Icarus Class: SeqAli

A sequence alignment object. This includes database name, a list of sequences, and any comments.

name     Alignment name. dbName     Database name. cmnt     Comment. seqList Seq     List of sequence objects.

add	Adds a sequence object to a sequence alignment object. seq Seq   Sequence object to be added.
app	Appends a string (possibly only a single character) to a specified range of sequences of the multiple alignment object. Processed as a for loop of 'step' characters, appending to each sequence in turn. str   Additional sequence as a string. off   Offset from the start of 'str'. step 1  Step forward (1 is the next character, 2 skips alternate characters) when processing 'str'. first 1  First sequence number in the alignment to be extended. last   |Last sequence number in the alignment to be extended.
len	Returns the length of an alignment.
make	Must be called to commit all sequence objects within an alignment. SeqAli
mismatch	Returns a string containing a space-delimited list of all mismatches in an alignment.
seq	Returns one of the sequences in an alignment. seqn   Sequence number in the alignment.
seqName	Returns the name of one sequence in an alignment. seqn   Sequence number in the alignment.
seqgaps	Returns a string containing a space-delimited list of all gaps in one sequence of an alignment. The coordinates are based on the sequence. Initial gaps start at zero, a gap after the first base or residue starts at 1. seqn   Sequence number in the alignment. align   If not zero, report alignment coordinates
seqlen	Returns the length of one sequence in an alignment. seqn   Sequence number in the alignment.
seqnogap	Returns one of the sequences in an alignment, with gaps removed, as a string. seqn   Sequence number in the alignment.
seqnogaplen	Returns the length of one (ungapped) sequence in an alignment. seqn   Sequence number in the alignment.
seqtype	Returns the type of one sequence in an alignment seqn   Sequence number in the alignment.
size	Returns the number of sequences in an alignment.
str	Represents a sequence alignment in one of various formats. format fasta  Name of a defined sequence output format Supported formats are: EMBL, swissprot, fasta, pir (these print just a block of sequences in these formats) msf, clustal, color, jalview and alignscroll. useStream n  y n Specifies whether the method should print to a stream already opened.