A.6. Calculated Attributes
Calculated attributes are datatype-specific attributes that are assigned values after the data definition has been processed, for example, once a sequence has been read in from file. Their value is calculated automatically during ACD file processing. This allows data definitions to refer to attributes whose value depends on the input data. The available calculated attributes are summarised in the table and described in detail below.
Values of calculated attributes for ACD data definitions are retrieved by an operation from within the ACD file. This is done using the $ ("get value of") syntax before a pair of parentheses enclosing the parameter and attribute name as follows:
$(ParameterName.CalculatedAttributeName)
A.6.1. "Simple" ACD Datatypes
A.6.1.1.1. length: integer
The length of the string.
A.6.2. "Input" ACD Datatypes
A.6.2.1.1.1. begin: integer
Start of the first sequence used.
A.6.2.1.1.2. end: integer
End of the first sequence used.
A.6.2.1.1.3. length: integer
Total length of the first sequence.
A.6.2.1.1.4. protein: Y/N
Boolean, indicates if sequence is protein.
A.6.2.1.1.5. nucleic: Y/N
Boolean, indicates if sequence is DNA.
A.6.2.1.1.6. name: string
The name/ID/accession of the sequence.
A.6.2.1.2.1. begin: integer
The beginning of the selection of the sequence.
A.6.2.1.2.2. end: integer
The end of the selection of the sequence.
A.6.2.1.2.3. length: integer
The maximum length of the sequence set.
A.6.2.1.2.4. protein: Y/N
Boolean, indicates if sequence set is protein.
A.6.2.1.2.5. nucleic: Y/N
Boolean, indicates if sequence set is DNA.
A.6.2.1.2.6. name: string
The name of the sequence set.
A.6.2.1.2.7. totweight: float
Float, total sequence weight for a set.
A.6.2.1.2.8. count: integer
Integer, number of sequences in the set.
A.6.2.1.3.1. begin: integer
The beginning of the selection of the sequence.
A.6.2.1.3.2. end: integer
The end of the selection of the sequence.
A.6.2.1.3.3. length: integer
The maximum length of the sequence set.
A.6.2.1.3.4. protein: Y/N
Boolean, indicates if sequence set is protein.
A.6.2.1.3.5. nucleic: Y/N
Boolean, indicates if sequence set is DNA.
A.6.2.1.3.6. name: string
The name of the sequence set.
A.6.2.1.3.7. totweight: float
Float, total sequence weight for each set.
A.6.2.1.3.8. count: integer
Integer, number of sequences in each set.
A.6.2.1.3.9. multicount: integer
Integer, number of sets of sequences.
A.6.2.1.4.1. begin: integer
Start of the sequence used.
A.6.2.1.4.2. end: integer
End of the sequence used.
A.6.2.1.4.3. length: integer
Total length of the sequence.
A.6.2.1.4.4. protein: Y/N
Boolean, indicates if sequence is protein.
A.6.2.1.4.5. nucleic: Y/N
Boolean, indicates if sequence is DNA.
A.6.2.1.4.6. name: string
The name/ID/accession of the sequence.
A.6.2.2. Sequence Features
A.6.2.2.1.1. fbegin: integer
Start of the features to be used.
A.6.2.2.1.2. fend: integer
End of the features to be used.
A.6.2.2.1.3. flength: integer
Total length of sequence (fsize is feature count).
A.6.2.2.1.4. fprotein: Y/N
Feature table is protein.
A.6.2.2.1.5. fnucleic: Y/N
Feature table is nucleotide.
A.6.2.2.1.6. fname: string
The name of the feature table.
A.6.2.2.1.7. fsize: string
Integer, number of features.
A.6.2.3. Other Inputs (not sequences or features)
A.6.2.3.1.1. distancesize: integer
Number of distance rows.
A.6.2.3.1.2. replicates: Y/N
Replicates data found in input.
A.6.2.3.1.3. hasmissing: Y/N
Missing values found (replicates=N).
A.6.2.3.2.1. freqlength: integer
Number of frequency values per set.
A.6.2.3.2.2. freqsize: integer
Number of frequency sets.
A.6.2.3.2.3. freqloci: integer
Number of frequency loci.
A.6.2.3.2.4. freqgenedata: Y/N
Gene frequency data.
A.6.2.3.2.5. freqcontinuous: Y/N
Continuous frequency data.
A.6.2.3.2.6. freqwithin: Y/N
Individual within species frequency data.
A.6.2.3.3.1. propertylength: integer
Number of property values per set.
A.6.2.3.3.2. propertysize: integer
Number of property sets.
A.6.2.3.4.1. length: integer
The length of the regular expression.
A.6.2.3.5.1. treecount: integer
Number of trees.
A.6.2.3.5.2. speciescount: integer
Number of species.
A.6.2.3.5.3. haslengths: Y/N
Branch lengths defined.