import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
-import jalview.analysis.AnnotationSorter;
-import jalview.analysis.AnnotationSorter.SortOrder;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
- for (int i = 0; i < aa.length; i++)
+ for (int i = 0; aa != null && 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[]
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();
copyAnn.visible = true;
}
}
- // TODO: save annotation sort order on AlignViewport
- // do sorting from AlignmentPanel.updateAnnotation()
- new AnnotationSorter(this.ap.getAlignment()).sort(this.ap
- .getAlignment().getAlignmentAnnotation(),
- SortOrder.SEQUENCE_AND_TYPE);
refresh();
}
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true);
+ jalview.io.AppletFormatAdapter.FILE, sequence, true,
+ Desktop.instance);
}
}