X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=3e689d1ad1fed2ed7ff85c1b8e16994be1b42a8d;hb=ae3fad8019274ca3ab1258a480ba15dd9adac1e9;hp=24020e57fcd29750c5a0c0594f569fcfd7e43e7e;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 24020e5..3e689d1 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,8 @@ package jalview.api;
 
 import java.util.List;
 
+import jalview.io.DataSourceType;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -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();
+
 }