JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 56d25d5..d15c5fb 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;
@@ -108,9 +109,9 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  Hashtable[] getComplementConsensusHash();
+  Hashtable<String, Object>[] getComplementConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  Hashtable<String, Object>[] getRnaStructureConsensusHash();
 
   boolean isIgnoreGapsConsensus();
 
@@ -178,7 +179,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setComplementConsensusHash(Hashtable[] hconsensus);
+  void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
 
   /**
    * 
@@ -192,7 +193,8 @@ 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
@@ -498,9 +500,18 @@ public interface AlignViewportI extends ViewStyleI
   @Override
   void setProteinFontAsCdna(boolean b);
 
-  public abstract TreeModel getCurrentTree();
+  TreeModel getCurrentTree();
 
-  public abstract void setCurrentTree(TreeModel tree);
+  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
@@ -535,9 +546,9 @@ public interface AlignViewportI extends ViewStyleI
    * regions of the alignment
    * 
    * @param selectedRegionOnly
-   *                             if true, and the view has a selection region,
-   *                             then only the intersection of visible columns
-   *                             with the selection region is returned
+   *          if true, and the view has a selection region, then only the
+   *          intersection of visible columns with the selection region is
+   *          returned
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);