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Merge branch 'patch/JAL-2238_tcoffee_subgroups' into develop
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewControllerI.java
diff --git
a/src/jalview/api/AlignViewControllerI.java
b/src/jalview/api/AlignViewControllerI.java
index
fef9f14
..
26966ba
100644
(file)
--- a/
src/jalview/api/AlignViewControllerI.java
+++ b/
src/jalview/api/AlignViewControllerI.java
@@
-20,6
+20,8
@@
*/
package jalview.api;
*/
package jalview.api;
+import java.util.List;
+
/**
* prototype abstract controller for a Jalview alignment view
*
/**
* prototype abstract controller for a Jalview alignment view
*
@@
-62,19
+64,25
@@
public interface AlignViewControllerI
* @return true if operation affected state
*/
boolean markColumnsContainingFeatures(boolean invert,
* @return true if operation affected state
*/
boolean markColumnsContainingFeatures(boolean invert,
- boolean extendCurrent, boolean clearColumns, String featureType);
+ boolean extendCurrent, boolean toggle, String featureType);
/**
/**
- * sort the alignment or current selection by average score over the given set of features
- * @param typ list of feature names or null to use currently displayed features
+ * sort the alignment or current selection by average score over the given set
+ * of features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
*/
*/
- void sortAlignmentByFeatureScore(String[] typ);
+ void sortAlignmentByFeatureScore(List<String> typ);
/**
/**
- * sort the alignment or current selection by distribution of the given set of features
- * @param typ list of feature names or null to use currently displayed features
+ * sort the alignment or current selection by distribution of the given set of
+ * features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
*/
*/
- void sortAlignmentByFeatureDensity(String[] typ);
+ void sortAlignmentByFeatureDensity(List<String> typ);
/**
* add a features file of some kind to the current view
/**
* add a features file of some kind to the current view