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Commit 236b8b01 authored by J.F.J. Laros's avatar J.F.J. Laros
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Some more modifications on the classes slides.

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classes.ipynb
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− 152
View file @ 236b8b01
......@@ -27,6 +27,22 @@
"License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%html\n",
"<style type=\"text/css\">\n",
"/* Remove the vertical scrollbar added by nbconvert. */\n",
".reveal {\n",
" overflow-y: hidden;\n",
"}\n",
"</style>"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
......@@ -52,6 +68,7 @@
"collapsed": false,
"input": [
"from IPython.display import HTML, Image, IFrame\n",
"from person import Person\n",
"%pylab inline"
],
"language": "python",
......@@ -69,7 +86,7 @@
]
}
],
"prompt_number": 128
"prompt_number": 1
},
{
"cell_type": "markdown",
......@@ -79,9 +96,11 @@
}
},
"source": [
"Imagine we are collecting a number of attributes of some persons:\n",
"Keeping track of attributes\n",
"===\n",
"\n",
"Suppose we want to keep track of some properties in a population:\n",
"\n",
"* Eye colour.\n",
"* Hair colour.\n",
"* Weight.\n",
"* Length."
......@@ -95,6 +114,9 @@
}
},
"source": [
"Non-object oriented\n",
"===\n",
"\n",
"Should we use simple lists?"
]
},
......@@ -102,12 +124,11 @@
"cell_type": "code",
"collapsed": false,
"input": [
"eye_colour = ['blue', 'blue', 'grey', 'green', 'brown']\n",
"hair_colour = ['black', 'red', 'white', 'blue', 'red']\n",
"weight = [80, 75, 130, 90, 64]\n",
"length = [180, 174, 230, 161, 149]\n",
"\n",
"eye_colour[3], hair_colour[3], weight[3], length[3]"
"hair_colour[3], weight[3], length[3]"
],
"language": "python",
"metadata": {},
......@@ -115,13 +136,20 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 129,
"prompt_number": 2,
"text": [
"('green', 'blue', 90, 161)"
"('blue', 90, 161)"
]
}
],
"prompt_number": 129
"prompt_number": 2
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Getting all attributes is a bit of a hastle."
]
},
{
"cell_type": "code",
......@@ -135,22 +163,32 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 130,
"prompt_number": 3,
"text": [
"90"
]
}
],
"prompt_number": 130
"prompt_number": 3
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Getting one attribute is easy though."
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "subslide"
}
},
"source": [
"Non-object oriented\n",
"===\n",
"\n",
"Or nested lists?"
]
},
......@@ -158,13 +196,13 @@
"cell_type": "code",
"collapsed": false,
"input": [
"person = [['blue', 'black', 80, 180],\n",
" ['blue', 'red', 75, 174],\n",
" ['grey', 'white', 130, 230],\n",
" ['green', 'blue', 90, 161],\n",
" ['brown', 'red', 64, 149]]\n",
"persons = [['black', 80, 180],\n",
" ['red', 75, 174],\n",
" ['white', 130, 230],\n",
" ['blue', 90, 161],\n",
" ['red', 64, 149]]\n",
"\n",
"person[3]"
"persons[3]"
],
"language": "python",
"metadata": {},
......@@ -172,19 +210,26 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 131,
"prompt_number": 4,
"text": [
"['green', 'blue', 90, 161]"
"['blue', 90, 161]"
]
}
],
"prompt_number": 131
"prompt_number": 4
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now all attributes are nicely grouped."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"person[3][2]"
"persons[3][2]"
],
"language": "python",
"metadata": {},
......@@ -192,22 +237,32 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 132,
"prompt_number": 5,
"text": [
"90"
"161"
]
}
],
"prompt_number": 132
"prompt_number": 5
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Accessing a single attribute is a bit cryptic though."
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "subslide"
}
},
"source": [
"Non-object oriented\n",
"===\n",
"\n",
"Or a list of dictionaries?"
]
},
......@@ -215,13 +270,13 @@
"cell_type": "code",
"collapsed": false,
"input": [
"person = [{'eye_colour': 'blue', 'hair_colour': 'black', 'weight': 80, 'length': 180},\n",
" {'eye_colour': 'blue', 'hair_colour': 'red', 'weight': 75, 'length': 174},\n",
" {'eye_colour': 'grey', 'hair_colour': 'white', 'weight': 130, 'length': 230},\n",
" {'eye_colour': 'green', 'hair_colour': 'blue', 'weight': 90, 'length': 161},\n",
" {'eye_colour': 'brown', 'hair_colour': 'red', 'weight': 64, 'length': 149}]\n",
"persons = [{'hair_colour': 'black', 'weight': 80, 'length': 180},\n",
" {'hair_colour': 'red', 'weight': 75, 'length': 174},\n",
" {'hair_colour': 'white', 'weight': 130, 'length': 230},\n",
" {'hair_colour': 'blue', 'weight': 90, 'length': 161},\n",
" {'hair_colour': 'red', 'weight': 64, 'length': 149}]\n",
"\n",
"person[3]"
"persons[3]"
],
"language": "python",
"metadata": {},
......@@ -229,19 +284,19 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 133,
"prompt_number": 6,
"text": [
"{'eye_colour': 'green', 'hair_colour': 'blue', 'length': 161, 'weight': 90}"
"{'hair_colour': 'blue', 'length': 161, 'weight': 90}"
]
}
],
"prompt_number": 133
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"person[3]['weight']"
"persons[3]['weight']"
],
"language": "python",
"metadata": {},
......@@ -249,13 +304,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 134,
"prompt_number": 7,
"text": [
"90"
]
}
],
"prompt_number": 134
"prompt_number": 7
},
{
"cell_type": "markdown",
......@@ -265,68 +320,22 @@
}
},
"source": [
"Object Oriented Programming\n",
"Classes\n",
"===\n",
"\n",
"A class as a simple container:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"class Person(object):\n",
" weight = 80\n",
" \n",
" def __init__(self, eye_colour='unknown', hair_colour='unknown', weight=0, length=0):\n",
" self.eye_colour = eye_colour\n",
" self.hair_colour = hair_colour\n",
" if weight:\n",
" self.weight = weight\n",
" self.length = length\n",
" \n",
" def __str__(self):\n",
" return \"Eye colour: {0}, Hair colour: {1}, Weight: {2}, Length: {3}\".format(\n",
" self.eye_colour, self.hair_colour, self.weight, self.length)\n",
" \n",
" def __len__(self):\n",
" return self.length\n",
"\n",
" def feed(self, amount=3):\n",
" self.weight += amount\n",
" \n",
" def bleach(self):\n",
" self.hair_colour = 'white'\n",
" \n",
" def _convert_weight(self, multiplier):\n",
" return self.weight * multiplier\n",
" \n",
" def weight_in_pounds(self):\n",
" return self._convert_weight(2.20462)\n",
" \n",
" def weight_in_grams(self):\n",
" return self._convert_weight(1000)"
],
"language": "python",
"metadata": {
"slideshow": {
"slide_type": "skip"
}
},
"outputs": [],
"prompt_number": 135
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "-"
}
},
"source": [
" class Person(object):\n",
" def __init__(self, eye_colour='unknown', hair_colour='unknown', weight=0, length=0):\n",
" self.eye_colour = eye_colour\n",
" def __init__(self, hair_colour='unknown', weight=0, length=0):\n",
" self.hair_colour = hair_colour\n",
" self.weight = weight\n",
" self.length = length"
......@@ -336,7 +345,7 @@
"cell_type": "code",
"collapsed": false,
"input": [
"someone = Person('green', 'blue', 90, 161)\n",
"someone = Person('blue', 90, 161)\n",
"\n",
"someone.weight"
],
......@@ -346,39 +355,57 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 136,
"prompt_number": 8,
"text": [
"90"
]
}
],
"prompt_number": 136
"prompt_number": 8
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "subslide"
}
},
"source": [
"Classes\n",
"===\n",
"\n",
"Makes initialisation a lot easier."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"person = [Person(),\n",
" Person('blue', 'red'),\n",
" Person('grey', 'white', 130, 230),\n",
" Person(weight=90),\n",
" Person(weight=64, length=149)]\n",
"persons = [Person(),\n",
" Person('red'),\n",
" Person('white', 130, 230),\n",
" Person(weight=90),\n",
" Person(weight=64, length=149)]\n",
"\n",
"person[3].weight"
"persons[3].weight"
],
"language": "python",
"metadata": {},
"metadata": {
"slideshow": {
"slide_type": "-"
}
},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 137,
"prompt_number": 9,
"text": [
"90"
]
}
],
"prompt_number": 137
"prompt_number": 9
},
{
"cell_type": "markdown",
......@@ -387,11 +414,23 @@
"slide_type": "slide"
}
},
"source": [
"Methods\n",
"==="
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "-"
}
},
"source": [
" class Person(object):\n",
" ...\n",
" \n",
" def feed(self, amount=3):\n",
" def eat(self, amount=3):\n",
" self.weight += amount\n",
" \n",
" def bleach(self):\n",
......@@ -402,9 +441,9 @@
"cell_type": "code",
"collapsed": false,
"input": [
"person = Person('green', 'blue', 90, 161)\n",
"someone = Person('blue', 90, 161)\n",
"\n",
"person.weight, person.hair_colour"
"someone.weight, someone.hair_colour"
],
"language": "python",
"metadata": {},
......@@ -412,21 +451,21 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 138,
"prompt_number": 10,
"text": [
"(90, 'blue')"
]
}
],
"prompt_number": 138
"prompt_number": 10
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"person.feed()\n",
"person.bleach()\n",
"person.weight, person.hair_colour"
"someone.eat()\n",
"someone.bleach()\n",
"someone.weight, someone.hair_colour"
],
"language": "python",
"metadata": {},
......@@ -434,13 +473,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 139,
"prompt_number": 11,
"text": [
"(93, 'white')"
]
}
],
"prompt_number": 139
"prompt_number": 11
},
{
"cell_type": "markdown",
......@@ -449,6 +488,18 @@
"slide_type": "slide"
}
},
"source": [
"Public and private methods\n",
"==="
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "-"
}
},
"source": [
" class Person(object):\n",
" ...\n",
......@@ -463,11 +514,20 @@
" return self._convert_weight(1000)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Private methods are prefixed with an underscore.\n",
"\n",
"* Note that this is a convention, it is not enforced."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"person.weight_in_pounds(), person.weight_in_grams()"
"someone.weight_in_pounds(), someone.weight_in_grams()"
],
"language": "python",
"metadata": {},
......@@ -475,13 +535,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 140,
"prompt_number": 12,
"text": [
"(205.02965999999998, 93000)"
]
}
],
"prompt_number": 140
"prompt_number": 12
},
{
"cell_type": "markdown",
......@@ -490,23 +550,43 @@
"slide_type": "slide"
}
},
"source": [
"Class variables vs. instance variables\n",
"==="
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "-"
}
},
"source": [
" class Person(object):\n",
" weight = 80\n",
" default_weight = 80\n",
" \n",
" def __init__(self, eye_colour='unknown', hair_colour='unknown', weight=0, length=0):\n",
" self.eye_colour = eye_colour\n",
" def __init__(self, hair_colour='unknown', weight=0, length=0):\n",
" self.hair_colour = hair_colour\n",
" if weight:\n",
" self.weight = weight\n",
" self.weight = weight or self.default_weight\n",
" self.length = length"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Class variables are defined outside the methods.\n",
"\n",
"* It is still refererenced as **self.** inside the methods."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"someone = Person()\n",
"\n",
"someone.weight"
],
"language": "python",
......@@ -515,13 +595,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 142,
"prompt_number": 13,
"text": [
"80"
]
}
],
"prompt_number": 142
"prompt_number": 13
},
{
"cell_type": "code",
......@@ -536,20 +616,21 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 143,
"prompt_number": 14,
"text": [
"79"
]
}
],
"prompt_number": 143
"prompt_number": 14
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"Person.weight = 90\n",
"Person.default_weight = 90\n",
"someone = Person()\n",
"\n",
"someone.weight"
],
"language": "python",
......@@ -558,13 +639,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 144,
"prompt_number": 15,
"text": [
"90"
]
}
],
"prompt_number": 144
"prompt_number": 15
},
{
"cell_type": "markdown",
......@@ -573,24 +654,55 @@
"slide_type": "slide"
}
},
"source": [
"Special methods\n",
"==="
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
" print someone\n",
" <__main__.Person instance at 0x321ebd8>"
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "-"
}
},
"source": [
" class Person(object):\n",
" ...\n",
" \n",
" def __str__(self):\n",
" return \"Eye colour: {0}, Hair colour: {1}, Weight: {2}, Length: {3}\".format(\n",
" self.eye_colour, self.hair_colour, self.weight, self.length)\n",
" return \"Person with hair colour: {0}, weight: {1} and length: {2}\".format(\n",
" self.hair_colour, self.weight, self.length)\n",
" \n",
" def __len__(self):\n",
" return self.length"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Special methods are prefixed and suffixed with double underscores.\n",
"\n",
"* There are methods for adding (**\\_\\_add\\_\\_**), subtracting (**\\_\\_sub\\_\\_**), etc."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print person\n",
"len(person)"
"someone = Person('blue', 90, 161)\n",
"\n",
"print someone\n",
"len(someone)"
],
"language": "python",
"metadata": {},
......@@ -599,19 +711,31 @@
"output_type": "stream",
"stream": "stdout",
"text": [
"Eye colour: green, Hair colour: white, Weight: 93, Length: 161\n"
"Person with hair colour: blue, weight: 90 and length: 161\n"
]
},
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 126,
"prompt_number": 16,
"text": [
"161"
]
}
],
"prompt_number": 126
"prompt_number": 16
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"Class inheritance\n",
"==="
]
},
{
"cell_type": "code",
......@@ -619,23 +743,30 @@
"input": [
"class DutchPerson(Person):\n",
" def __str__(self):\n",
" return \"Oogkleur: {0}, Haarkleur: {1}, Gewicht: {2}, Lengte: {3}\".format(\n",
" self.eye_colour, self.hair_colour, self.weight, self.length)"
" return \"Persoon met haarkleur: {0}, gewicht: {1} en lengte: {2}\".format(\n",
" self.hair_colour, self.weight, self.length)"
],
"language": "python",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "-"
}
},
"outputs": [],
"prompt_number": 127
"prompt_number": 17
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"A subclass can have added functionality, or it can override some functionality."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"sinterklaas = DutchPerson('blue', 'white', 85, 191)\n",
"sinterklaas = DutchPerson('white', 85, 191)\n",
"\n",
"print sinterklaas"
],
......@@ -646,11 +777,23 @@
"output_type": "stream",
"stream": "stdout",
"text": [
"Oogkleur: blue, Haarkleur: white, Gewicht: 85, Lengte: 191\n"
"Persoon met haarkleur: white, gewicht: 85 en lengte: 191\n"
]
}
],
"prompt_number": 86
"prompt_number": 18
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
}
},
"source": [
"An object oriented solution for the Sequencer assignment.\n",
"==="
]
},
{
"cell_type": "code",
......@@ -658,14 +801,14 @@
"input": [
"class Read(object):\n",
" def __init__(self):\n",
" self.read = \"\"\n",
" self.read = []\n",
" self.qual = []\n",
" \n",
" def __str__(self):\n",
" return self.read\n",
" return \"\".join(self.read)\n",
" \n",
" def add(self, base):\n",
" self.read += base[0]\n",
" def append(self, base):\n",
" self.read.append(base[0])\n",
" self.qual.append(base[1])\n",
" \n",
" def quality(self):\n",
......@@ -674,16 +817,18 @@
" def trim(self, score):\n",
" for position in range(len(self.read) - 1, -1, -1):\n",
" if self.qual[position] >= score:\n",
" return self.read[:position]"
" self.read = self.read[:position]\n",
" self.qual = self.qual[:position]\n",
" break"
],
"language": "python",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "-"
}
},
"outputs": [],
"prompt_number": 7
"prompt_number": 19
},
{
"cell_type": "code",
......@@ -697,16 +842,17 @@
"reads = [Read() for _ in range(spots)]\n",
"for tile in run:\n",
" for read_id, base in enumerate(tile):\n",
" reads[read_id].add(base)\n",
" reads[read_id].append(base)\n",
"\n",
"for i in reads:\n",
" print i, i.quality()\n",
" print i.trim(39)"
" i.trim(39)\n",
" print i, i.quality()"
],
"language": "python",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "subslide"
}
},
"outputs": [
......@@ -714,14 +860,14 @@
"output_type": "stream",
"stream": "stdout",
"text": [
"GGTGTGATTCCCGTTCGGTGGGCCGCCTTGGGTCATTGCTCGGTTGAGGAGGGAAGACCT 30\n",
"GGTGTGATTCCCGTTCGGTGGGCCGCCTTGGGTCAT\n",
"GGCTTTAGAATGTCTCCTGCATCTGATGCTATTAAAAGCTATGTTTTTCACATAGTACGG 29\n",
"GGCTTTAGAATGTCTCCTGCATCTGATGCTATTAAAAGCTATGTTTTTCACATAGT\n"
"ATCATTAATTCTAAGTAGTCACACCGGATTAACGATCCCTCTTAGCCAACGCTTTTAGTC 29\n",
"ATCATTAATTCTAAGTAGTCACACCGGATTAACGATCCCTCTTAGCCAACGCTTT 30\n",
"TCCACTAGTGGGAATACTTAGTATTACACGGACATAGTTTACTCCCATTATATGCTAGAA 27\n",
"TCCACTAGTGGGAATACT 36\n"
]
}
],
"prompt_number": 8
"prompt_number": 20
}
],
"metadata": {}
......
person.py 0 → 100644
+ 29
− 0
View file @ 236b8b01
class Person(object):
default_weight = 80
def __init__(self, hair_colour='unknown', weight=0, length=0):
self.hair_colour = hair_colour
self.weight = weight or self.default_weight
self.length = length
def __str__(self):
return "Person with hair colour: {0}, weight: {1} and length: {2}".format(
self.hair_colour, self.weight, self.length)
def __len__(self):
return self.length
def eat(self, amount=3):
self.weight += amount
def bleach(self):
self.hair_colour = 'white'
def _convert_weight(self, multiplier):
return self.weight * multiplier
def weight_in_pounds(self):
return self._convert_weight(2.20462)
def weight_in_grams(self):
return self._convert_weight(1000)
0% or .
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