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

Diff of /FigKernelPackages/FIGO.pm

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

revision 1.15, Sun Mar 4 18:49:52 2007 UTC revision 1.16, Sun Mar 11 00:21:50 2007 UTC
# Line 1256  Line 1256 
1256    
1257  Numerical value.  Numerical value.
1258    
1259  =items RETURNS:  =item RETURNS:
1260    
1261  The smaller of the two numerical values C<$x> and C<$y>.  The smaller of the two numerical values C<$x> and C<$y>.
1262    
# Line 1273  Line 1273 
1273    
1274  =head3 covers  =head3 covers
1275    
1276    (Question: Should this function be considered "PRIVATE" ???)
1277    
1278    USAGE:
1279        C<< if (&covers(\@hits, $len, $diff, $must_shift)) { #...Do stuff } >>
1280    
1281    Returns boolean C<TRUE> if a set of BLAST HSPs "cover" more than 90%
1282    of the database sequence(?).
1283    
1284  =cut  =cut
1285    
1286  sub covers {  sub covers {
# Line 1292  Line 1300 
1300      return (($hsp1->[0] % 3) != ($hsp2->[0] % 3));      return (($hsp1->[0] % 3) != ($hsp2->[0] % 3));
1301  }  }
1302    
1303    
1304    
1305  =head3 merge  =head3 merge
1306    
1307    Merge two HSPs unless their overlap or separation is too large.
1308    
1309    RETURNS: Merged boundaries if merger succeeds, and C<undef> if merger fails.
1310    
1311  =cut  =cut
1312    
1313  sub merge {  sub merge {
# Line 1308  Line 1322 
1322    
1323  =head3 sims  =head3 sims
1324    
1325    =over 4
1326    
1327    =item FUNCTION:
1328    
1329    Returns precomputed "Sim.pm" objects from the SEED.
1330    
1331    =item USAGE:
1332    
1333    C<< my @sims = $pegO->sims( -all, -cutoff => 1.0e-10); >>
1334    
1335    C<< my @sims = $pegO->sims( -max => 50, -cutoff => 1.0e-10); >>
1336    
1337    =item RETURNS: List of sim objects.
1338    
1339    =back
1340    
1341  =cut  =cut
1342    
1343  use Sim;  use Sim;
# Line 1328  Line 1358 
1358    
1359  =head3 bbhs  =head3 bbhs
1360    
1361    =over 4
1362    
1363    =item FUNCTION:
1364    
1365    Given a PEG-type "FeatureO" object, returns the list of BBHO objects
1366    corresponding to the pre-computed BBHs for that PEG.
1367    
1368    =item USAGE:
1369    
1370    C<< my @bbhs = $pegO->bbhs(); >>
1371    
1372    =item List of BBHO objects.
1373    
1374    =back
1375    
1376  =cut  =cut
1377    
1378  sub bbhs {  sub bbhs {
# Line 1347  Line 1392 
1392    
1393  =head3 display  =head3 display
1394    
1395    Prints info about a "FeatureO" object to STDOUT.
1396    
1397    USAGE:
1398    
1399    C<< $pegO->display(); >>
1400    
1401  =cut  =cut
1402    
1403  sub display {  sub display {
# Line 1365  Line 1416 
1416    
1417  =head1 BBHO  =head1 BBHO
1418    
1419    Methods for accessing "Bidirectiona Best Hits" (BBHs).
1420    
1421  =cut  =cut
1422    
1423    
1424  =head3 new  =head3 new
1425    
1426    Constructor of BBHO objects.
1427    
1428    (NOTE: The "average user" should never need to invoke this method.)
1429    
1430  =cut  =cut
1431    
1432  sub new {  sub new {
# Line 1385  Line 1442 
1442  }  }
1443    
1444    
1445    
1446  =head3 peg1  =head3 peg1
1447    
1448    =over 4
1449    
1450    =item USAGE:
1451    
1452    C<< my $peg1 = $bbh->peg1(); >>
1453    
1454    =item RETURNS:
1455    
1456    A "FeatureO" object corresponding to the "query" sequence
1457    in a BBH pair.
1458    
1459    =back
1460    
1461  =cut  =cut
1462    
1463  sub peg1 {  sub peg1 {
# Line 1398  Line 1469 
1469    
1470  =head3 peg2  =head3 peg2
1471    
1472    =over 4
1473    
1474    =item USAGE:
1475    
1476    C<< my $peg2 = $bbh->peg2(); >>
1477    
1478    =item RETURNS:
1479    
1480    A "FeatureO" object corresponding to the "database" sequence
1481    in a BBH pair.
1482    
1483    =back
1484    
1485  =cut  =cut
1486    
1487  sub peg2 {  sub peg2 {
# Line 1411  Line 1495 
1495    
1496  =head3 psc  =head3 psc
1497    
1498    =over 4
1499    
1500    =item USAGE:
1501    
1502    C<< my $psc = $bbh->psc(); >>
1503    
1504    =item RETURNS:
1505    
1506    The numerical value of the BLAST E-value for the pair.
1507    
1508    =back
1509    
1510  =cut  =cut
1511    
1512  sub psc {  sub psc {
# Line 1423  Line 1519 
1519    
1520  =head3 norm_bitscore  =head3 norm_bitscore
1521    
1522    
1523    =over 4
1524    
1525    =item USAGE:
1526    
1527    C<< my $bsc = $bbh->norm_bitscore(); >>
1528    
1529    =item RETURNS:
1530    
1531    The "BLAST bit-score per aligned character" for the pair.
1532    
1533    =back
1534    
1535  =cut  =cut
1536    
1537  sub norm_bitscore {  sub norm_bitscore {
# Line 1439  Line 1548 
1548    
1549  =head1 AnnotationO  =head1 AnnotationO
1550    
1551    Methods for accessing SEED annotations.
1552    
1553  =cut  =cut
1554    
1555    
# Line 1536  Line 1647 
1647    
1648  =head1 CouplingO  =head1 CouplingO
1649    
1650    Methods for accessing the "Functional coupling scores"
1651    of PEGs in close physical proximity to each other.
1652    
1653  =cut  =cut
1654    
1655    
# Line 1673  Line 1787 
1787    
1788  =head3 usable  =head3 usable
1789    
1790    
1791  =cut  =cut
1792    
1793  sub usable {  sub usable {

Legend:
Removed from v.1.15  
changed lines
  Added in v.1.16

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3