+ // search for alignment sequences to update coordinate frame for\r
+ for (int alsq = 0; alsq<alseqs.length; alsq++)\r
+ {\r
+ if (alseqs[alsq].getDatasetSequence()==sequence)\r
+ {\r
+ String ngAlsq = AlignSeq.extractGaps("-. ",\r
+ alseqs[alsq].getSequenceAsString()).toUpperCase();\r
+ int oldstrt = alseqs[alsq].getStart();\r
+ alseqs[alsq].setStart(sequence.getSequenceAsString().toUpperCase().indexOf(ngAlsq)+sequence.getStart());\r
+ if (oldstrt != alseqs[alsq].getStart()) {\r
+ alseqs[alsq].setEnd(ngAlsq.length()+alseqs[alsq].getStart()-1);\r
+ }\r
+ }\r
+ }\r
+ // TODO: search for all other references to this dataset sequence, and update start/end\r
+ // TODO: update all AlCodonMappings which involve this alignment sequence (e.g. Q30167 cdna translation from exon2 product (vamsas demo)\r