X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=9d5c075b1248e158575f26ffbe2d9601c01e6a56;hb=e7b6c76c3b028aeeef7770c99c87d895c1b46172;hp=f40b73b1c62ab4ca0a40868551656621739216d5;hpb=1f959f4a5bc07769cde4c2577022ad64e55b4a1a;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f40b73b..9d5c075 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -240,6 +240,19 @@ public interface AlignViewportI extends ViewStyleI
    * @return String[]
    */
   String[] getViewAsString(boolean selectedRegionOnly);
+  
+  /**
+   * This method returns the visible alignment as text, as seen on the GUI, ie
+   * if columns are hidden they will not be returned in the result. However, If
+   * there are hidden sequences, isExportHiddenSeqs flag decides if they would
+   * be exported or not. Use this for calculating trees, PCA, redundancy etc on
+   * views which contain hidden columns.
+   * 
+   * @param selectedRegionOnly
+   * @param isExportHiddenSeqs
+   * @return String[]
+   */
+  String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -376,20 +389,6 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-  /**
-   * Set whether hidden Sequences should be trimmed off during an export
-   * operation.
-   * 
-   * @param isExportHiddenSeqs
-   */
-  public void setExportHiddenSeqs(boolean isExportHiddenSeqs);
-
-  /**
-   * If true hidden Sequences are exported otherwise they aren't
-   * 
-   * @return
-   */
-  public boolean isExportHiddenSeqs();
 
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 }