The raw text of the program output
A reference to an array of hashes of scores for each state and the
assigned state. Each element in the array is a residue (indexed from 0).
An array of Bio::SeqFeature::Generic objects where each feature is a
predicted unit of secondary structure. Only stretches of helix/sheet
predictions for longer than 4 residues are defined as helices.
So, in order to add features to an existing Bio::Seq object;
A Bio::Seq::Meta::Array implementing sequence.
This is a Bio::Seq object that can also hold data about each residue in the sequence. In this case, the sequence can be associated with a single array of Domcut prediction scores. e.g.,
Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase.
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Seq::Meta::Array, Bio::WebAgent
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Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
Richard Adams, Richard.Adams@ed.ac.uk,
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Name : result Purpose : To retrieve results of analysis in one of several formats. Usage : $job->result (...) Returns : a result created by running an analysis Args : various - see keysin $RESULT_SPEC.
The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data.
This implementation returns differently processed data depending on argument:
undef Returns the raw ASCII data stream but without HTML tags Bio::SeqFeatureI The argument string defines the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic. Tagnames are score and rank. parsed Array of array references of [score, rank]. all A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence name is Domcut.
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