X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=3e689d1ad1fed2ed7ff85c1b8e16994be1b42a8d;hb=d42b7588a34477b24ce97ba75788536e74e6cf86;hp=17a15630bb4b5f7eb74f2670d66f4e4afc740f66;hpb=08c587d9947f357382199bdb6900c263efc62739;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 17a1563..3e689d1 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -22,6 +22,8 @@ package jalview.api;
 
 import java.util.List;
 
+import jalview.io.DataSourceType;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -64,7 +66,7 @@ public interface AlignViewControllerI
    * @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
@@ -88,13 +90,33 @@ public interface AlignViewControllerI
    * add a features file of some kind to the current view
    * 
    * @param file
-   * @param protocol
+   * @param sourceType
    * @param relaxedIdMatching
    *          if true, try harder to match up IDs with local sequence data
    * @return true if parsing resulted in something being imported to the view or
    *         dataset
    */
-  public boolean parseFeaturesFile(String file, String protocol,
+  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();
+
 }