git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace
[jalview.git]
/
src
/
jalview
/
workers
/
AlignmentAnnotationFactory.java
diff --git
a/src/jalview/workers/AlignmentAnnotationFactory.java
b/src/jalview/workers/AlignmentAnnotationFactory.java
index
b0392d4
..
8b5240c
100644
(file)
--- a/
src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/
src/jalview/workers/AlignmentAnnotationFactory.java
@@
-20,6
+20,8
@@
*/
package jalview.workers;
*/
package jalview.workers;
+import java.awt.Color;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Jalview;
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 jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
-import java.awt.Color;
-
/**
* Factory class with methods which allow clients (including external scripts
/**
* Factory class with methods which allow clients (including external scripts
- * such as Groovy) to 'register and forget' an alignment annotation calculator. <br>
+ * such as Groovy) to 'register and forget' an alignment annotation calculator.
+ * <br>
* Currently supports two flavours of calculator:
* <ul>
* <li>a simple 'feature counter' which counts any desired score derivable from
* Currently supports two flavours of calculator:
* <ul>
* <li>a simple 'feature counter' which counts any desired score derivable from
- * residue value and any sequence features at each position of the alignment</li>
+ * residue value and any sequence features at each position of the
+ * alignment</li>
* <li>a 'general purpose' calculator which computes one or more complete
* AlignmentAnnotation objects</li>
* </ul>
* <li>a 'general purpose' calculator which computes one or more complete
* AlignmentAnnotation objects</li>
* </ul>
@@
-50,11
+52,12
@@
public class AlignmentAnnotationFactory
*/
public static void newCalculator(FeatureSetCounterI counter)
{
*/
public static void newCalculator(FeatureSetCounterI counter)
{
- AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
+ AlignmentViewPanel currentAlignFrame = Jalview.getInstance()
+ .getCurrentAlignFrame().alignPanel;
if (currentAlignFrame == null)
{
if (currentAlignFrame == null)
{
- 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");
return;
}
new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
return;
}
new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
@@
-71,7
+74,8
@@
public class AlignmentAnnotationFactory
{
// TODO need an interface for AlignFrame by which to access
// its AlignViewportI and AlignmentViewPanel
{
// 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)
{
new AnnotationWorker(currentAlignFrame.getViewport(),
if (currentAlignFrame != null)
{
new AnnotationWorker(currentAlignFrame.getViewport(),
@@
-79,8
+83,8
@@
public class AlignmentAnnotationFactory
}
else
{
}
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");
}
}
}
}
@@
-111,7
+115,8
@@
public class AlignmentAnnotationFactory
public static Annotation newAnnotation(String displayChar, String desc,
char secondaryStructure, float val, Color color)
{
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);
}
/**
}
/**