X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=d8ba30d007abda84883e1ef0f4ead7f8199c5e6e;hb=5720f2cea034f014f366886b3cb9a170a909e988;hp=ab9efb164a835304991570aeb22ba87ded8b8121;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index ab9efb1..d8ba30d 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,23 +1,44 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.api;
 
+import java.awt.Color;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Map;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.RNAHelicesColour;
 
 /**
  * @author jimp
- *
+ * 
  */
 public interface AlignViewportI
 {
@@ -28,6 +49,14 @@ public interface AlignViewportI
 
   int getCharHeight();
 
+  /**
+   * calculate the height for visible annotation, revalidating bounds where
+   * necessary ABSTRACT GUI METHOD
+   * 
+   * @return total height of annotation
+   */
+  public int calcPanelHeight();
+
   boolean hasHiddenColumns();
 
   boolean isValidCharWidth();
@@ -57,23 +86,28 @@ public interface AlignViewportI
   AlignmentAnnotation getAlignmentQualityAnnot();
 
   AlignmentAnnotation getAlignmentConservationAnnotation();
+
   /**
    * get the container for alignment consensus annotation
+   * 
    * @return
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
    * Test to see if viewport is still open and active
-   * @return true indicates that all references to viewport should be dropped 
+   * 
+   * @return true indicates that all references to viewport should be dropped
    */
   boolean isClosed();
+
   /**
    * get the associated calculation thread manager for the view
+   * 
    * @return
    */
   AlignCalcManagerI getCalcManager();
-  
+
   /**
    * get the percentage gaps allowed in a conservation calculation
    * 
@@ -82,24 +116,28 @@ public interface AlignViewportI
 
   /**
    * set the consensus result object for the viewport
+   * 
    * @param hconsensus
    */
   void setSequenceConsensusHash(Hashtable[] hconsensus);
 
   /**
    * 
-   * @return the alignment annotatino row for the structure consensus calculation
+   * @return the alignment annotatino row for the structure consensus
+   *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
 
   /**
    * set the Rna structure consensus result object for the viewport
-   * @param hStrucConsensus 
+   * 
+   * @param hStrucConsensus
    */
   void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
 
   /**
    * set global colourscheme
+   * 
    * @param rhc
    */
   void setGlobalColourScheme(ColourSchemeI rhc);
@@ -109,4 +147,57 @@ public interface AlignViewportI
   void setHiddenRepSequences(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
 
+  /**
+   * hides or shows dynamic annotation rows based on groups and group and
+   * alignment associated auto-annotation state flags apply the current
+   * group/autoannotation settings to the alignment view. Usually you should
+   * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
+   * ensure the annotation panel bounds are set correctly.
+   * 
+   * @param applyGlobalSettings
+   *          - apply to all autoannotation rows or just the ones associated
+   *          with the current visible region
+   * @param preserveNewGroupSettings
+   *          - don't apply global settings to groups which don't already have
+   *          group associated annotation
+   */
+  void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings);
+
+  void setSequenceColour(SequenceI seq, Color col);
+
+  Color getSequenceColour(SequenceI seq);
+
+  void updateSequenceIdColours();
+
+  SequenceGroup getSelectionGroup();
+
+  SequenceI[] getSequenceSelection();
+
+  void clearSequenceColours();
+
+  CigarArray getViewAsCigars(boolean selectedRegionOnly);
+
+  AlignmentView getAlignmentView(boolean selectedOnly);
+
+  AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+  String[] getViewAsString(boolean selectedRegionOnly);
+
+  void setSelectionGroup(SequenceGroup sg);
+
+  char getGapCharacter();
+
+  void setColumnSelection(ColumnSelection cs);
+
+  void setConservation(Conservation cons);
+
+  /**
+   * 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
+   */
+  List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+          boolean selectedOnly);
+
 }