import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
SecondaryStructureListener, InterfaceVARNASelectionListener,
VamsasSource
{
- private static final byte[] PAIRS = new byte[]
- { '(', ')', '[', ']', '{', '}', '<', '>' };
+ private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+ '}', '<', '>' };
private AppVarnaBinding vab;
String theTitle = sname
+ (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
theTitle = MessageManager.formatMessage("label.varna_params",
- new String[]
- { theTitle });
+ new String[] { theTitle });
setTitle(theTitle);
String gappedTitle = sname + " (with gaps)";
vab.setSelectedIndex(0);
}
-
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ HiddenColumns hidden, SelectionSource source)
{
if (source != ap.av)
{
ShiftList offset = new ShiftList();
int ofstart = -1;
int sleng = seq.getLength();
- char[] seqChars = seq.getSequence();
for (int i = 0; i < sleng; i++)
{
- if (Comparison.isGap(seqChars[i]))
+ if (Comparison.isGap(seq.getCharAt(i)))
{
if (ofstart == -1)
{
vab.setSelectedIndex(selectedIndex);
}
-
/**
* Add a model with associated Varna session file
*
}
}
-
/**
* Replace everything except RNA secondary structure characters with a period
*