From 3f136acb9684e4f8440522c41b67a81d5577ba38 Mon Sep 17 00:00:00 2001 From: "j.procter@dundee.ac.uk" Date: Fri, 18 Jul 2014 13:33:42 +0100 Subject: [PATCH] JAL-674 futzing with bugs --- src/jalview/ext/jmol/PDBFileWithJmol.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java index 6553e26..009b9e8 100644 --- a/src/jalview/ext/jmol/PDBFileWithJmol.java +++ b/src/jalview/ext/jmol/PDBFileWithJmol.java @@ -157,7 +157,7 @@ public class PDBFileWithJmol extends AlignFile implements { char newseq[] = new char[len]; System.arraycopy(seq, 0, newseq, 0, len); - Annotation asecstr[] = new Annotation[len]; + Annotation asecstr[] = new Annotation[len+firstrnum-1]; for (int p = 0; p < len; p++) { if (secstr[p] >= 'A' && secstr[p] <= 'z') @@ -181,8 +181,13 @@ public class PDBFileWithJmol extends AlignFile implements AlignmentAnnotation ann = new AlignmentAnnotation( "Secondary Structure", "Secondary Structure from PDB File", asecstr); + ann.belowAlignment=true; + ann.visible=true; + ann.autoCalculated=false; ann.setCalcId(getClass().getName()); sq.addAlignmentAnnotation(ann); + ann.adjustForAlignment(); + ann.validateRangeAndDisplay(); annotations.add(ann); } } -- 1.7.10.2