import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
{
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[]
@Override
public void actionPerformed(ActionEvent e)
{
- // System.out.println("1:"+structureLine);
- System.out.println("1:sname" + seq.getName());
- System.out.println("2:seq" + seq);
-
- // System.out.println("3:"+seq.getSequenceAsString());
- System.out.println("3:strucseq" + rnastruc);
- // System.out.println("4:struc"+seq.getRNA());
- System.out.println("5:name" + seq.getName());
- System.out.println("6:ap" + ap);
+ // // System.out.println("1:"+structureLine);
+ // System.out.println("1:sname" + seq.getName());
+ // System.out.println("2:seq" + seq);
+ //
+ // // System.out.println("3:"+seq.getSequenceAsString());
+ // System.out.println("3:strucseq" + rnastruc);
+ // // System.out.println("4:struc"+seq.getRNA());
+ // System.out.println("5:name" + seq.getName());
+ // System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
// new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
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();
true,
true,
false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ (ap.getSeqPanel().seqCanvas.fr != null) ? ap.getSeqPanel().seqCanvas.fr.minmax
: null);
contents.append("</p>");
}
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);
}
}
System.arraycopy(features, 0, tfeatures, 0, rsize);
features = tfeatures;
seqs = rseqs;
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- EditCommand.REPLACE, dialog.getName().replace(' ',
+ Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());