From 57d863cc978bfd638da0e21a37b425be6251ce13 Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Mon, 23 May 2011 19:26:01 +0200 Subject: [PATCH] 'Update to Covariaton color scheme' merge; JAL-580 Change-Id: Iaf439847f280e8be7336437a8447f3a439098b09 --- src/jalview/datamodel/AlignmentAnnotation.java | 2 +- src/jalview/io/AlignFile.java | 12 +++++++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index c4268e2..9037008 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -339,7 +339,7 @@ public class AlignmentAnnotation * checks graphMin and graphMax, secondary structure symbols, sets graphType * appropriately, sets null labels to the empty string if appropriate. */ - private void validateRangeAndDisplay() + public void validateRangeAndDisplay() { if (annotations == null) diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 1e1b777..abc7a16 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -127,7 +127,17 @@ public abstract class AlignFile extends FileParse addProperties(al); for (int i = 0; i < annotations.size(); i++) { - al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i)); + // detect if annotations.elementAt(i) rna secondary structure + // if so then do: + /* + * SequenceFeature[] pairArray = + * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i)); + * Rna.HelixMap(pairArray); + */ + AlignmentAnnotation an = (AlignmentAnnotation) annotations + .elementAt(i); + an.validateRangeAndDisplay(); + al.addAnnotation(an); } } -- 1.7.10.2