X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=8343f0b0691d74c61de042e9056e090aa35974be;hb=69f930f786254940db0a7c247cc350098e940bbf;hp=9d5c075b1248e158575f26ffbe2d9601c01e6a56;hpb=e7b6c76c3b028aeeef7770c99c87d895c1b46172;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9d5c075..8343f0b 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -235,21 +235,27 @@ public interface AlignViewportI extends ViewStyleI
    * 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. Use this for
    * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
+   * columns. This method doesn't exclude hidden sequences from the output.
+   *
+   * @param selectedRegionOnly
+   *          - determines if only the selected region or entire alignment is
+   *          exported
    * @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.
+   * if columns are hidden they will not be returned in the result. Use this for
+   * calculating trees, PCA, redundancy etc on views which contain hidden
+   * columns.
    * 
    * @param selectedRegionOnly
+   *          - determines if only the selected region or entire alignment is
+   *          exported
    * @param isExportHiddenSeqs
+   *          - determines if hidden sequences would be exported or not.
+   * 
    * @return String[]
    */
   String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);