static final String CUTOFF_EVALUE = "label.evalue";
- static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+ static final String REPORTING_SEQ_EVALUE_KEY = "label.reporting_seq_evalue";
- static final String DOM_EVALUE_KEY = "label.dom_evalue";
+ static final String REPORTING_DOM_EVALUE_KEY = "label.reporting_dom_evalue";
- static final String SEQ_SCORE_KEY = "label.seq_score";
+ static final String REPORTING_SEQ_SCORE_KEY = "label.reporting_seq_score";
- static final String DOM_SCORE_KEY = "label.dom_score";
+ static final String REPORTING_DOM_SCORE_KEY = "label.reporting_dom_score";
+
+ static final String INCLUSION_SEQ_EVALUE_KEY = "label.inclusion_seq_evalue";
+
+ static final String INCLUSION_DOM_EVALUE_KEY = "label.inclusion_dom_evalue";
+
+ static final String INCLUSION_SEQ_SCORE_KEY = "label.inclusion_seq_score";
+
+ static final String INCLUSION_DOM_SCORE_KEY = "label.inclusion_dom_score";
static final String ARG_TRIM = "--trim";
+ static final String INCLUSION_THRESHOLD_KEY = "label.inclusion_threshold";
+
/**
* Constructor
*
}
/**
- * Answers the HMM profile for the profile sequence the user selected (default
- * is just the first HMM sequence in the alignment)
+ * Answers the query sequence the user selected (default is just the first
+ * sequence in the alignment)
*
* @return
*/