X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=d8ba30d007abda84883e1ef0f4ead7f8199c5e6e;hb=5720f2cea034f014f366886b3cb9a170a909e988;hp=224ba0f5e6fca44608bbdcdd70279274ec50091f;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 224ba0f..d8ba30d 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -6,20 +6,23 @@
*
* 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.
+ * 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 .
+ * 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.api;
import java.awt.Color;
import java.util.Hashtable;
+import java.util.List;
import java.util.Map;
import jalview.analysis.Conservation;
@@ -189,5 +192,12 @@ public interface AlignViewportI
void setConservation(Conservation cons);
+ /**
+ * get a copy of the currently visible alignment annotation
+ * @param selectedOnly if true - trim to selected regions on the alignment
+ * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+ */
+ List getVisibleAlignmentAnnotation(
+ boolean selectedOnly);
}