X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=f92160e66d29b95717eb5f173e8a50242fcf6b2d;hb=f2b03e9fecf41886ebf5f747fd4be02edf042bee;hp=5df38d600d8efbb01db37592e92522741035a88d;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 5df38d6..f92160e 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -31,7 +31,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
-import java.awt.Color;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -53,6 +52,18 @@ public interface AlignViewportI extends ViewStyleI
    */
   public int calcPanelHeight();
 
+  /**
+   * Answers true if the viewport has at least one column selected
+   * 
+   * @return
+   */
+  boolean hasSelectedColumns();
+
+  /**
+   * Answers true if the viewport has at least one hidden column
+   * 
+   * @return
+   */
   boolean hasHiddenColumns();
 
   boolean isValidCharWidth();
@@ -179,9 +190,9 @@ public interface AlignViewportI extends ViewStyleI
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
 
-  void setSequenceColour(SequenceI seq, Color col);
+  void setSequenceColour(SequenceI seq, ColorI col);
 
-  Color getSequenceColour(SequenceI seq);
+  ColorI getSequenceColour(SequenceI seq);
 
   void updateSequenceIdColours();
 
@@ -235,11 +246,30 @@ 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. 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. 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);
+  String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -375,4 +405,15 @@ 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);
+
+  /**
+   * check if current selection group is defined on the view, or is simply a
+   * temporary group.
+   * 
+   * @return true if group is defined on the alignment
+   */
+  boolean isSelectionDefinedGroup();
 }