Fixed malformed POD in Bio::Tree::Tree method descriptions

bioperl · May 8, 2012 · 1453b66 · 1453b66
1 parent 558efd6
commit 1453b66
Showing 1 changed file with 113 additions and 116 deletions.
diff --git a/Bio/Tree/Tree.pm b/Bio/Tree/Tree.pm
@@ -113,20 +113,19 @@ use base qw(Bio::Root::Root Bio::Tree::TreeI Bio::Tree::TreeFunctionsI);
 
 =head2 new
 
-Title   : new
-Usage   : my $obj = Bio::Tree::Tree->new();
-Function: Builds a new Bio::Tree::Tree object 
-Returns : Bio::Tree::Tree
-Args    : -root     => L<Bio::Tree::NodeI> object which is the root
-             OR
-          -node     => L<Bio::Tree::NodeI> object from which the root will be
+ Title   : new
+ Usage   : my $obj = Bio::Tree::Tree->new();
+ Function: Builds a new Bio::Tree::Tree object 
+ Returns : Bio::Tree::Tree
+ Args    : -root     => L<Bio::Tree::NodeI> object which is the root
+              OR
+           -node     => L<Bio::Tree::NodeI> object from which the root will be
                         determined
-
-          -nodelete => boolean, whether or not to try and cleanup all
-                                 the nodes when this this tree goes out
-                                 of scope.
-          -id       => optional tree ID
-          -score    => optional tree score value
+ 
+           -nodelete => boolean, whether or not to try and cleanup all
+                        the nodes when this this tree goes out of scope.
+           -id       => optional tree ID
+           -score    => optional tree score value
 
 =cut
 
@@ -168,13 +167,13 @@ sub new {
 
 =head2 nodelete
 
-Title   : nodelete
-Usage   : $obj->nodelete($newval)
-Function: Get/Set Boolean whether or not to delete the underlying
+ Title   : nodelete
+ Usage   : $obj->nodelete($newval)
+ Function: Get/Set Boolean whether or not to delete the underlying
            nodes when it goes out of scope.  By default this is false
            meaning trees are cleaned up.
-Returns : boolean
-Args    : on set, new boolean value
+ Returns : boolean
+ Args    : on set, new boolean value
 
 =cut
 
@@ -187,11 +186,11 @@ sub nodelete {
 
 =head2 get_nodes
 
-Title   : get_nodes
-Usage   : my @nodes = $tree->get_nodes()
-Function: Return list of Bio::Tree::NodeI objects
-Returns : array of Bio::Tree::NodeI objects
-Args    : (named values) hash with one value 
+ Title   : get_nodes
+ Usage   : my @nodes = $tree->get_nodes()
+ Function: Return list of Bio::Tree::NodeI objects
+ Returns : array of Bio::Tree::NodeI objects
+ Args    : (named values) hash with one value 
            order => 'b|breadth' first order or 'd|depth' first order
            sortby => [optional] "height", "creation", "alpha", "revalpha",
            or coderef to be used to sort the order of children nodes. See L<Bio::Tree::Node> for details
@@ -230,12 +229,12 @@ sub get_nodes {
 
 =head2 get_root_node
 
-Title   : get_root_node
-Usage   : my $node = $tree->get_root_node();
-Function: Get the Top Node in the tree, in this implementation
+ Title   : get_root_node
+ Usage   : my $node = $tree->get_root_node();
+ Function: Get the Top Node in the tree, in this implementation
            Trees only have one top node.
-Returns : Bio::Tree::NodeI object
-Args    : none
+ Returns : Bio::Tree::NodeI object
+ Args    : none
 
 =cut
 
@@ -247,11 +246,11 @@ sub get_root_node {
 
 =head2 set_root_node
 
-Title   : set_root_node
-Usage   : $tree->set_root_node($node)
-Function: Set the Root Node for the Tree
-Returns : Bio::Tree::NodeI
-Args    : Bio::Tree::NodeI
+ Title   : set_root_node
+ Usage   : $tree->set_root_node($node)
+ Function: Set the Root Node for the Tree
+ Returns : Bio::Tree::NodeI
+ Args    : Bio::Tree::NodeI
 
 =cut
 
@@ -271,11 +270,11 @@ sub set_root_node {
 
 =head2 total_branch_length
 
-Title   : total_branch_length
-Usage   : my $size = $tree->total_branch_length
-Function: Returns the sum of the length of all branches
-Returns : real
-Args    : none
+ Title   : total_branch_length
+ Usage   : my $size = $tree->total_branch_length
+ Function: Returns the sum of the length of all branches
+ Returns : real
+ Args    : none
 
 =cut
 
@@ -284,13 +283,13 @@ sub total_branch_length { shift->subtree_length }
 
 =head2 subtree_length
 
-Title   : subtree_length
-Usage   : my $subtree_size = $tree->subtree_length($internal_node)
-Function: Returns the sum of the length of all branches in a subtree
+ Title   : subtree_length
+ Usage   : my $subtree_size = $tree->subtree_length($internal_node)
+ Function: Returns the sum of the length of all branches in a subtree
            under the node. Calculates the size of the whole tree
            without an argument (but only if root node is defined)
-Returns : real or undef
-Args    : Bio::Tree::NodeI object, defaults to the root node
+ Returns : real or undef
+ Args    : Bio::Tree::NodeI object, defaults to the root node
 
 =cut
 
@@ -308,11 +307,11 @@ sub subtree_length {
 
 =head2 id
 
-Title   : id
-Usage   : my $id = $tree->id();
-Function: An id value for the tree
-Returns : scalar
-Args    : [optional] new value to set
+ Title   : id
+ Usage   : my $id = $tree->id();
+ Function: An id value for the tree
+ Returns : scalar
+ Args    : [optional] new value to set
 
 =cut
 
@@ -327,13 +326,13 @@ sub id {
 
 =head2 score
 
-Title   : score
-Usage   : $obj->score($newval)
-Function: Sets the associated score with this tree
+ Title   : score
+ Usage   : $obj->score($newval)
+ Function: Sets the associated score with this tree
            This is a generic slot which is probably best used 
            for log likelihood or other overall tree score
-Returns : value of score
-Args    : newvalue (optional)
+ Returns : value of score
+ Args    : newvalue (optional)
 
 =cut
 
@@ -350,35 +349,33 @@ sub score {
 
 =head2 height
 
-Title   : height
-Usage   : my $height = $tree->height
-Function: Gets the height of tree - this LOG_2($number_nodes)
+ Title   : height
+ Usage   : my $height = $tree->height
+ Function: Gets the height of tree - this LOG_2($number_nodes)
            WARNING: this is only true for strict binary trees.  The TreeIO
            system is capable of building non-binary trees, for which this
            method will currently return an incorrect value!!
-Returns : integer
-Args    : none
+ Returns : integer
+ Args    : none
 
 =head2 number_nodes
 
-Title   : number_nodes
-Usage   : my $size = $tree->number_nodes
-Function: Returns the number of nodes in the tree
-Returns : integer
-Args    : none
-
-=cut
+ Title   : number_nodes
+ Usage   : my $size = $tree->number_nodes
+ Function: Returns the number of nodes in the tree
+ Returns : integer
+ Args    : none
 
 =head2 as_text
 
-Title   : as_text
-Usage   : my $tree_as_string = $tree->as_text($format)
-Function: Returns the tree as a string representation in the 
+ Title   : as_text
+ Usage   : my $tree_as_string = $tree->as_text($format)
+ Function: Returns the tree as a string representation in the 
            desired format (currently 'newick', 'nhx', or 
-           'tabtree')
-Returns : scalar string
-Args    : format type as specified by Bio::TreeIO
-Note    : This method loads the Bio::TreeIO::$format module
+          'tabtree')
+ Returns : scalar string
+ Args    : format type as specified by Bio::TreeIO
+ Note    : This method loads the Bio::TreeIO::$format module
            on the fly, and commandeers the _write_tree_Helper
            routine therein to create the tree string. 
 
@@ -411,13 +408,13 @@ These methods associate tag/value pairs with a Tree
 
 =head2 set_tag_value
 
-Title   : set_tag_value
-Usage   : $tree->set_tag_value($tag,$value)
+ Title   : set_tag_value
+ Usage   : $tree->set_tag_value($tag,$value)
            $tree->set_tag_value($tag,@values)
-Function: Sets a tag value(s) to a tree. Replaces old values.
-Returns : number of values stored for this tag
-Args    : $tag   - tag name
-          $value - value to store for the tag
+ Function: Sets a tag value(s) to a tree. Replaces old values.
+ Returns : number of values stored for this tag
+ Args    : $tag   - tag name
+           $value - value to store for the tag
 
 =cut
 
@@ -434,12 +431,12 @@ sub set_tag_value {
 
 =head2 add_tag_value
 
-Title   : add_tag_value
-Usage   : $tree->add_tag_value($tag,$value)
-Function: Adds a tag value to a tree 
-Returns : number of values stored for this tag
-Args    : $tag   - tag name
-          $value - value to store for the tag
+ Title   : add_tag_value
+ Usage   : $tree->add_tag_value($tag,$value)
+ Function: Adds a tag value to a tree 
+ Returns : number of values stored for this tag
+ Args    : $tag   - tag name
+           $value - value to store for the tag
 
 =cut
 
@@ -455,11 +452,11 @@ sub add_tag_value {
 
 =head2 remove_tag
 
-Title   : remove_tag
-Usage   : $tree->remove_tag($tag)
-Function: Remove the tag and all values for this tag
-Returns : boolean representing success (0 if tag does not exist)
-Args    : $tag - tagname to remove
+ Title   : remove_tag
+ Usage   : $tree->remove_tag($tag)
+ Function: Remove the tag and all values for this tag
+ Returns : boolean representing success (0 if tag does not exist)
+ Args    : $tag - tagname to remove
 
 =cut
 
@@ -476,11 +473,11 @@ sub remove_tag {
 
 =head2 remove_all_tags
 
-Title   : remove_all_tags
-Usage   : $tree->remove_all_tags()
-Function: Removes all tags 
-Returns : None
-Args    : None
+ Title   : remove_all_tags
+ Usage   : $tree->remove_all_tags()
+ Function: Removes all tags 
+ Returns : None
+ Args    : None
 
 =cut
 
@@ -493,11 +490,11 @@ sub remove_all_tags {
 
 =head2 get_all_tags
 
-Title   : get_all_tags
-Usage   : my @tags = $tree->get_all_tags()
-Function: Gets all the tag names for this Tree
-Returns : Array of tagnames
-Args    : None
+ Title   : get_all_tags
+ Usage   : my @tags = $tree->get_all_tags()
+ Function: Gets all the tag names for this Tree
+ Returns : Array of tagnames
+ Args    : None
 
 =cut
 
@@ -510,11 +507,11 @@ sub get_all_tags {
 
 =head2 get_tag_values
 
-Title   : get_tag_values
-Usage   : my @values = $tree->get_tag_values($tag)
-Function: Gets the values for given tag ($tag)
-Returns : Array of values or empty list if tag does not exist
-Args    : $tag - tag name
+ Title   : get_tag_values
+ Usage   : my @values = $tree->get_tag_values($tag)
+ Function: Gets the values for given tag ($tag)
+ Returns : Array of values or empty list if tag does not exist
+ Args    : $tag - tag name
 
 =cut
 
@@ -527,11 +524,11 @@ sub get_tag_values {
 
 =head2 has_tag
 
-Title   : has_tag
-Usage   : $tree->has_tag($tag)
-Function: Boolean test if tag exists in the Tree
-Returns : Boolean
-Args    : $tag - tagname
+ Title   : has_tag
+ Usage   : $tree->has_tag($tag)
+ Function: Boolean test if tag exists in the Tree
+ Returns : Boolean
+ Args    : $tag - tagname
 
 =cut
 
@@ -545,13 +542,13 @@ sub has_tag {
 
 =head2 clone
 
-Title   : clone
-Alias   : _clone
-Usage   : $tree_copy = $tree->clone();
-          $subtree_copy = $tree->clone($internal_node);
-Function: Safe tree clone that doesn't segfault
-Returns : Bio::Tree::Tree object
-Args    : [optional] $start_node, Bio::Tree::Node object
+ Title   : clone
+ Alias   : _clone
+ Usage   : $tree_copy = $tree->clone();
+           $subtree_copy = $tree->clone($internal_node);
+ Function: Safe tree clone that doesn't segfault
+ Returns : Bio::Tree::Tree object
+ Args    : [optional] $start_node, Bio::Tree::Node object
 
 =cut