From 6684899d56d5bfb61faf814560010d7cb7b8bd95 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 4 May 2017 11:37:19 +0100 Subject: [PATCH] fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label or 'isRNA' RNA secondary structure annotation flag --- src/jalview/io/StockholmFile.java | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 2061f29..3b0dab4 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -978,15 +978,19 @@ public class StockholmFile extends AlignFile { for (int j = 0; j < alAnot.length; j++) { - if (ds.getSequenceFeatures() != null) + + String key = type2id(alAnot[j].label); + boolean isrna = alAnot[j].isValidStruc(); + + if (isrna) { - feature = ds.getSequenceFeatures()[0].type; + // hardwire to secondary structure if there is RNA secondary + // structure on the annotation + key = "SS"; } - // ?bug - feature may still have previous loop value - String key = type2id(feature); - if (key == null) { + continue; } @@ -994,7 +998,6 @@ public class StockholmFile extends AlignFile out.append(new Format("%-" + maxid + "s").form("#=GR " + printId(s[i], jvSuffix) + " " + key + " ")); ann = alAnot[j].annotations; - boolean isrna = alAnot[j].isValidStruc(); String seq = ""; for (int k = 0; k < ann.length; k++) { -- 1.7.10.2