X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=7463187d51cc7d2296ff79c31b38590bd7d32b59;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=61b295011936780382499de3c3e2101457d9e1b6;hpb=752bd6197b82c59d196b26a62edba81f16be2604;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 61b2950..7463187 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,23 +1,41 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.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
 {
@@ -31,7 +49,7 @@ public interface AlignViewportI
   /**
    * calculate the height for visible annotation, revalidating bounds where
    * necessary ABSTRACT GUI METHOD
-   *
+   * 
    * @return total height of annotation
    */
   public int calcPanelHeight();
@@ -65,23 +83,28 @@ 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
    * 
@@ -90,24 +113,28 @@ 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);
@@ -118,13 +145,49 @@ public interface AlignViewportI
           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
+   * 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);
+
+
 }