X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=8b0734035cef58585f485ec3870fe0fb2d868f34;hb=84724ad7b25f65eb6009f70d9b4cb89fc6796622;hp=7985504cc96dc6eb02658375c6a15be421a2c376;hpb=1c757dc1e6ee864277825c1ebd9c6a9fbe0da7b2;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 7985504..8b07340 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,16 +21,19 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.util.Hashtable;
@@ -44,7 +47,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getEndRes();
+  /**
+   * Get the ranges object containing details of the start and end sequences and
+   * residues
+   * 
+   * @return
+   */
+  public ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -78,11 +87,19 @@ public interface AlignViewportI extends ViewStyleI
 
   ColourSchemeI getGlobalColourScheme();
 
+  /**
+   * Returns an object that describes colouring (including any thresholding or
+   * fading) of the alignment
+   * 
+   * @return
+   */
+  ResidueShaderI getResidueShading();
+
   AlignmentI getAlignment();
 
   ColumnSelection getColumnSelection();
 
-  Profile[] getSequenceConsensusHash();
+  ProfilesI getSequenceConsensusHash();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -109,6 +126,13 @@ public interface AlignViewportI extends ViewStyleI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for alignment gap annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getAlignmentGapAnnotation();
+
+  /**
    * get the container for cDNA complement consensus annotation
    * 
    * @return
@@ -145,7 +169,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(Profile[] hconsensus);
+  void setSequenceConsensusHash(ProfilesI hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -156,7 +180,7 @@ public interface AlignViewportI extends ViewStyleI
 
   /**
    * 
-   * @return the alignment annotatino row for the structure consensus
+   * @return the alignment annotation row for the structure consensus
    *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
@@ -169,11 +193,13 @@ public interface AlignViewportI extends ViewStyleI
   void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
 
   /**
-   * set global colourscheme
+   * Sets the colour scheme for the background alignment (as distinct from
+   * sub-groups, which may have their own colour schemes). A null value is used
+   * for no residue colour (white).
    * 
-   * @param rhc
+   * @param cs
    */
-  void setGlobalColourScheme(ColourSchemeI rhc);
+  void setGlobalColourScheme(ColourSchemeI cs);
 
   Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
 
@@ -261,7 +287,7 @@ 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. Use this for
@@ -276,7 +302,8 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return String[]
    */
-  String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
+  String[] getViewAsString(boolean selectedRegionOnly,
+          boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -413,7 +440,6 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
@@ -423,4 +449,25 @@ public interface AlignViewportI extends ViewStyleI
    * @return true if group is defined on the alignment
    */
   boolean isSelectionDefinedGroup();
+
+  /**
+   * 
+   * @return true if there are search results on the view
+   */
+  boolean hasSearchResults();
+
+  /**
+   * set the search results for the view
+   * 
+   * @param results
+   *          - or null to clear current results
+   */
+  void setSearchResults(SearchResultsI results);
+
+  /**
+   * get search results for this view (if any)
+   * 
+   * @return search results or null
+   */
+  SearchResultsI getSearchResults();
 }