Families and Family Groups

Gene sequences are divided into groups in order to build more reliable gene trees. In Softparsmap this kind of group is referred to as a family. Families are also divided into groups and they are called family groups. A family is represented by the class Family and a family group by the interface FamilyGroup. Instances of this interface are responsible of providing everything needed to perform a task on a family, including the families. In order to create your own family group, extend AbstractFamilyGroup and the abstract family group tag found in def.xml. For more information see section Create a Tag Instance.

FamilyGroupTreesInFiles retrieves gene trees from files, one tree and family per file. There are four different tags allowed under this tag in order to fill this family group with families. The pair <include_directory>, <exclude_directory> are used to include or exclude files from a family group. The attribute tree_files_directory is used in these two tags to specify the directory to include or exclude. Last two tags are <include_group>, <exclude_group> which are used to include and exclude other groups. These two tags have following attributes.

• family_group - defines the did attribute of the family group to include or exclude

• family_numbers - can be 'all' to include or exclude all families from the given family group, or comma separated family numbers on those families to include or exclude from the given family group

• min_family_number and max_family_number - give an upper and a lower limit on those families to include or exclude from the given family group

• marker_family_number - is the marker for the file number. It is used to find the number in the file name.

• template_tree_file_name - is the template for all files that will be included or excluded from given directories

     
  <family_group did="my_super" eid="trees_in_files"
                data_source="my_data_source"
                />
      
  <family_group did="all" eid="my_super">
    <include_directory tree_files_directory="trees/dir_a"/>
    <include_directory tree_files_directory="trees/dir_b"/>
  </family_group>
      
  <family_group did="not_yet_valid" eid="my_super">
    <include_group eid="super" family_group="all"
                   family_numbers="123, 456, 789"/>
  </family_group>
		       
  <family_group did="small_trees" eid="my_super">
    <include_group eid="super" family_group="all"
                   max_number_leaves="20"/>
  </family_group>

  <family_group did="the_rest" eid="my_super">
    <include_group eid="super" family_group="all"/>
    <exclude_group eid="super" family_group="not_yet_valid"/>
    <exclude_group eid="super" family_group="small_trees"/>
  </family_group>