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POD fixes

svn path=/bioperl-pedigree/trunk/; revision=12052
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1 parent 2709278 commit 9fc21ba2e486831651c94c5311edcec42acf02c5 @heikkil heikkil committed Jul 7, 2001
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6 Bio/Pedigree.pm
@@ -18,7 +18,6 @@ which there are results.
=head1 SYNOPSIS
-{
use Bio::Pedigree;
use Bio::Pedigree::PedIO;
# get a Bio::Pedigree object somehow (PedIO system typically)
@@ -27,7 +26,7 @@ which there are results.
print "date is ", $pedigree->date, "\n";
print "comment is ", $pedigree->comment ,"\n";
-
+
print "markers are :\n";
foreach my $markername ( $pedigree->each_Marker('name') ) {
print "$markername\n";
@@ -38,7 +37,7 @@ which there are results.
print $person->personid, " ", $person->gender, "\n";
}
}
-}
+
=head1 DESCRIPTION
@@ -399,6 +398,7 @@ sub comment{
Args : Type of warning to use 'warnOnError', 'failOnError', or
do not report warnings.
See also L<Bio::Pedigree::Group>
+
=cut
sub calculate_all_relationships {
View
4 Bio/Pedigree/Draw/GD.pm
@@ -80,6 +80,7 @@ $DEFAULTTYPE = 'png';
Args : -fh => filehandle to write to
-type => format to use 'png' or 'gif' are supported by GD
only png depending on your version of GD
+
=cut
sub new {
@@ -223,6 +224,7 @@ sub type{
ending Y point
width of line (in points)
color of line (string)
+
=cut
sub draw_line {
@@ -246,6 +248,7 @@ sub draw_line {
width of line (in points)
color of line (string)
box fill color (string)
+
=cut
sub draw_box {
@@ -274,6 +277,7 @@ sub draw_box {
width of line (in points)
color of line (string)
oval fill color (string)
+
=cut
sub draw_oval {
View
6 Bio/Pedigree/Draw/PedPlot.pm
@@ -15,13 +15,12 @@
Bio::Pedigre::Draw::PedPlot - An object to plot pedigrees
=head1 SYNOPSIS
-{
+
use Bio::Pedigree::Draw::PedPlot;
# get a Bio::Pedigree somehow
my $plotter = new Bio::Pedigree::Draw::PedPlot(-drawingengine => $de);
$plotter->add_group_to_draw($group,$dxmarker);
$plotter->write();
-}
=head1 DESCRIPTION
@@ -106,13 +105,14 @@ sub new {
Usage : $renderer->add_group_to_draw($group,$marker)
Function: Draws a group on a page, can be called multiple times
and will insure that no group overwrites another.
-
+
Data is not final until renderer object is closed
(data is synced out to disk/filestream at that point).
Returns : none
Args : group to draw
marker which will determine affection status (if not defined
affection status will not be reported)
+
=cut
sub add_group_to_draw {
View
2 Bio/Pedigree/Draw/PedRenderI.pm
@@ -77,7 +77,7 @@ sub _abstractDeath {
Usage : $renderer->add_group_to_draw($group,$marker)
Function: Draws a group on a page, can be called multiple times
and will insure that no group overwrites another.
-
+
Data is not final until renderer object is closed
(data is synced out to disk/filestream at that point).
Returns : none
View
3 Bio/Pedigree/Group.pm
@@ -108,6 +108,7 @@ BEGIN {
-type => 'FAMILY' or 'GROUP' - 'FAMILY' by default
-people => (optional) initial people arrayref to initialize
object with
+
=cut
sub new {
@@ -231,6 +232,7 @@ sub num_of_people{
Args : (optional) 'id' will cause method to only return a list of ids
for the people stored within the group rather than the
Bio::Pedigree::PersonI objects
+
=cut
sub each_Person{
@@ -305,6 +307,7 @@ sub center{
Args : integer (optional) integer to set the group id to
Note : We try and be explicit about what type of id we have here
to avoid future confusion with databaseids.
+
=cut
sub groupid {
View
5 Bio/Pedigree/GroupI.pm
@@ -17,9 +17,7 @@ Bio::Pedigree::GroupI - DESCRIPTION of Object
=head1 SYNOPSIS
# get a Group object somehow
-
print "group is ", $group->center, " ", $group->groupid, "\n";
-
=head1 DESCRIPTION
@@ -86,6 +84,7 @@ sub _abstractDeath {
id.
Throws : Exception if a person with the id $person->id already exists
unless $overwrite is true
+
=cut
sub add_Person{
@@ -138,6 +137,7 @@ sub num_of_people{
Args : (optional) 'id' will cause method to only return a list of ids
for the people stored within the group rather than the
Bio::Pedigree::PersonI objects
+
=cut
sub each_Person{
@@ -268,6 +268,7 @@ sub type {
'failOnError' - to throw and exception when an error is found
passing anything else (or no argument) will cause method to
update errors quietly
+
=cut
sub calculate_relationships {
View
4 Bio/Pedigree/Marker/variation.pm
@@ -73,7 +73,7 @@ use Bio::PrimarySeq;
-fwdflank => $seqfwd,
-revflank => $seqrev,
);
-
+
Function: build a Bio::Pedigree::Variation object
Returns : Bio::Pedigree::Variation
Args : All fields are required unless specified as optional
@@ -91,6 +91,7 @@ use Bio::PrimarySeq;
-revflank => Bio::PrimarySeqI object or DNA string for the
reverse flanking sequence of the marker
(optional)
+
=cut
sub _initialize {
@@ -292,6 +293,7 @@ sub known_alleles {
Returns : none
Args : name => Allele name
freq => (optional) allele frequency
+
=cut
sub add_allele{
View
2 Bio/Pedigree/PedIO.pm
@@ -79,7 +79,7 @@ BEGIN { $DEFAULTDIGITLEN = 4; }
Usage : do not use this module directly it is an interface
Function: initializes a PedIO object, constructor for shared
data initialization.
-
+
IO is initialized in the read/write methods since
a single stream can really only support one pedigree
at a time.
View
2 Bio/Pedigree/PedIO/lapis.pm
@@ -303,7 +303,7 @@ sub read_pedigree {
-pedfile / -pedfh => pedigree output location
-datfile / -datfh => (if needed) marker data output location
(datfile not needed for lapis format)
-
+
=cut
sub write_pedigree {
View
2 Bio/Pedigree/PersonI.pm
@@ -19,7 +19,6 @@ Bio::Pedigree::PersonI - Interface defining the methods for a Person in a Pedigr
# get a PersonI object somehow
print "id is ", $person->personid, " father id is ", $person->fatherid,
" motherid is ", $person->motherid, "\n";
-
=head1 DESCRIPTION
@@ -161,6 +160,7 @@ sub displayid{
boolean if existing results should be overwritten
Throws : Exception if a result with the name $result->name already exists
unless $overwrite is true
+
=cut
sub add_Result{
View
1 Bio/Pedigree/Result.pm
@@ -78,6 +78,7 @@ use Bio::Root::RootI;
Args : All fields are required unless specified as optional
-name => unique name for this variation.
-alleles => (optional) array ref of alleles to initialize object
+
=cut
sub new {

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