+
+ /**
+ * @param seq
+ * @return true if seq is a member of the group
+ */
+
+ public boolean contains(SequenceI seq1)
+ {
+ return sequences.contains(seq1);
+ }
+
+ /**
+ * @param seq
+ * @param apos
+ * @return true if startRes<=apos and endRes>=apos and seq is in the group
+ */
+ public boolean contains(SequenceI seq, int apos)
+ {
+ return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+ }
+
+ public boolean isShowInformationHistogram()
+ {
+ return showInformationHistogram;
+ }
+
+ public void setShowInformationHistogram(boolean state)
+ {
+ if (showInformationHistogram != state && informationContent != null)
+ {
+ this.showInformationHistogram = state;
+ // recalcConservation(); TODO don't know what to do here next
+ }
+ this.showInformationHistogram = state;
+
+ }
+
+ public boolean isShowHMMSequenceLogo()
+ {
+ // TODO Auto-generated method stub
+ return showHMMSequenceLogo;
+ }
+
+ public void setshowHMMSequenceLogo(boolean state)
+ {
+ showHMMSequenceLogo = state;
+
+ }
+
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ // TODO Auto-generated method stub
+ return normaliseHMMSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+