From e3ff86bf4b17ec3cf58bfe8fdb152bfc431765b3 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 7 Oct 2013 17:02:45 +0100
Subject: [PATCH] JAL-1385 expose core view model methods in interface

---
 src/jalview/api/AlignViewportI.java          |   23 +++++++++++++++++++++++
 src/jalview/viewmodel/AlignmentViewport.java |    7 +++++++
 2 files changed, 30 insertions(+)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f42293d..15e5f1d 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -17,13 +17,17 @@
  */
 package jalview.api;
 
+import java.awt.Color;
 import java.util.Hashtable;
 import java.util.Map;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+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;
 
@@ -155,4 +159,23 @@ public interface AlignViewportI
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
 
+
+  SequenceGroup getSelectionGroup();
+
+  SequenceI[] getSequenceSelection();
+
+
+  CigarArray getViewAsCigars(boolean selectedRegionOnly);
+
+  AlignmentView getAlignmentView(boolean selectedOnly);
+
+  AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+  String[] getViewAsString(boolean selectedRegionOnly);
+
+  void setSelectionGroup(SequenceGroup sg);
+
+  char getGapCharacter();
+
+
 }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d65486d..dc352f4 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -594,6 +594,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return null or the currently selected sequence region
    */
+  @Override
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -606,6 +607,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          - group holding references to sequences in this alignment view
    * 
    */
+  @Override
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
@@ -1054,6 +1056,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return array of references to sequence objects
    */
+  @Override
   public SequenceI[] getSequenceSelection()
   {
     SequenceI[] sequences = null;
@@ -1076,6 +1079,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
@@ -1092,6 +1096,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          boolean true to just return the selected view
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1110,6 +1115,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          is true)
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
@@ -1125,6 +1131,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
     String[] selection = null;
-- 
1.7.10.2