/**
* group members
*/
- private List<SequenceI> sequences = new ArrayList<>();
+ private List<SequenceI> sequences;
/**
* representative sequence for this group (if any)
private int startRes = 0;
/**
- * end column (base 0)
+ * end column (base 0)
*/
private int endRes = 0;
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
-
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
}
}
+ /**
+ * Constructor that copies the given list of sequences
+ *
+ * @param seqs
+ */
+ public SequenceGroup(List<SequenceI> seqs)
+ {
+ this();
+ this.sequences.addAll(seqs);
+ }
+
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
for (int i = 0, ipos = 0; i < inorder.length; i++)
{
SequenceI seq = inorder[i];
- SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+ SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
+ endRes + 1);
if (seqipos != null)
{
seqipos.setDescription(seq.getDescription());
public void setStartRes(int newStart)
{
int before = startRes;
- startRes= Math.max(0,newStart); // sanity check for negative start column positions
- changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
-
-
+ startRes = Math.max(0, newStart); // sanity check for negative start column
+ // positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
}