- if (colourScheme instanceof UserColourScheme)
- {
- residueShading = new ResidueShader(
- UserDefinedColours.loadDefaultColours());
- residueShading.setThreshold(0, isIgnoreGapsConsensus());
- }
-
- if (residueShading != null)
- {
- residueShading.setConsensus(hconsensus);
- }
- }
- }
-
- /**
- * get the consensus sequence as displayed under the PID consensus annotation
- * row.
- *
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
- {
- if (consensus == null)