/**
* group members
*/
- private List<SequenceI> sequences = new ArrayList<>();
+ private List<SequenceI> sequences;
/**
* representative sequence for this group (if any)
*/
public ResidueShaderI cs;
- // start column (base 0)
- int startRes = 0;
+ /**
+ * start column (base 0)
+ */
+ private int startRes = 0;
- // end column (base 0)
- int endRes = 0;
+ /**
+ * end column (base 0)
+ */
+ private int endRes = 0;
public Color outlineColour = Color.black;
{
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];
-
- seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
- if (seqs[ipos] != null)
+ SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
+ endRes + 1);
+ if (seqipos != null)
{
- seqs[ipos].setDescription(seq.getDescription());
- seqs[ipos].setDBRefs(seq.getDBRefs());
- seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+ seqipos.setDescription(seq.getDescription());
+ seqipos.setDBRefs(seq.getDBRefs());
+ seqipos.setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
- seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+ seqipos.setDatasetSequence(seq.getDatasetSequence());
}
if (seq.getAnnotation() != null)
if (alann != null)
{
boolean found = false;
- for (int pos = 0; pos < alann.length; pos++)
+ for (int pos = 0, np = alann.length; pos < np; pos++)
{
if (alann[pos] == tocopy)
{
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
- seqs[ipos].addAlignmentAnnotation(newannot);
+ seqipos.addAlignmentAnnotation(newannot);
}
}
ipos++;
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
- * @param i
+ * @param newStart
*/
- public void setStartRes(int i)
+ public void setStartRes(int newStart)
{
int before = startRes;
- startRes = i;
+ startRes = Math.max(0, newStart); // sanity check for negative start column
+ // positions
changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
}
/**