X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fstructures%2FJalviewStructureDisplayI.java;h=abb23f89c22d0c58c8c48c8040ff5472d99fcd69;hb=61aa0f698c7494efa3e6408ce54fac4e8400053c;hp=a27cec6ea3502e7c2afc3a20eab800f102e6e5e8;hpb=e06ef51ba3dd8cdae7632d71db162ff416b88256;p=jalview.git

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index a27cec6..abb23f8 100644
--- 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 toFront();
+
 }