JAL-1944 java doc update and minor house keeping

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9d5c075..8343f0b 100644 (file)
--- 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);

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 7cea5a3..0f6d66b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1593,7 +1593,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly,
-          boolean isExportHiddenSeqs)
+          boolean exportHiddenSeqs)
   {
     String[] selection = null;
     SequenceI[] seqs = null;
@@ -1608,13 +1608,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows() && isExportHiddenSeqs)
+      if (hasHiddenRows() && exportHiddenSeqs)
       {
-        iSize = alignment.getHiddenSequences().getFullAlignment()
-                .getHeight();
-        seqs = alignment.getHiddenSequences().getFullAlignment()
-                .getSequencesArray();
-        end = alignment.getHiddenSequences().getFullAlignment().getWidth();
+        AlignmentI fullAlignment = alignment.getHiddenSequences()
+                .getFullAlignment();
+        iSize = fullAlignment.getHeight();
+        seqs = fullAlignment.getSequencesArray();
+        end = fullAlignment.getWidth();
       }
       else
       {