X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=3e689d1ad1fed2ed7ff85c1b8e16994be1b42a8d;hb=d42b7588a34477b24ce97ba75788536e74e6cf86;hp=b868ee5770fb5a732892f8e68ef6221c622d36e3;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index b868ee5..3e689d1 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -20,10 +20,10 @@
  */
 package jalview.api;
 
-import jalview.io.DataSourceType;
-
 import java.util.List;
 
+import jalview.io.DataSourceType;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -96,7 +96,27 @@ public interface AlignViewControllerI
    * @return true if parsing resulted in something being imported to the view or
    *         dataset
    */
-  public boolean parseFeaturesFile(String file, DataSourceType sourceType,
+  public boolean parseFeaturesFile(Object file, DataSourceType sourceType,
           boolean relaxedIdMatching);
 
+  /**
+   * mark columns containing highlighted regions (e.g. from search, structure
+   * highlight, or a mouse over event in another viewer)
+   * 
+   * @param invert
+   * @param extendCurrent
+   * @param toggle
+   * @return
+   */
+  boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
+          boolean toggle);
+
+  /**
+   * copies each distinct highlighted region on the current view as a new
+   * sequence on the clipboard
+   * 
+   * @return
+   */
+  boolean copyHighlightedRegionsToClipboard();
+
 }