From 236b8b01d5df51dd246a2c543968a92d416fc698 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <jlaros@obscured.morspoort.fixedpoint.nl>
Date: Thu, 8 Aug 2013 18:47:45 +0200
Subject: [PATCH] Some more modifications on the classes slides.
---
classes.ipynb | 450 +++++++++++++++++++++++++++++++++-----------------
person.py | 29 ++++
2 files changed, 327 insertions(+), 152 deletions(-)
create mode 100644 person.py
diff --git a/classes.ipynb b/classes.ipynb
index 5ea4e0d..71aaf87 100644
--- a/classes.ipynb
+++ b/classes.ipynb
@@ -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": {}
diff --git a/person.py b/person.py
new file mode 100644
index 0000000..857cc10
--- /dev/null
+++ b/person.py
@@ -0,0 +1,29 @@
+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)
--
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