From aafcc446eb4b421b7c6362afa7afa7c6f6db8b87 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 9 Nov 2015 07:01:14 +0000 Subject: [PATCH] JAL-1950 magic keys for different parts of the JSON object --- src/jalview/ws/ebi/HmmerJSONProcessor.java | 30 ++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/src/jalview/ws/ebi/HmmerJSONProcessor.java b/src/jalview/ws/ebi/HmmerJSONProcessor.java index 611f99e..4d30b3b 100644 --- a/src/jalview/ws/ebi/HmmerJSONProcessor.java +++ b/src/jalview/ws/ebi/HmmerJSONProcessor.java @@ -77,6 +77,36 @@ public class HmmerJSONProcessor } } + // encodings for JSON keys + /** + * score becomes sequence associated AlignmentAnnotation + */ + private String[] score = { "aliId", "ali_IdCount", "bitscore", "ievalue", + "aliSim", "aliSimCount", "aliL", "aliSim", "ievalue", "cevalue" }; + + /** + * attrib becomes numeric or binary attribute for sequence with respect to + * this hmmsearch run + */ + private String[] attrib = { "bias", "oasc", "is_included", "is_reported" }; + + /** + * name of the hmmsearch query + */ + private String[] label = { "alihmmname" // (query label?)}, + }; + + /** + * integer attributes for each + */ + private String[] ipos = { "alihmmfrom", "alihmmto" }, pos_l = { + "alimline", "alimodel", "alirfline" }; + + /** + * positional quantitative annotation encoded as strings. + */ + private String[] pos_nscore = { "alippline" }; + // // mapping of keys to types of property on sequence // -- 1.7.10.2