X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=9d5c075b1248e158575f26ffbe2d9601c01e6a56;hb=e7b6c76c3b028aeeef7770c99c87d895c1b46172;hp=93b2134bb15830d5d98cc6524d838d9dc2ee4a38;hpb=294cc8b0cf3d28310a95e1ffdb2a0f871304b70d;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 93b2134..9d5c075 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -178,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI
    */
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
-  
+
   void setSequenceColour(SequenceI seq, Color col);
 
   Color getSequenceColour(SequenceI seq);
@@ -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);
 
@@ -251,8 +264,11 @@ public interface AlignViewportI extends ViewStyleI
 
   /**
    * get a copy of the currently visible alignment annotation
-   * @param selectedOnly if true - trim to selected regions on the alignment
-   * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+   * 
+   * @param selectedOnly
+   *          if true - trim to selected regions on the alignment
+   * @return an empty list or new alignment annotation objects shown only
+   *         visible columns trimmed to selected region only
    */
   List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly);
@@ -372,4 +388,7 @@ public interface AlignViewportI extends ViewStyleI
    * Set whether view should scroll to show the highlighted region of a sequence
    */
   void setFollowHighlight(boolean b);
+
+
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 }