From a16e1965f87dc25c9d6bc6672fbf3a8ad703357e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 21 Nov 2014 08:54:11 +0000 Subject: [PATCH] JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated from sequence associated structure lines --- src/jalview/gui/PopupMenu.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 1c7be46..36811c7 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -374,10 +374,10 @@ public class PopupMenu extends JPopupMenu .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { - if (aa[i].getRNAStruc() != null) + if (aa[i].isValidStruc() && aa[i].sequenceRef == null) { final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label; + final String structureLine = aa[i].label + " (alignment)"; menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( "label.2d_rna_structure_line", new String[] @@ -414,7 +414,7 @@ public class PopupMenu extends JPopupMenu AlignmentAnnotation seqAnno[] = seq.getAnnotation(); for (int i = 0; i < seqAnno.length; i++) { - if (seqAnno[i].getRNAStruc() != null) + if (seqAnno[i].isValidStruc()) { final String rnastruc = seqAnno[i].getRNAStruc(); -- 1.7.10.2