1. 1 Drawing phylogenies We've seen several tree data structures but we still can't draw a tree  In today's first exercise we write a drawtree module for the Phylogeny class:

2. 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. Phylogeny-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. 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. 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

5. 5 New version of drawtree module All functions that take a node some_node as argument should also take a converter object converter 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. 6 Example: converter for XML DOM trees - pretty simple, huh? Recall: a DOM tree consists of nodes representing tags in the XML data

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

8. 8 Drawing article2.xml

9. 9 And now for something completely different os module: Interface to operating system functionality os.linesep The string used to separate (or, rather, 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. 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.basename( path ), os.path.dirname( 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 valid format. E.g. os.path.join( "/users/chili/PBI", "plan.html" )

11. 11 os.walk( top ) walk() generates the file names in a directory tree, by walking the tree either top down or bottom up. For each directory in the tree rooted at directory top (including top itself), it 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. os.walk - recursively traverse directory Programs_from_ book symbolic link not included

12. 12 Calculate size of all files in PBI directories dirwalk.py No path info in dirs and files lists; join with root Traversal is top-down by default: OK to remove a directory from the dirs list to avoid visiting it

13. 13 /users/chili/PBI/ consumes 155940 bytes in 45 non-directory files /users/chili/PBI/Exercises consumes 1289251 bytes in 148 non- directory files /users/chili/PBI/Exercises/Solutions consumes 1095594 bytes in 109 non-directory files /users/chili/PBI/Slides consumes 4974264 bytes in 22 non-directory files /users/chili/PBI/Slides/Images consumes 1173961 bytes in 70 non- directory files /users/chili/PBI/Mail consumes 6625 bytes in 7 non-directory files /users/chili/PBI/NoAccess consumes 0 bytes in 0 non-directory files /users/chili/PBI/ExamplePrograms consumes 770219 bytes in 160 non- directory files Note: Project not visited

14. 14 Now that we have a drawtree function.. dirdraw.py

15. 15 Tadaa! +---Solutions +---------Exercises+ | +-----Project | +------------Slides+------Images ---PBI+ +--------------Mail | +----------NoAccess | +---ExamplePrograms