[Bio] / FigKernelPackages / FIGO.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/FIGO.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.23, Mon May 7 00:43:26 2007 UTC revision 1.24, Tue Sep 25 08:47:33 2007 UTC
# Line 35  Line 35 
35  (Likewise, in principle one might like to attach an "annotation"  (Likewise, in principle one might like to attach an "annotation"
36  to any type of object  to any type of object
37    
38  Four of the modules dealing with "genomes" have a reasonable clear  The four modules dealing with "genomes" have a reasonable clear
39  "implied heirarchy:"  "implied heirarchy:"
40    
41  =over 4  =over 4
# Line 52  Line 52 
52  We have chosen to in many cases sidestep the entire issue of inheritance  We have chosen to in many cases sidestep the entire issue of inheritance
53  via an I<ad hoc> mechanism:  via an I<ad hoc> mechanism:
54  If a "child" object needs access to its "ancestors'" methods,  If a "child" object needs access to its "ancestors'" methods,
55  we pass it references to its "ancestors" using subroutine arguments.  we will explicitly pass it references to its "ancestors,"
56    as subroutine arguments.
57  This is admittedly ugly, clumsy, and potentially error-prone ---  This is admittedly ugly, clumsy, and potentially error-prone ---
58  but it has the advantage that, unlike multiple inheritance,  but it has the advantage that, unlike multiple inheritance,
59  we understand how to do it...  we understand how to do it...
# Line 716  Line 717 
717    
718  =head3 new  =head3 new
719    
720  Constructor of "FeatureO" objects  Constructor of new "FeatureO" objects
721    
722  =over 4  =over 4
723    
# Line 1024  Line 1025 
1025    
1026  =item RETURNS:  =item RETURNS:
1027    
1028  A list of L<CouplingO> objects describing the evidence for functional coupling  A list of "CouplingO" objects describing the evidence for functional coupling
1029  between this feature and other nearby features.  between this feature and other nearby features.
1030    
1031  =back  =back
# Line 1059  Line 1060 
1060    
1061  =item RETURNS:  =item RETURNS:
1062    
1063  A list of L<AnnotationO> objects allowing access to the annotations for this feature.  A list of "AnnotationO" objects allowing access to the annotations for this feature.
1064    
1065  =back  =back
1066    
# Line 1085  Line 1086 
1086    
1087  =item RETURNS:  =item RETURNS:
1088    
1089  A list of L<SubsystemO> objects allowing access to the subsystems  A list of "SubsystemO" objects allowing access to the subsystems
1090  that this feature particupates in.  that this feature particupates in.
1091    
1092  =back  =back
# Line 1284  Line 1285 
1285    
1286  C<< my $max = $feature->max($x, $y); >>  C<< my $max = $feature->max($x, $y); >>
1287    
1288  =item C<$x>  =item C<$x> and  C<$y>
1289    
1290  Numerical value.  Numerical values.
1291    
1292  =item C<$y>  =item RETURNS:
   
 Numerical value.  
   
 =items RETURNS:  
1293    
1294  The larger of the two numerical values C<$x> and C<$y>.  The larger of the two numerical values C<$x> and C<$y>.
1295    
# Line 1317  Line 1314 
1314    
1315  C<< my $min = $feature->min($x, $y); >>  C<< my $min = $feature->min($x, $y); >>
1316    
1317  =item C<$x>  =item C<$x> and C<$y>
1318    
1319  Numerical value.  Numerical values.
   
 =item C<$y>  
   
 Numerical value.  
1320    
1321  =item RETURNS:  =item RETURNS:
1322    
# Line 1449  Line 1442 
1442    
1443  C<< my @bbhs = $pegO->bbhs(); >>  C<< my @bbhs = $pegO->bbhs(); >>
1444    
1445  =item List of BBHO objects.  =item RETURNS:
1446    
1447    List of BBHO objects.
1448    
1449  =back  =back
1450    
# Line 1470  Line 1465 
1465                                                  },'BBHO') } @bbhs;                                                  },'BBHO') } @bbhs;
1466  }  }
1467    
1468    
1469  =head3 display  =head3 display
1470    
1471    =over 4
1472    
1473    =item FUNCTION:
1474    
1475  Prints info about a "FeatureO" object to STDOUT.  Prints info about a "FeatureO" object to STDOUT.
1476    
1477  USAGE:  =item USAGE:
1478    
1479  C<< $pegO->display(); >>  C<< $pegO->display(); >>
1480    
1481    =item RETURNS;
1482    
1483    (void)
1484    
1485    =back
1486    
1487  =cut  =cut
1488    
1489  sub display {  sub display {
# Line 1636  Line 1642 
1642    
1643  =head3 new  =head3 new
1644    
1645    =over 4
1646    
1647    =item FUNCTION:
1648    
1649    Cronstruct a new "AnnotationO" object
1650    
1651    =item USAGE:
1652    
1653    C<< my $annotO = AnnotationO->new( $fid, $timestamp, $who, $text); >>
1654    
1655    =item C<$fid>
1656    
1657    A feature identifier.
1658    
1659    =item C<$timestamp>
1660    
1661    The C<UN*X> timestamp one wishes to associate with the annotation.
1662    
1663    =item C<$who>
1664    
1665    The annotator's user-name.
1666    
1667    =item C<$text>
1668    
1669    The textual content of the annotation.
1670    
1671    =item RETURNS:
1672    
1673    An "AnnotationO" object.
1674    
1675    =back
1676    
1677  =cut  =cut
1678    
1679  sub new {  sub new {
# Line 1653  Line 1691 
1691    
1692  =head3 fid  =head3 fid
1693    
1694    =over 4
1695    
1696    =item FUNCTION:
1697    
1698    Extract the feature-ID that was annotated.
1699    
1700    =item USAGE:
1701    
1702    C<< my $fid = $annotO->fid(); >>
1703    
1704    =item RETURNS;
1705    
1706    The feature-ID as a string.
1707    
1708    =back
1709    
1710  =cut  =cut
1711    
1712  sub fid {  sub fid {
# Line 1665  Line 1719 
1719    
1720  =head3 timestamp  =head3 timestamp
1721    
1722    =over 4
1723    
1724    =item FUNCTION:
1725    
1726    Extract the C<UN*X> timestamp of the annotation.
1727    
1728    =item USAGE:
1729    
1730    C<< my $fid = $annotO->timestamp(); >>
1731    
1732    =item RETURNS;
1733    
1734    The timestamp as a string.
1735    
1736    =back
1737    
1738  =cut  =cut
1739    
1740  sub timestamp {  sub timestamp {
# Line 1684  Line 1754 
1754    
1755  =head3 made_by  =head3 made_by
1756    
1757    =over 4
1758    
1759    =item FUNCTION:
1760    
1761    Extract the annotator's user-name.
1762    
1763    =item USAGE:
1764    
1765    C<< my $fid = $annotO->made_by(); >>
1766    
1767    =item RETURNS;
1768    
1769    The username of the annotator, as a string.
1770    
1771    =back
1772    
1773  =cut  =cut
1774    
1775  sub made_by {  sub made_by {
# Line 1698  Line 1784 
1784    
1785  =head3 text  =head3 text
1786    
1787    =over 4
1788    
1789    =item FUNCTION:
1790    
1791    Extract the text of the annotation.
1792    
1793    =item USGAE:
1794    
1795    C<< my $text = $annotO->text(); >>
1796    
1797    =item RETURNS:
1798    
1799    The text of the annotation, as a string.
1800    
1801    =back
1802    
1803  =cut  =cut
1804    
1805  sub text {  sub text {
# Line 1710  Line 1812 
1812    
1813  =head3 display  =head3 display
1814    
1815    =over 4
1816    
1817    =item FUNCTION:
1818    
1819    Print the contents of an "AnnotationO" object to B<STDOUT>
1820    in human-readable form.
1821    
1822    =item USAGE:
1823    
1824    C<< my $annotO->display(); >>
1825    
1826    =item RETURNS:
1827    
1828    (void)
1829    
1830    =back
1831    
1832  =cut  =cut
1833    
1834  sub display {  sub display {
# Line 1736  Line 1855 
1855    
1856  =head3 new  =head3 new
1857    
1858    =over 4
1859    
1860    =item FUNCTION:
1861    
1862    Construct a new "CouplingO" object
1863    encapsulating the "functional coupling" score
1864    between a pair of features in some genome.
1865    
1866    =item USAGE:
1867    
1868    C<< $couplingO = CouplingO->new($figO, $fid1, $fid2, $sc); >>
1869    
1870    =item C<$figO>
1871    
1872    Parent "FIGO" object.
1873    
1874    =item C<$fid1> and C<$fid2>
1875    
1876    A pair of feature-IDs.
1877    
1878    =item C<$sc>
1879    
1880    A functional-coupling score
1881    
1882    =item RETURNS:
1883    
1884    A "CouplingO" object.
1885    
1886    =back
1887    
1888  =cut  =cut
1889    
1890  sub new {  sub new {
# Line 1755  Line 1904 
1904    
1905  =head3 peg1  =head3 peg1
1906    
1907    =over 4
1908    
1909    =item FUNCTION:
1910    
1911    Returns a "FeatureO" object corresponding to the first FID in a coupled pair.
1912    
1913    =item USAGE:
1914    
1915    C<< my $peg1 = $couplingO->peg1(); >>
1916    
1917    =item RETURNS:
1918    
1919    A "FeatureO" object.
1920    
1921    =back
1922    
1923  =cut  =cut
1924    
1925  sub peg1 {  sub peg1 {
# Line 1766  Line 1931 
1931    
1932    
1933    
1934  =head3 peg1  =head3 peg2
1935    
1936    =over 4
1937    
1938    =item FUNCTION:
1939    
1940    Returns a "FeatureO" object corresponding to the second FID in a coupled pair.
1941    
1942    =item USAGE:
1943    
1944    C<< my $peg2 = $couplingO->peg2(); >>
1945    
1946    =item RETURNS:
1947    
1948    A "FeatureO" object.
1949    
1950    =back
1951    
1952  =cut  =cut
1953    
# Line 1781  Line 1962 
1962    
1963  =head3 sc  =head3 sc
1964    
1965    =over 4
1966    
1967    =item FUNCTION:
1968    
1969    Extracts the "functional coupling" score from a "CouplingO" object.
1970    
1971    =item USAGE:
1972    
1973    C<< my $sc = $couplingO->sc(); >>
1974    
1975    =item RETURNS:
1976    
1977    A scalar score.
1978    
1979    =back
1980    
1981  =cut  =cut
1982    
1983  sub sc {  sub sc {
# Line 1793  Line 1990 
1990    
1991  =head3 evidence  =head3 evidence
1992    
1993    =over 4
1994    
1995    =item FUNCTION:
1996    
1997    Fetch the evidence for a "functional coupling" between two close PEGs,
1998    in the form of a list of objects describing the "Pairs of Close Homologs" (PCHs)
1999    supporting the existence of a functional coupling between the two close PEGs.
2000    
2001    =item USAGE:
2002    
2003    C<< my $evidence = $couplingO->evidence(); >>
2004    
2005    =item RETURNS
2006    
2007    List of pairs of "FeatureO" objects.
2008    
2009    =back
2010    
2011  =cut  =cut
2012    
2013  sub evidence {  sub evidence {
# Line 1815  Line 2030 
2030    
2031  =head3 display  =head3 display
2032    
2033    =over 4
2034    
2035    =item FUNCTION:
2036    
2037    Print the contents of a "CouplingO" object to B<STDOUT> in human-readable form.
2038    
2039    =item USAGE:
2040    
2041    C<< $couplingO->display(); >>
2042    
2043    =item RETURNS:
2044    
2045    (Void)
2046    
2047    =back
2048    
2049  =cut  =cut
2050    
2051  sub display {  sub display {

Legend:
Removed from v.1.23  
changed lines
  Added in v.1.24

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3