+ /**\r
+ * get the consensus sequence as displayed under the PID consensus annotation row.\r
+ * @return consensus sequence as a new sequence object\r
+ */\r
+ /**\r
+ * get the consensus sequence as displayed under the PID consensus annotation row.\r
+ * @return consensus sequence as a new sequence object\r
+ */\r
+ public SequenceI getConsensusSeq() {\r
+ if (consensus==null)\r
+ updateConsensus();\r
+ if (consensus==null)\r
+ return null;\r
+ StringBuffer seqs=new StringBuffer();\r
+ for (int i=0; i<consensus.annotations.length; i++) {\r
+ if (consensus.annotations[i]!=null) {\r
+ if (consensus.annotations[i].description.charAt(0) == '[')\r
+ seqs.append(consensus.annotations[i].description.charAt(1));\r
+ else\r
+ seqs.append(consensus.annotations[i].displayCharacter);\r
+ }\r
+ }\r
+ SequenceI sq = new Sequence("Consensus", seqs.toString());\r
+ sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));\r
+ return sq;\r
+ }\r