Clarence Leung clarle

## Standa.cpp
///////////////////////////////////////////////////////////////////////////////
// FILE:          Standa.cpp
// PROJECT:       Micro-Manager
// SUBSYSTEM:     DeviceAdapters
//-----------------------------------------------------------------------------
// DESCRIPTION:   Standa device adapters: 8SMC1-USBhF Microstep Driver
//
// COPYRIGHT:     Leslie Lab, McGill University, Montreal, 2013
//
// LICENSE:       This file is distributed under the BSD license.

## MMCore.h
///////////////////////////////////////////////////////////////////////////////
// FILE:          MMCore.h
// PROJECT:       Micro-Manager
// SUBSYSTEM:     MMCore
//-----------------------------------------------------------------------------
// DESCRIPTION:   The interface to the MM core services.
//
// COPYRIGHT:     University of California, San Francisco, 2006,
//                100X Imaging Inc, www.100ximaging.com, 2008
//                All Rights reserved

## manage.py
import os
from time import sleep
from optparse import OptionParser

# Remember to add the trailing slash!

SERVER_FOLDER = "/home/2010/cleung24/comp512/a3/servercode/"
CLIENT_FOLDER = "/home/2010/cleung24/comp512/a3/clientsrc/"
MIDDLEWARE_PORT = 5678

## consensus.py
import re
import operator
from math import sqrt
from itertools import product

ALPHABET = ["A", "C", "G", "T", "[AC]", "[AG]",
            "[AT]", "[CG]", "[CT]", "[GT]", "[ACGT]"]

NUC_PROBS = {
    "A": 0.25,

## nj.r
library(ape)
m = c(0, 13, 8, 20, 21, 13, 0, 9, 16, 17, 8, 9, 0, 15, 16, 20, 16, 15, 0, 13, 21, 17, 16, 13, 0)
dim(m) = c(5, 5)
colnames(m) = c('A', 'B', 'C', 'D', 'E')
rownames(m) = colnames(m)
d = as.dist(m)
tr = nj(d)
plot(tr, cex=2, tip.color=rainbow(6))
axisPhylo()

## NI100X.cpp
///////////////////////////////////////////////////////////////////////////////
// FILE:          NI100X.cpp
// PROJECT:       100X micro-manager extensions
// SUBSYSTEM:     DeviceAdapters
//-----------------------------------------------------------------------------
// DESCRIPTION:   NI control with multiple devices
//
// AUTHOR:        Nenad Amodaj, January 2010
//
// COPYRIGHT:     100X Imaging Inc, 2010

## forget-the-past.tex
\begin{algorithm}
\caption{Calculates the optimal alignment using ForgetThePast-NW}
\begin{algorithmic}
\Procedure{LinearSpaceAlignment}{$S$, $T$}
\State m = \textbf{length}(S)
\State n = \textbf{length}(T)
\If {$m <= 1$ \textbf{or} $n <= 1$}
\State \textbf{return} NW(S, T) \Comment Use the regular NW algorithm
\Else \Comment Divide and conquer with recursion
\State Middle = \textbf{round}(m/2)

## app.coffee
YUI.add "todo-app", ((Y) ->
  "use strict"

  # Dependencies from MVC namespace.
  TodoList = Y.TodoMVC.TodoList
  TodoView = Y.TodoMVC.TodoView
  TodoApp = undefined

  # -- Main Application --------------
  TodoApp = Y.Base.create("todoApp", Y.App, [],

## js-frameworks.md

      
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                clarle
                / js-frameworks.md
            
            
              Created
              August 19, 2012 16:54
            
              
                Mojito/Derby/Meteor comparison (Public WIP)
              
          
    Next-generation JavaScript frameworks

Web application frameworks have been developing fast in the past few years, and as the technologies that they're built on top of get more advanced, each of these frameworks is able to provide newer features to help developers build more complex applications.  This year, we've seen the release of a new class of application frameworks that takes advantage of JavaScript's ability to be both on the client and the server.  What this allows these frameworks to do is provide both a new level of abstraction by sharing code between client and server, as well as embrace the benefits of both client-side rendering and server-side rendering.
For the end user, they get smooth, desktop-like responsiveness from client-side rendering, while still being able to maintain the SEO and accessbility benefits of server-side rendering.  For developers, that means writing less boilerplate code, and being able to focus more on writing the application logic.
Today, there are three main framew

  
## index.html
<!doctype html>
<html>
  <head>
    <script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script>
    <script type="text/javascript">
        $(document).ready(function () {
            $('#user-submit').click(function () {
                var payload = {
                    name: $('#user-name').val(),
                    msg: $('#user-msg').val()
	///////////////////////////////////////////////////////////////////////////////
	// FILE: Standa.cpp
	// PROJECT: Micro-Manager
	// SUBSYSTEM: DeviceAdapters
	//-----------------------------------------------------------------------------
	// DESCRIPTION: Standa device adapters: 8SMC1-USBhF Microstep Driver
	//
	// COPYRIGHT: Leslie Lab, McGill University, Montreal, 2013
	//
	// LICENSE: This file is distributed under the BSD license.
	///////////////////////////////////////////////////////////////////////////////
	// FILE: MMCore.h
	// PROJECT: Micro-Manager
	// SUBSYSTEM: MMCore
	//-----------------------------------------------------------------------------
	// DESCRIPTION: The interface to the MM core services.
	//
	// COPYRIGHT: University of California, San Francisco, 2006,
	// 100X Imaging Inc, www.100ximaging.com, 2008
	// All Rights reserved
	import os
	from time import sleep
	from optparse import OptionParser

	# Remember to add the trailing slash!

	SERVER_FOLDER = "/home/2010/cleung24/comp512/a3/servercode/"
	CLIENT_FOLDER = "/home/2010/cleung24/comp512/a3/clientsrc/"
	MIDDLEWARE_PORT = 5678
	import re
	import operator
	from math import sqrt
	from itertools import product

	ALPHABET = ["A", "C", "G", "T", "[AC]", "[AG]",
	"[AT]", "[CG]", "[CT]", "[GT]", "[ACGT]"]

	NUC_PROBS = {
	"A": 0.25,
	library(ape)
	m = c(0, 13, 8, 20, 21, 13, 0, 9, 16, 17, 8, 9, 0, 15, 16, 20, 16, 15, 0, 13, 21, 17, 16, 13, 0)
	dim(m) = c(5, 5)
	colnames(m) = c('A', 'B', 'C', 'D', 'E')
	rownames(m) = colnames(m)
	d = as.dist(m)
	tr = nj(d)
	plot(tr, cex=2, tip.color=rainbow(6))
	axisPhylo()
	///////////////////////////////////////////////////////////////////////////////
	// FILE: NI100X.cpp
	// PROJECT: 100X micro-manager extensions
	// SUBSYSTEM: DeviceAdapters
	//-----------------------------------------------------------------------------
	// DESCRIPTION: NI control with multiple devices
	//
	// AUTHOR: Nenad Amodaj, January 2010
	//
	// COPYRIGHT: 100X Imaging Inc, 2010
	\begin{algorithm}
	\caption{Calculates the optimal alignment using ForgetThePast-NW}
	\begin{algorithmic}
	\Procedure{LinearSpaceAlignment}{$S$, $T$}
	\State m = \textbf{length}(S)
	\State n = \textbf{length}(T)
	\If {$m <= 1$ \textbf{or} $n <= 1$}
	\State \textbf{return} NW(S, T) \Comment Use the regular NW algorithm
	\Else \Comment Divide and conquer with recursion
	\State Middle = \textbf{round}(m/2)
	YUI.add "todo-app", ((Y) ->
	"use strict"

	# Dependencies from MVC namespace.
	TodoList = Y.TodoMVC.TodoList
	TodoView = Y.TodoMVC.TodoView
	TodoApp = undefined

	# -- Main Application --------------
	TodoApp = Y.Base.create("todoApp", Y.App, [],
	<!doctype html>
	<html>
	<head>
	<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script>
	<script type="text/javascript">
	$(document).ready(function () {
	$('#user-submit').click(function () {
	var payload = {
	name: $('#user-name').val(),
	msg: $('#user-msg').val()