Merge branch 'releases/Release_2_10_4_Branch'

[jalview.git] / src / jalview / api / structures / JalviewStructureDisplayI.java

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index a27cec6..8f778f7 100644 (file)
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -72,12 +72,32 @@ public interface JalviewStructureDisplayI
    */
   boolean hasMapping();
 
-  // construction method - move to another interface ?
+  /**
+   * Checks if the PDB file is already loaded in this viewer, if so just adds
+   * mappings as necessary and answers true, else answers false. This supports
+   * the use case of adding additional chains of the same structure to a viewer.
+   * 
+   * @param seq
+   * @param chains
+   * @param apanel
+   * @param pdbId
+   * @return
+   */
   boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
           AlignmentViewPanel apanel, String pdbId);
 
-  // construction method - move to another interface ?
-  boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+  /**
+   * Adds one or more chains (sequences) of a PDB structure to this structure
+   * viewer
+   * 
+   * @param pdbentry
+   * @param seq
+   * @param chains
+   * @param apanel
+   * @param pdbId
+   * @return
+   */
+  void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
           String[] chains, AlignmentViewPanel apanel, String pdbId);
 
   /**
@@ -85,8 +105,24 @@ public interface JalviewStructureDisplayI
    */
   void updateTitleAndMenus();
 
+  /**
+   * Answers true if the viewer should attempt to align any added structures,
+   * else false
+   * 
+   * @return
+   */
   boolean isAlignAddedStructures();
 
+  /**
+   * Sets the flag for whether added structures should be aligned
+   * 
+   * @param alignAdded
+   */
   void setAlignAddedStructures(boolean alignAdded);
 
+  /**
+   * Raise the panel to the top of the stack...
+   */
+  void raiseViewer();
+
 }