broad.core.multiplealignment.MAFIO Member List

This is the complete list of members for broad.core.multiplealignment.MAFIO, including all inherited members.

createUnloadedAlignment(String fileName)	broad.core.multiplealignment.MAFIO
destroyFileHandle()	broad.core.multiplealignment.MAFIO
getPreferredFileExtension()	broad.core.multiplealignment.MAFIO
load(List< String > sequencesToLoad, int start, int end)	broad.core.multiplealignment.MAFIO
load(String fileName)	broad.core.multiplealignment.MAFIO
load(String fileName, List< String > sequencesToLoad)	broad.core.multiplealignment.MAFIO
load(InputStream in)	broad.core.multiplealignment.MAFIO
load(String fileName, List< String > sequencesToLoad, int start, int end)	broad.core.multiplealignment.MAFIO
load(InputStream in, List< String > sequencesToLoad)	broad.core.multiplealignment.MAFIO
MAFIO(String alignmentFile, boolean keepFileHandle)	broad.core.multiplealignment.MAFIO
MAFIO()	broad.core.multiplealignment.MAFIO
write(BufferedWriter bw, MultipleAlignment ma)	broad.core.multiplealignment.MAFIO
write(BufferedWriter bw, MultipleAlignment ma, List< String > sequenceOrder)	broad.core.multiplealignment.MAFIO