X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=64c1547904427d0fea146dcf47eb1b0440eb964d;hb=33b66c03f2b63cc80b6d7e697c02530209041990;hp=563f0e7a4983fecff5afb3ab0176d5ab93a2c672;hpb=a06dd69fae641b3f5a8f202b439796df8469abb6;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 563f0e7..64c1547 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -388,6 +388,9 @@ public class StructureSelectionManager
    * @param IProgressIndicator
    *          reference to UI component that maintains a progress bar for the
    *          mapping operation
+   * @param tft - specify how to interpret the temperature factor column in the atom data
+   * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
+   * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray 
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile computeMapping(boolean forStructureView,