@@ -158,7 +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);
}
/**