+
+ public ScalePanel getScalePanel()
+ {
+ return scalePanel;
+ }
+
+ public void setScalePanel(ScalePanel scalePanel)
+ {
+ this.scalePanel = scalePanel;
+ }
+
+ public SeqPanel getSeqPanel()
+ {
+ return seqPanel;
+ }
+
+ public void setSeqPanel(SeqPanel seqPanel)
+ {
+ this.seqPanel = seqPanel;
+ }
+
+ public AnnotationPanel getAnnotationPanel()
+ {
+ return annotationPanel;
+ }
+
+ public void setAnnotationPanel(AnnotationPanel annotationPanel)
+ {
+ this.annotationPanel = annotationPanel;
+ }
+
+ public AnnotationLabels getAlabels()
+ {
+ return alabels;
+ }
+
+ public void setAlabels(AnnotationLabels alabels)
+ {
+ this.alabels = alabels;
+ }
+
+ public IdPanel getIdPanel()
+ {
+ return idPanel;
+ }
+
+ public void setIdPanel(IdPanel idPanel)
+ {
+ this.idPanel = idPanel;
+ }
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param verticalOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ public void scrollToCentre(SearchResults sr, int verticalOffset)
+ {
+ /*
+ * To avoid jumpy vertical scrolling (if some sequences are gapped or not
+ * mapped), we can make the scroll-to location a sequence above the one
+ * actually mapped.
+ */
+ SequenceI mappedTo = sr.getResultSequence(0);
+ List<SequenceI> seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ boolean matched = false;
+ for (SequenceI seq : seqs)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+
+ /*
+ * Scroll to position but centring the target residue.
+ */
+ scrollToPosition(sr, verticalOffset, true, true);
+ }
+
+ /**
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setDontScrollComplement(boolean b)
+ {
+ this.dontScrollComplement = b;
+ }
+
+ protected boolean isDontScrollComplement()
+ {
+ return this.dontScrollComplement;
+ }