Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview...

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 389d9cf..cec61f4 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -23,6 +23,7 @@ package jalview.api;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -107,9 +108,9 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  Hashtable[] getComplementConsensusHash();
+  Hashtable<String, Object>[] getComplementConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  Hashtable<String, Object>[] getRnaStructureConsensusHash();
 
   boolean isIgnoreGapsConsensus();
 
@@ -177,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setComplementConsensusHash(Hashtable[] hconsensus);
+  void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
 
   /**
    * 
@@ -191,13 +192,20 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hStrucConsensus
    */
-  void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+  void setRnaStructureConsensusHash(
+          Hashtable<String, Object>[] hStrucConsensus);
 
   /**
    * 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).
    * 
+   * BH Note: It is critical that any call to
+   * AlignViewportI.setGlobalColourScheme is followed closely, if not
+   * immediately, by a call to AlignPanel.repaint(true, true) so that the
+   * overview is updated. When that happens, the sequence overview color caches
+   * are cleared.
+   * 
    * @param cs
    */
   void setGlobalColourScheme(ColourSchemeI cs);
@@ -487,9 +495,18 @@ public interface AlignViewportI extends ViewStyleI
   @Override
   void setProteinFontAsCdna(boolean b);
 
-  public abstract TreeModel getCurrentTree();
+  TreeModel getCurrentTree();
+
+  void setCurrentTree(TreeModel tree);
 
-  public abstract void setCurrentTree(TreeModel tree);
+  /**
+   * Answers a data bean containing data for export as configured by the
+   * supplied options
+   * 
+   * @param options
+   * @return
+   */
+  AlignmentExportData getAlignExportData(AlignExportSettingsI options);
 
   /**
    * @param update