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Drawing phylogenies

Drawing phylogenies. We've seen several tree data structures but we still can't draw a tree  In the tree drawing exercise we write a drawtree function for the Node class:. Drawing other trees. Can we reuse this phylogeny drawtree method with other trees?

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Drawing phylogenies

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  1. Drawing phylogenies We've seen several tree data structures but we still can't draw a tree  In the tree drawing exercise we write a drawtree function for the Node class:

  2. Drawing other trees Can we reuse this phylogeny drawtree method with other trees? • drawtree needs to know child nodes and name of node No problem: A node in any tree has some sons (or none) and a name. Node specifics for drawtree: • uses method get_sons (returns list of child nodes) • used method get_name (returns string) Problem: Corresponding methods in other trees may have different names

  3. Can't use drawtree directly We want: General tree drawing tool that can draw any tree if given a converter object: an "interpreter" which knows what methods to call for the given kind of node instead of get_sons get_name • For each tree data structure we need to write a converter • Need to modify drawtree slightly to use a converter

  4. A converter class for tree data structure X • Should have two methods, each taking an X node as argument: • one for returning a list of the node's sons • one for returning the name of the node node

  5. New version of drawtree module • All functions that call get_name or get_sons on a node some_node must also take a converter object converteras argument • All occurrences of some_node.get_name() and some_node.get_sons() are replaced with converter.get_name( some_node ) and converter.get_sons( some_node )

  6. Example: converter for XML DOM trees A DOM tree consists of nodes representing tags in the XML data xml_draw.py (part 1) drawtree doesn’t knowhow to get to the sons and the name of a DOM tree node, but this XML converter tells it how

  7. Drawing XML DOM trees Import modified drawtree module xml_draw.py (part 2) Parse XML file, obtain DOM tree Please draw this tree, here is how (neat!)

  8. Drawing article2.xml

  9. And now for something completely different os module: Interface to operating system functionality os.linesep The string used to terminate lines on the current platform. This may be a single character, such as '\n' for Unix or '\r' for Mac OS, or multiple characters, for example, '\r\n' for Windows. os.getcwd() Returns a string representing the current directory os.mkdir( path ) Creates a directory with the given name os.listdir( path ) Returns a list of all entries in the given directory path

  10. os.path module: functions on pathnames os.path.split( path ) Split the pathname path into a pair, (head, tail) where tail is the part after the last / and head is everything leading up to that. os.path.dirname( path ) , os.path.basename( path ) Returns the head and tail of path, respectively. os.path.splitext( path ) Split the path into a pair (root, ext) such that root + ext == path, and ext is the extension. os.path.exists( path ) Returns true if the given file or directory exists, false otherwise. os.path.join( path1[, path2[, ...]] ) Joins the paths to form a new path in format valid on current platform: os.path.join( "/users/chili/PBI", "plan.html" ) gives /users/chili/PBI/plan.html

  11. os.walk - recursively traverse directory os.walk( top ) walk() generates the entries in a directory tree, by walking the tree either top down or bottom up. It returns a list of tuples: Each directory in the tree rooted at directory top (including top itself) yields a 3-tuple (dirpath, dirnames, filenames). dirpath is a string, the path to the directory. dirnames is a list of the names of the subdirectories in dirpath (excluding '.' and '..'). filenames is a list of the names of the non-directory files in dirpath. Notes ProgramExamples figures FromCourseNotes

  12. Find all python programs in PBI directories dirwalk.py Traversal is top-down by default: OK to remove a directory from the subdirs list to avoid visiting it

  13. Notes ProgramExamples figures FromCourseNotes /users/chili/PBI/Exercises contains 3 .py files (out of 211 files) /users/chili/PBI/Exercises/Solutions contains 29 .py files (out of 67 files) /users/chili/PBI/ProgramExamples contains 48 .py files (out of 89 files) /users/chili/PBI/ProgramExamples/FromCourseNotes contains 25 .py files (out of 27 files)

  14. Now that we have a drawtree function.. entry names only local: join with root to get full path dirdraw.py

  15. Tadaa!

  16. ..on to the exercises

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