this.sequence = new ext.vamsas.Sequence();\r
this.sequence.setId(msf[0].getName());\r
this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));\r
- jalview.io.MSFfile mwrite = new jalview.io.MSFfile();\r
+ jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
this.msa = new ext.vamsas.Msfalignment();\r
msa.setMsf(mwrite.print(msf));\r
}\r