From a0bd24f90375fc1d4be619bf65746a912dfcfc89 Mon Sep 17 00:00:00 2001 From: James Procter Date: Wed, 6 Sep 2023 12:39:44 +0100 Subject: [PATCH] JAL-629 javadoc on new setMapping variant for structureselectionmanager --- .../structure/StructureSelectionManager.java | 25 ++++++++++++++++++++ 1 file changed, 25 insertions(+) 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>, 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, -- 1.7.10.2