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python-biopython  1.60
Public Member Functions | Public Attributes | Private Member Functions
Bio.GenBank.Record.Reference Class Reference

List of all members.

Public Member Functions

def __init__
def __str__

Public Attributes

 number
 bases
 authors
 consrtm
 title
 journal
 medline_id
 pubmed_id
 remark

Private Member Functions

def _reference_line
def _authors_line
def _consrtm_line
def _title_line
def _journal_line
def _medline_line
def _pubmed_line
def _remark_line

Detailed Description

Hold information from a GenBank reference.

Attributes:
o number - The number of the reference in the listing of references.
o bases - The bases in the sequence the reference refers to.
o authors - String with all of the authors.
o consrtm - Consortium the authors belong to. 
o title - The title of the reference.
o journal - Information about the journal where the reference appeared.
o medline_id - The medline id for the reference.
o pubmed_id - The pubmed_id for the reference.
o remark - Free-form remarks about the reference.

Definition at line 500 of file Record.py.


Constructor & Destructor Documentation

Definition at line 514 of file Record.py.

00514 
00515     def __init__(self):
00516         self.number = ''
00517         self.bases = ''
00518         self.authors = ''
00519         self.consrtm = ''
00520         self.title = ''
00521         self.journal = ''
00522         self.medline_id = ''
00523         self.pubmed_id = ''
00524         self.remark = ''

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Member Function Documentation

Definition at line 525 of file Record.py.

00525 
00526     def __str__(self):
00527         output = self._reference_line()
00528         output += self._authors_line()
00529         output += self._consrtm_line()
00530         output += self._title_line()
00531         output += self._journal_line()
00532         output += self._medline_line()
00533         output += self._pubmed_line()
00534         output += self._remark_line()
00535         
00536         return output

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Output for AUTHORS information.

Definition at line 551 of file Record.py.

00551 
00552     def _authors_line(self):
00553         """Output for AUTHORS information.
00554         """
00555         output = ""
00556         if self.authors:
00557             output += Record.INTERNAL_FORMAT % "AUTHORS"
00558             output += _wrapped_genbank(self.authors, Record.GB_BASE_INDENT)
00559         return output

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Output for CONSRTM information.

Definition at line 560 of file Record.py.

00560 
00561     def _consrtm_line(self):
00562         """Output for CONSRTM information.
00563         """
00564         output = ""
00565         if self.consrtm:
00566             output += Record.INTERNAL_FORMAT % "CONSRTM"
00567             output += _wrapped_genbank(self.consrtm, Record.GB_BASE_INDENT)
00568         return output

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Output for JOURNAL information.

Definition at line 578 of file Record.py.

00578 
00579     def _journal_line(self):
00580         """Output for JOURNAL information.
00581         """
00582         output = ""
00583         if self.journal:
00584             output += Record.INTERNAL_FORMAT % "JOURNAL"
00585             output += _wrapped_genbank(self.journal, Record.GB_BASE_INDENT)
00586         return output

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Output for MEDLINE information.

Definition at line 587 of file Record.py.

00587 
00588     def _medline_line(self):
00589         """Output for MEDLINE information.
00590         """
00591         output = ""
00592         if self.medline_id:
00593             output += Record.INTERNAL_FORMAT % "MEDLINE"
00594             output += self.medline_id + "\n"
00595         return output
    

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Output for PUBMED information.

Definition at line 596 of file Record.py.

00596 
00597     def _pubmed_line(self):
00598         """Output for PUBMED information.
00599         """
00600         output = ""
00601         if self.pubmed_id:
00602             output += Record.OTHER_INTERNAL_FORMAT % "PUBMED"
00603             output += self.pubmed_id + "\n"
00604         return output
    

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Output for REFERENCE lines.

Definition at line 537 of file Record.py.

00537 
00538     def _reference_line(self):
00539         """Output for REFERENCE lines.
00540         """
00541         output = Record.BASE_FORMAT % "REFERENCE"
00542         if self.number:
00543             if self.bases:
00544                 output += "%-3s" % self.number
00545                 output += "%s" % self.bases
00546             else:
00547                 output += "%s" % self.number
00548 
00549         output += "\n"
00550         return output

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Output for REMARK information.

Definition at line 605 of file Record.py.

00605 
00606     def _remark_line(self):
00607         """Output for REMARK information.
00608         """
00609         output = ""
00610         if self.remark:
00611             output += Record.INTERNAL_FORMAT % "REMARK"
00612             output += _wrapped_genbank(self.remark, Record.GB_BASE_INDENT)
        return output

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def Bio.GenBank.Record.Reference._title_line (   self) [private]
Output for TITLE information.

Definition at line 569 of file Record.py.

00569 
00570     def _title_line(self):
00571         """Output for TITLE information.
00572         """
00573         output = ""
00574         if self.title:
00575             output += Record.INTERNAL_FORMAT % "TITLE"
00576             output += _wrapped_genbank(self.title, Record.GB_BASE_INDENT)
00577         return output

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Member Data Documentation

Definition at line 517 of file Record.py.

Definition at line 516 of file Record.py.

Definition at line 518 of file Record.py.

Definition at line 520 of file Record.py.

Definition at line 521 of file Record.py.

Definition at line 515 of file Record.py.

Definition at line 522 of file Record.py.

Definition at line 523 of file Record.py.

Definition at line 519 of file Record.py.


The documentation for this class was generated from the following file: