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

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

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 ofget_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

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

Example: converter for XML DOM trees

- pretty simple, huh?

Recall: a DOM tree consists of nodes representing tags in the XML data

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

Drawing article2.xml

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

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

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

Calculate size of all files in PBI directoriesdi

rwal

k.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

/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

Now that we have a drawtree function..di

rdra

w.p

y

15

Tadaa!

+---Solutions +---------Exercises+ | +-----Project | +------------Slides+------Images---PBI+ +--------------Mail | +----------NoAccess | +---ExamplePrograms