From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 6 Sep 2023 11:39:44 +0000 (+0100)
Subject: JAL-629 javadoc on new setMapping variant for structureselectionmanager
X-Git-Tag: Release_2_11_4_0~191
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a0bd24f90375fc1d4be619bf65746a912dfcfc89;p=jalview.git

JAL-629 javadoc on new setMapping variant for structureselectionmanager
---

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 8968742..9bd247a 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -357,6 +357,31 @@ public class StructureSelectionManager
             pdbFile, sourceType, tft, paeFilename, true);
   }
 
+
+  /**
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol). Either constructs a mapping
+   * using NW alignment or derives one from any available SIFTS mapping data.
+   * 
+   * @param forStructureView
+   *          when true, record the mapping for use in mouseOvers
+   * 
+   * @param sequenceArray
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChainIds
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+   *          - this should be List<List<String>>, empty lists indicate no
+   *          predefined mappings
+   * @param pdbFile
+   *          - structure data resource
+   * @param sourceType
+   *          - how to resolve data from resource
+   * @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 setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile, DataSourceType sourceType, TFType tft,