JAL-1944 updated bugfix implementation

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f40b73b..9d5c075 100644 (file)
--- 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);
 }