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JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated...
author
Jim Procter
<jprocter@dundee.ac.uk>
Fri, 21 Nov 2014 08:54:11 +0000
(08:54 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Fri, 21 Nov 2014 08:54:11 +0000
(08:54 +0000)
src/jalview/gui/PopupMenu.java
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diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
1c7be46
..
36811c7
100644
(file)
--- 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++)
{
.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 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[]
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++)
{
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();
{
final String rnastruc = seqAnno[i].getRNAStruc();