In file blastConfig.h:

class blastConfig

This class stores program settings, constants & static functions

Public Fields

[more]int NumDbs
number of databases (10)
[more]int pdb
index for PDB database (0)
[more]int gb
index for GenBank (GB) database
[more]int gi
index for GenBank (GI) database
[more]int sp
index for SWISS-PROT database
[more]int pir
index for PIR database
[more]int emb
index for EMBL database
[more]int dbj
index for DBJ database
[more]int prf
index for PRF database
[more]int ref
index for REF database
[more]int none
index for unknown database (9)
[more]int NumCols
number of columns in data entry
[more]string strFlag
start of data section in query result (see .cc for definition)
[more]string endFlag
end of data section in query result (see .cc for definition)
[more]int MaxXEntries
max. number of non-pdb entries to keep
[more]int lengthOffset
"Length =" with 10 spaces in front is the end of entries

Public Methods

[more]string getName ( const string& code )
returns db name or NULL
[more]int getNameIdx ( const string& name )
returns index of db name or -1
[more]string getCode ( const string& name )
returns db code or NULL
[more]int getCodeIdx ( const string& code )
returns index of db name or -1
[more]char* getBlastHost () const
returns URL of the blast server
[more]char* getBlastProg () const
returns CGI script name
[more]unsigned getBlastPort () const
returns port number on the blast server
[more]char* getCommentFile () const
returns name of comment file
[more]char* getQueryFile () const
returns path to temp. file where query result is saved
[more]bool isQuiet () const
returns true if blast was started with "quiet" ("-q") flag
[more]void setQuiet ( bool q )
sets "quiet" flag
[more]bool isSeqDet () const
returns true if blast was started with "seq.details" ("-seqdet") flag
[more]void setSeqDet ( bool q )
sets "sequence details" flag
[more]DataValueNode::ValType findNeededQuoteStyle ( const string& searchme )
returns quote style constant for the string
[more] blastConfig ()
constructor


Documentation

This class stores program settings, constants & static functions.

Settings that are loaded from blastrc file:
url (blasthost), port number, CGI script name and comment file name.
Settings that are read from command line:
"quiet" flag (-q), "sequence details" flag (-seqdet).
Other: temp. file name to store query result, map of database names and codes.

BlastConfig provides Java-style accessor methods: getXXX/setXXX/isXXX.

oint NumDbs
number of databases (10)

oint pdb
index for PDB database (0)

oint gb
index for GenBank (GB) database

oint gi
index for GenBank (GI) database

oint sp
index for SWISS-PROT database

oint pir
index for PIR database

oint emb
index for EMBL database

oint dbj
index for DBJ database

oint prf
index for PRF database

oint ref
index for REF database

oint none
index for unknown database (9)

oint NumCols
number of columns in data entry

ostring strFlag
start of data section in query result (see .cc for definition)

ostring endFlag
end of data section in query result (see .cc for definition)

oint MaxXEntries
max. number of non-pdb entries to keep

oint lengthOffset
"Length =" with 10 spaces in front is the end of entries

ostring getName( const string& code )
returns db name or NULL.
It is overloaded to accept either string (code) or int (index) parameter (pdb..none).
See Also:
pdb

oint getNameIdx( const string& name )
returns index of db name or -1.
See Also:
pdb

ostring getCode( const string& name )
returns db code or NULL.
It is overloaded to accept either string (name) or int (index) parameter (pdb..none).
See Also:
pdb

oint getCodeIdx( const string& code )
returns index of db name or -1.
See Also:
pdb

ochar* getBlastHost() const
returns URL of the blast server

ochar* getBlastProg() const
returns CGI script name

ounsigned getBlastPort() const
returns port number on the blast server

ochar* getCommentFile() const
returns name of comment file

ochar* getQueryFile() const
returns path to temp. file where query result is saved

obool isQuiet() const
returns true if blast was started with "quiet" ("-q") flag

ovoid setQuiet( bool q )
sets "quiet" flag

obool isSeqDet() const
returns true if blast was started with "seq.details" ("-seqdet") flag

ovoid setSeqDet( bool q )
sets "sequence details" flag

oDataValueNode::ValType findNeededQuoteStyle( const string& searchme )
returns quote style constant for the string.
Quote styles are defined in starlib (ast.h), they're just an enum of none, single quote, double quote or semicolon (for multi-line entries).

It is static so we don't need an object to call it.

Returns:
quote style.
Parameters:
searchme - string to check.

o blastConfig()
constructor.
Set blast host, program etc. to compile-time defaults,
try opening blastrc file and read new values from it,
see if TMPDIR envvar is set,
and set temporary file to $TMPDIR/blast_out,
otherwise set it to P_tmpdir/blast_out (P_tmpdir is defined in stdio.h)


This class has no child classes.

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