Understanding Symmetry Breaking (Part II) Tweet
Fourth of July
It was the fourth of July in 2012. I was a new college graduate and was working at a science museum when the Higgs Boson discovery was announced! From what I’ve heard later on from people working at CERN, both ATLAS and CMS have already found signs of a “Higgs-like” particle a year earlier. But these guys are very careful. A 5-sigma result is required before any discovery can be claimed in particle physics. For those more familiar with the p-value, corresponds to a p-value equal to . Pretty far from the 0.05 threshold!
Take a look at the evolution of the CMS data over time!
What does the Higgs do?
We talked about fermions (fundamental matter particles) and gauge bosons, the particles that guide their interactions and mediate the four fundamental fources (except the graviton hasn’t been found yet!). What does the Higgs do?
So, if I was back with my Lyft Driver from Chicago, I’d talk to him about the beginning of the universe which he was very fascinated about. Right after the bigbang, most particles were massless and were zipping through space at the speed of light. It was very hot then. It began to be slightly cooler, and some form of symmetry breaking occured and here the Higgs field turned on and permeated the entire universe. The Higgs field is often likened to a thick syrup that slows down the particles, essentially by making them massive. This field gives mass to fundamental particles like the electrons, quarks, the W and Z bosons. Protons and other composite particles, particles that can be broken down into pieces, do not get their masses from the Higgs field.
Spontaneous Symmetry Breaking
The W and Z bosons acquire mass through Higgs field through the process of “spontaneous symmetry breaking”. I think every particle physicist should be able to explain this to a guy or girl in a bar. Three groups of physicists independently proposed this mechanism, but the process was only oddly named after Peter Higgs. The other guys were Englert and Brout, and Guralnik, Hagen and Kibble. I think it’s because “Higgs” is super easy to pronounce and super catchy. But at some point it also got really famous as the “God” particle.
Here, I will be a little technical. Spontaneous symmetry breaking occurs through the introduction of a complex scalar field that gives rise the the SM Higgs boson. Fermions acquire mass through a Yukawa interaction of the Higgs boson.
A good visual example of a spontaneous symmetry breaking occurs in a ferromagnet. One can imagine the magnet to have little tiny arrows arranged in a grid. At first they are pointing in different directions and they have no preffered direction. So if you were living inside the magnet, you’d probably get lost. This occurs at high temperature. When you lower the temperature just enough, these arrows would then begin to align themselves. The magnetization then becomes zero because of this. Here, symmetry is broken.
Here is another visual image of symmetry being broken. If you rotate a rod about its axis, it doesn’t look different. In that case, you call it “rotationally invariant”. If there is a force that starts to bend the rod, you could then tell that it is being rotated.
I got the image from this nice write-up. The article also nicely explains the difference between “spontaneous” and “explicit” symmetry breaking. The latter occurs when there is an external force that actively breaks the symmetry. In math-y particle physics parlance you will find a symmetry breaking term in the Lagrangian, e.g. a mass term. In the case of the rod, that is called explicit symmetry breaking.
To generate mass via “spontaneous symmetry breaking”, instead of writing a mass term in a Lagrangian by hand, we can do something else. This is a typical example. Here I am simply regurgitating the discussion from Halzen and Martin Chapter 14. For a world composed only of scalars, we can write the Lagrangian as . Here . The second set of terms in the parenthesis is the potential .
The idea here is that if is negative, the mass term sign is incorrect! And the potential would look like this.
You can try to do some calculus for yourself and get and solve for to get the extremum/extrema You will find that when is negative, the extremum where you were supposed to expect symmetry, does not correspond to the minimum. If we do some rewriting of the scalar field as a sum of the minimum and some quantum fluctuation about the minimum, , the Lagrangian then will have a mass term with the right sign!
\[ \mathcal{L} = \frac{1}{2} \left(\partial_{\mu} \eta\right)^2 - \lambda v^2 \eta^2 - \lambda v \eta^3 - \frac{1}{4} \lambda \eta^4 + const. \]
It’s pretty late now. Around 1:30 am and still in my office. I should get back home and get some sleep. I’m also hungry. I’ll talk about the Higgs mechanism after this.


This test is expected to fail.
Failure
This test is used to check that the runTotals test executes successfully on a test with the @ExpectedToFail annotation.


--- layout: post title: 'LIFT07: What happens when 1st life meets 2nd life, Julian Bleecker' date: 2007-02-08 00:00:00 categories: digital-media interfaces-&-interaction play social ---
LIFT07: What happens when 1st life meets 2nd life, Julian Bleecker
2nd life worlds are made out of bits, which are supported by hardware atoms (no, really), customer support resources, energy. According to Nicolas Carr, an avatar uses 1752kwh/year of energy. A real person, 2436kwh. We're not thinking that coal is being burned to support these.
There's also a debt to our bodies: obesity from a sedentary lifestyle, etc. (Not that in days of Wii, this is necessarily the case).
How to bridge the two? Make 2nd life worlds remind us of the material contingencies of the real world (I'd argue that escapism is part of the point of them)?
Start by bringing back motion, time and distance into 2nd life?
Examples:
Not sure I follow the argument here. TV uses more electricity than radio. Does this mean we should explore ways to make TV more radio-like?
Q: How should NGOs etc using Second Life best recognise their impact?
Q: There's been some research on Second Life as a place in which one projects ones consciousness, e.g. patients in burns units undergoing a virtual "snow" experience which reduces pain levels.
(Is this real? I can't find any reference online)
Q: If a user expends


iab!rpg is a game, run completely under the iab discord bot.
There are four stats to keep track of in combat.
First is HP.
Next is DEF. Defense reduces damage. Pretty standard stuff really.
Third is DMG. DMG determines how much damage you do.
Last is SPD. SPD determines when you act.
The interactions between the stats are pretty simple. Damage is equal to DMG - DEF. Health = HP - Damage. Low speed is better; think of it as 1 SPD = 1 second to act. Thusly, a SPD of 10 means you will attack half as often as something with a SPD of 5.
Let's say that a player is fighting an enemy. The player has a base SPD of 10, and the enemy has a base SPD of 15.
The player is wielding a staff with a SPD value of 10. Now, the player has a SPD of 20. The enemy is unarmed, and thus has no higher SPD.
At the beginning of combat, the SPD Counter (SPDC) - the amount of time elapsed in a fight, starts at 0. Both parties decide on their attacks. Let's say that both of the combatants go for a basic attack. Now, they both have a next action time. The player will get a new action when the SPD Counter is at 20, but the enemy will get a new turn when the SPD Counter is at 15.
Consequently, the player will take damage before their attack even goes out. Their attack will be sent on SPDC 20.
Let's say now that the player decides to cast a spell. The spell has a SPD value of 40 (it's a massive attack). The player will attack in 60 (10 base + 10 weapon + 40 spell) counts of the SPDC (simply referred to as a 'c' suffix on numbers.) The enemy will recieve four turns during the buildup for the spell. For this reason, it's very important to be careful with how you manage your SPD. It will most definitely be a matter of life or death.


The Farrago Spiritum Tarot - a farrago of all your hopes, dreams, doubts, & fears in a mixed fodder of imagery.
The deck is an electronic assemblage of the artwork of Yvette Endrijautzki, & based on the writings of astrologer, teacher, & tarot reader, Raven Bella Zingaro. Each card is a collage of information from several different realms & modalities. The deck is designed to be read easily, even by individuals with no tarot background. In addition to traditional tarot symbolism, our deck includes planetary and astrological references, crystals, chakras, Shamanic symbols, & depictions of flora and fauna. The Major Arcana & Court Cards are printed in Latin, which is our nod to the classic history of the Tarot. The Minor Arcana are in English. Each deck has 78 cards, 86x127mm (3.38" x 5") & is printed on 300gsm white core paper with a matte varnish finish. The deck comes in a 2-piece styled box.
The Farrago Spiritum Tarot - a farrago of all your hopes, dreams, doubts, & fears in a mixed fodder of imagery. The deck is an electronic assemblage of the artwork of Yvette Endrijautzki, & based on the writings of astrologer, teacher, & tarot reader, Raven Bella Zingaro. Each card is a collage of information from several different realms & modalities, & designed to be read easily, even by individuals with no tarot background.
In addition to traditional tarot symbolism, our deck includes planetary and astrological references, crystals, chakras, Shamanic symbols, & depictions of flora and fauna. The Major Arcana & Court Cards are printed in Latin, which is our nod to the classic history of the Tarot. The Minor Arcana are in English. Each deck has 78 cards, 86x127mm (3.38" x 5") & is printed on 300gsm white core paper with a matte varnish finish. The deck comes in a 2-piece styled box.
Raven & Yvette, friends & co-workers at Tenzing MoMo in Seattle's famed Pike Place Market, felt a strong connection to the project from its inception. The project spanned many years & the two continued their collaborative efforts even while living on separate continents. The deck was officially finished on 02.22.2020 at 11:59pm in Brussels, Belgium, just before the world shut down due to the pandemic.
Currently in its 2nd printing, the Farrago Spiritum Tarot is available for purchase on Etsy.


Lookup tables for estimating the likelihood of poverty using the Poverty Probability Index
(previously called Progress out of Poverty Index
) or PPI
from country-specific indicators collected from cross-sectional surveys. This lookup table is extracted from documentation of the PPI
found at https://www.povertyindex.org.
You can install ppitables
from CRAN with:
install.packages("ppitables")
library(ppitables)
You can install ppitables
from GitHub with:
# install.packages("devtools")
devtools::install_github("validmeasures/ppitables")
library(ppitables)
The ppitables
package contains PPI lookup tables for the 60 countries1 where PPI can currently be calculated. To be able to use the lookup tables in ppitables
appropriately, you need to be aware of the naming syntax used for the tables for each country. The name for each table will always have three fixed or constant components as follows:
ppiXXXYYYY
The name of any of the PPI tables contains:
ppi
in lower case letters;XXX
which is the the three letter ISO code
of the country of interest (all capitals); and,YYYY
which is the specific year at which the country PPI table was released.These three components are joined together without any spaces or gaps.
Some country lookup tables may have additional components to their name which are added after the year separated with an underscore. These usually signify that a lookup table released on a particular year has a subset table in which the poverty likelihoods for a given PPI
score are reported based on a different poverty definition or cut-off. This additional component to the table name is usually a character value or alphanumeric and is usually country-specific. To know more about what this additional component to some PPI
tables refer to, read the index table below of the PPI
tables available in this package.
Following are the available PPI country tables from the ppitables
package. This is updated as at 27 February 2018 using information from the PPI site.
| PPI Country Table Name | Description | PPI Release Date |
|---|---|---|
|
PPI for Afghanistan based on 2007/8 National Risk and Vulnerability Survey (NRVA) | 2012 |
|
PPI for Angola based on the 2008/2009 Household Living Standards Survey | 2015 |
|
PPI for Benin based on 2010 data | 2012 |
|
PPI for Burkina Faso using Burkina Faso’s 2014 Enquête Multisectorielle Continue (EMC) Survey | 2017 |
|
PPI for Bangladesh using Bangaldesh’s 2010 HIES Survey | 2013 |
|
PPI for Bolivia using Bolivia’s 2013 Household Survey | 2015 |
|
PPI for Brazil based on the 2008 PNAD | 2010 |
|
PPI for Ivory Coast using the Ivory Coast’s 2008 Household Living Standards Survey | 2013 |
|
PPI for Cameroon using Cameroon’s 2007 Household Survey | 2013 |
|
PPI for Colombia based on Colombia’s 2009 Encuesta Integrada de Hogares. This table uses the legacy poverty cutoffs. | 2018 |
ppiCOL2018_a |
PPI for Colombia based on Colombia’s 2009 Encuesta Integrada de Hogares. This table uses the new poverty cutoffs for Colombia. | 2018 |
|
PPI for Dominican Republic based on the 2007 Encuesta Nacional de Ingresos y Gastos de los Hogares (ENIGH) | 2010 |
|
PPI for Ecuador based on the 2013 Living Standards Survey | 2015 |
|
PPI for Egypt based on the 2004/5 HIECS | 2010 |
|
PPI for Ethiopia based on Ethiopia’s 2010/11 Household Consumption and Expenditure Survey | 2016 |
|
PPI for Fiji based on Fiji’s 2008/9 Household Income and Expenditure Survey | 2014 |
|
PPI for Ghana based on Ghana’s 2012/13 Living Standards Survey using legacy poverty lines | 2015 |
|
PPI for Ghana based on Ghana’s 2012/13 Living Standards Survey using the new-definition poverty lines deflated with Ghana’s CPI | 2015 |
|
PPI for Ghana based on Ghana’s 2012/13 Living Standards Survey using the new-definition poverty lines deflated with the change in 100% of national poverty line | 2015 |
|
PPI for Guatemala based on Guatemala’s 2014 Household Living Standards Survey | 2016 |
|
PPI for Honduras based on the 2007 EPHPM | 2010 |
|
PPI for Haiti based on Haiti’s 2012 Post-Earthquake Living Standards Survey | 2016 |
|
PPI for Indonesia based on data from 2010 using legacy poverty lines | 2012 |
|
PPI for Indonesia based on data from 2010 using new definition poverty lines | 2012 |
|
PPI for India using India’s 2011/12 Socio-Economic using the R59 legacy poverty lines using MRP consumption | 2016 |
|
PPI for India using India’s 2011/12 Socio-Economic using the R59 legacy poverty lines using MRP consumption | 2016 |
|
PPI for India using India’s 2011/12 Socio-Economic using the R66 legacy poverty lines using MRP consumption | 2016 |
|
PPI for India using India’s 2011/12 Socio-Economic using the R68 new poverty lines using MRP consumption | 2016 |
|
PPI for Jordan using Jordan’s 2006 Household Income and Expenditure Survey | 2010 |
|
PPI for Kenya using Kenya’s 2005/06 Integrated Household Budget Survey | 2011 |
|
PPI for Kyrgyzstan Kyrgyz Republic’s 2012 Integrated Household Survey | 2015 |
|
PPI for Cambodia using Cambodia’s 2011 Socio-Economic Survey based using legacy poverty lines | 2015 |
|
PPI for Cambodia using Cambodia’s 2011 Socio-Economic Survey based using government definition poverty lines | 2015 |
|
PPI for Cambodia using Cambodia’s 2011 Socio-Economic Survey based using World Bank definition poverty lines | 2015 |
|
PPI for Sri Lanka using Sri Lanka’s 2012/13 Household Income and Expenditure Survey | 2016 |
|
PPI for Morocco based on Morocco’s 2007 Households Living Standards Survey | 2013 |
|
PPI for Madagascar based on Madagascar’s 2010 Periodic Household Survey | 2015 |
|
PPI for Mexico based on Mexico’s Encuesta Nacional de Ingresos y Gastos de los Hogares de 2014 using legacy definitions of poverty | 2017 |
|
PPI for Mexico based on Mexico’s Encuesta Nacional de Ingresos y Gastos de los Hogares de 2014 using new definitions of poverty | 2017 |
|
PPI for Mali based on Mali’s 2001 Poverty Evalution Survey | 2010 |
|
PPI for Myanmar based on Myanmar’s 2009/10 Integrated Household Living Conditions Assessment | 2012 |
|
PPI for Mongolia based on Mongolia’s 2014 Household Socio-Economic Survey | 2016 |
|
PPI for Mozambique based on 2008/9 Household Budget Survey | 2013 |
|
PPI for Malawi based on Malawi’s 2010/11 Integrated Household Survey using legacy poverty definitions | 2015 |
|
PPI for Malawi based on Malawi’s 2010/11 Integrated Household Survey using government poverty definitions | 2015 |
|
PPI for Malawi based on Malawi’s 2010/11 Integrated Household Survey using PBM poverty definitions | 2015 |
|
PPI for Namibia based on Namibia’s 2009/10 Household Income and Expenditure Survey | 2013 |
|
PPI for Niger based on Niger’s 2007/8 National Household Budget and Expenditure Survey | 2013 |
|
PPI for Nigeria based on Nigeria’s 2012/13 General Household Panel Survey | 2015 |
|
PPI for Nicaragua based on Nicaragua’s 2009 Living Standards Measurement Survey | 2013 |
|
PPI for Nepal using legacy poverty definition lines | 2013 |
|
PPI for Nepal using new poverty definition lines | 2013 |
|
PPI for Pakistan using Pakistan 2005/6 Social and Living Standards Measurement Survey | 2009 |
|
PPI for Peru based on Peru’s 2010 National Household Survey | 2012 |
|
PPI for the Philippines based on Philippines 2009 FIES/LFS. | 2014 |
|
PPI for Paraguay based on Paraguay’s 2011 EPH | 2012 |
|
PPI for Palestine based on Palestine’s 2011 Expenditure and Consumption Survey | 2014 |
|
PPI for Romania based on the 2007 HBS | 2009 |
|
PPI for Russia based on 2007 HBS | 2010 |
|
PPI for Rwanda based on Rwanda’s 2010/11 Integrated Household Living Standards Survey | 2016 |
|
PPI for Senegal based on Senegal’s 2005/6 Enquête de Suivi de la Pauvreté au Sénégal (ESPS) | 2009 |
|
PPI for Sierra Leone based on Sierra Leone’s 2003/4 HIS | 2011 |
|
PPI for El Salvador based on the 2008 EHPM | 2010 |
|
PPI for Syria based on Syria’s 2006/7 Household Income and Expenditure Survey | 2010 |
|
PPI for Tajikistan based on 2007 data | 2015 |
|
PPI for Timor Leste based on Timor-Leste’s 2007 Survey of Living Standards | 2013 |
|
PPI for Tanzania based on Tanzania’s 2011/12 Household Budget Survey | 2016 |
|
PPI for Uganda based on Uganda’s 2012/13 National Household Survey | 2015 |
|
PPI for Vietnam based on the 2006 VHLSS | 2009 |
|
PPI for Yemen based on 2005/06 HBS | 2009 |
|
PPI for South Africa based on the 2005/6 IES | 2009 |
|
PPIi for Zambia based on Zambia’s 2015 Living Conditions Monitoring Survey (LCMS) | 2017 |


Welcome to Protomapper Search. This service searches UniprotKB for regular expressions. See the About section for features and query syntax, and Github for sources and documentation.


Last updated: 2018-03-17
Code version: 99848d1
Reassortment is the mixing of the genetic material of a species into new combinations in different individuals. It is particularly used when two similar viruses that are infecting the same cell exchange genetic material.
There are several interesting concepts in graph theory. Please look at the Figure 1.1, 1.2 and 1.3.
The degreeof node \(u\) is the sum of its indegree and outdegree.
A biconnected components is the maximal subgraph that is induced by set of edges and doesn’t contain a cut node. A good example is in Figure 1.3.
A graph \(G=(V,E)\) is called bipartite if and only if its set of nodes can be partitioned into subsets \(V_{1}\), \(V_{2}\),with \(V=V_{1}\cup V_{2}\) and \(V_{1}\cap V_{2}=\emptyset\), such that for every edge \(e \in E\),one of the endpoints lies in \(V_{1}\), another endpoint lies in \(V_{2}\). Explain Exercise 1.2.3.
Two nodes \(v\) and \(w\) are imcomparable, if neither node is lower than other; similarily, two edges \(e\) and \(f\) are imcomparable if neither is lower than other;
Different traversals give rise to different orders in which nodes are examined. Pay attention to preorder, postorder and breadth-first traversal in Figure 1.7. In particular, breadth-first traversal, please see reference here.
PS: Nodes are also called vertices, edges are also called branches or arcs. Bifurcating Tree = Resolve Tree = Binary Tree
Let \(\chi=\left\{x_{1},x_{2},...x_{n} \right\}\) be a set of taxa, a cluster is any subset of \(\chi\),excluding the empty set \(\emptyset\) and full set \(\chi\). The ultimate goal of phylogenetic analysis is to compute a set of clusters on \(\chi\) such that each cluster is monophyletic(also called clade. Monophyletic group contains all descendants of the common ancestor and the ancestor itself).
A split is any bipartitioning of \(\chi\) into two non-empty subsets \(A\) and \(B\) of \(\chi\), such that \(\chi=A \cup B\) and \(A\cap B=\emptyset\).
In phylogenetic analysis, a set of taxa \(\chi=\left\{x_{1},x_{2},...x_{n} \right\}\) is often represented by a set of molecular sequences \(A=\left\{a_{1},a_{2},...a_{n} \right\}\) where \(a_{i}\) comes from taxon \(x_{i}\) and correspond to some specific genes or locus. We also need to ensure that the sequences are homologous, that is, have evolved from a common ancestor sequence.
In Pairwise sequence alignment, with the help of substitution matrix, for example the BLOSSUM matrix, which assigns empirically score, we could calculate the score of each pair of residues and then sum over scores among all pairs would be the score of whole alignment.
Sequence are often aligned by inserting gaps into each sequence shown in Figure 2.6 such that all sequences have same length \(m\), forming a multiple sequence alignment of length \(m\). Our goal is to find a multiple sequence alignment that achieves the optimal score according to an appropriate score scheme. Progressive method as a heuristic approach, is used to align multiple sequences, its outline is shown in Figure 2.7. The core is to align a pair of similar sequences into profiles, then align profiles into final multiple sequence alignment.
Let \(M\) be a multiple sequence alignment on \(\chi\), each column of \(M\) is called a character, each symbol that occurs in this column is called a character state.
Now we are introducing some basic concepts and main methods for inferring phylogenetic trees.
Phylogenetic trees are usually computed from molecular sequences. They not only could uncover the relationship between different species or taxa, but also have many other applications. For instance, they are used to determine the age and the rate of diversification. In sequence-analysis method, they are allowed phylogenetic footprinting.
In practice, there are two types of analysis after the initial multiple sequence alignment: distance-based analysis and sequence-based one. Its outline is shown in Figure 3.1 at page 24.
Given a set of taxa \(\chi\), this is a phylogenetic tree \(T=(V,E)\) , its all nodes have degree \(\neq\) 2, together with a taxon labeling \(\lambda:\chi\to V\)that assigns actually one taxon to every leave and none to internal nodes.
From a theoretical and algorithmic point of view, unrooted phylogenetic trees are much more easier than rooted ones, however, in biology, rooted phylogenetic trees are usually more of interest. A phylogenetic tree is called an edge-weighted tree if we are given a map \(\omega\) that assigns a non-negative weight or length \(\omega(e)\) to every edge e of the tree. In drawings, we usually use length of the edge to indicate the scale rather than write the lengths explicitly next to edges.
Jukes-Cantor model tells us the probability formula of change during time \(t\) or along the edge, given the mutation rate. This model of DNA evolution assumes the fours bases (A,C,G and T) occur with equal frequencies(0.25) and change from one base to another occurs at the same rate. If we relax the conditions, for example, let the bases occur at different and arbitrary rates (although they have to sum to 1), change rates in transitions and transversions, then we could get more generate model, anyway, they are both special cases of general time reversible model.
Classical phylogenetic trees construction approaches consist of two following types:
Maximum parsimony method is to look for a phylogenetic tree that explains the given set of aligned sequences using a minimum number of evolutionary events.
The parsimony score of \(T\)(tree) and \(M\)(given multiple sequence alignment) is defined as:
\[\begin{equation} P S(T, M)=\min_{\alpha}\sum_{\left\{x,y\right\}}diff(x,y) \end{equation}\]where diff() function is known as hamming distance between sequence \(x=(x_{1},x_{2},...x_{m})\)and sequence \(y=(y_{1},y_{2},...y_{m})\) that describes the difference of \(x\) and \(y\) \[\begin{equation} diff(x, y)=| \left\{ i | x_{i}\neq y_{i} \right\} | \end{equation}\]
The minimum is taken over all possible assignments \(\alpha\) that make the sequences of length \(m\) to be the internal nodes, summation is taken over all possible pairs of \(x\) and \(y\) that are assigned at opposite end of edge of \(T\) .
This task of computing parsimony score is the known small parsimony problem. In small parsimony problem, input is aligned sequences and a tree with sequences at leaves, output is an sequences assignment of all internal nodes in this tree with minimum number of changes across all edges. For bifurcating tree, Fitch algorithm is used to calculate efficiently, in more general settings, Sankoff’s algorithm can be applied.
Let’s describe Fitch algorithm which has a linear time when solving above small parsimony problem. Assume we are given a multiple sequence alignment \(M\) and a bifurcating tree \(T\) on \(\chi\), we need to score each character (that is, column of the alignment)separately, and then obtain the parsimony score \(P S(T, M)\) by summing over all characters.
This algorithm proceeds in two parts, as shown in following pictures. The first part is called bottom up phrase, from leaves to root, finding sets of possible ancestral states (labels) for each internal node, next part is top down process, from root to leaves, determining ancestral states (labels) for internal nodes. Different site is independent, so we can solve one site at a time.
On the contrary, there is big parsimony(called large parsimony also). It’s related with a search through the space of trees. In big parsimony problem, input is only aligned sequences, output is a labeled tree with minimum number of changes across all edges (over all trees). It is a NP hard problem.
Bayesian inference employs MCMC to sample from the posterior probability distribution. Posterior probability distribution in phylogeny inference is the conditional probability of T given input dataset. Each step, Metropolis-Hastings algorithm is used here, each step we propose a modified new tree topology, then accept it with the probability of \(min(1, \alpha)\), \(\alpha\) is the ratio of new prior times transition kernel divide the old one, otherwise, we reject and still use the current one. Therefore, a suitable modification of this proposed new tree should be taken into account with care. After discarding the burn in, sometimes we would also do sparsely sampling from output a series of trees, retaining only 1000th tree, say, in order to avoid the problem of autocorrelation, since the samples the not independent in this case. Let’s talk about the modification in detail.
The first one is called local algorithm, which is a modification of NNI(Nearest neighbor interchange). This algorithm is very magic and powerful. Through a path in a tree, then update length of different nodes and even topology by introducing random number. Regarding parameters in evolutionary model, like mutation rate \(\mu\) in Jukes Cantor model, are modified by adding a random number uniformly chosen from an appropriate interval centered at 0. For a set of parameters that is constrained to sum to some specific value, such as 1 in the case of probabilities, the values are randomly modified according to a Dirichlet distribution.
Modifying the tree and proposal for new parameters are generated independently and simultaneously, and then accept or reject by a single Metropolis-Hastings ratio.
The second one is called Metropolis-coupled MCMC or (\(MC^3\)) , this is a variant of MCMC which are suitable if there are a large amount of parameters. The first chain \(Z_{1}\) is called cold chain, other chains \(Z_{2},...Z_{K}\) are called heated chains, all chains are run parallel. After all chains have moved one step, Let \(T_{i}\) denote the current state of all chains, for all i =1 ,2 … K, then after randomly choosing two chains \(Z_{i}\) and \(Z_{j}\), swap the result with specific probability. Swapping of chains can help the cold chains to move a new part of of parameter space that it may have difficulty in reaching. At the end of run, discard all heated chains and cold chain is processed as before.
A challenge here is we may not know whether this chain has converged. Two approaches are introduced here: one is to monitor whether there there is no further increase in likelihood, another one is run multiple chains in parallel, to keep them running until appear to sample from the same distribution. In addition, areas like choosing prior distribution and check convergence is ongoing research.
When researchers explore the bifurcating trees space, they actually move from one bifurcating tree \(T\) to another bifurcating tree \(T'\) by applying Branch-swapping method to rearrange a part of tree \(T\). There are three methods : NNI(Nearest neighbor interchange),SPR(Subtree prune and regraft) and TBR(Tree bisection and reconnection). In order to show this three methods vividly, please look at the figures 3.14-3.16 which are all from this book. Let NNI(T), SPR(T) and TBR(T) represent the set of all possible trees that can be obtained by applying NNI,SPR and TBR respectively. It is not difficult to note that:
\[\begin{equation} NNI(T) \subseteq SPR(T) \subseteq TBR(T) \end{equation}\]Each of these three methods could be used to define distance of two phylogenetic trees. For example, the SPR distance of two trees is minimum number of SPR operations necessary to transform from one tree into another.
Figure 3.14-16 are all from original paper
In order to evaluate the robustness of estimated phylogenetic tree, bootstrapping is employed. Given a multiple sequence alignment \(M\) of length \(m\) and phylogenetic tree construction method, first step is to get bootstrap replicate \(M'\) by randomly sampling from \(M\) that consists of \(m\) columns, with replacement, normally a set of 100 or 1000, noted \(\left\{M^{1},M^{2},...M^{1000}\right\}\)(say 1000), the method is applied in each replicate, producing a collection of phylogenetic trees \(B=\left\{{T^{1},T^{2},...T^{1000}}\right\}\), then use these trees to determine bootstrap support of each split. In practice, a bootstrap support of at least 70%, is required for a split to be considered trustworthy.
Neighbour-joining is the most popular method for computing the phylogenetic tree, viewed as a modification of UPGMA. In biology, molecular clock hypothesis states the mutation rate is constant over all sites of sequence and over all edges of the model tree. It implies that all leaves of tree all have same distance from the root. Actually, any tree produced by UPGMA algorithm has the property that all leaves have the same distance to the root.
The steps of UPGMA are pretty easy to understand: given a set of sequences, first calculate a table showing the hamming distance. Then merge the smallest distance in pairs of sequences to one cluster, creating a new node. After that, calculate the new distance table again. UPDMA is assembled bottom-up.
Neighbour-joining doesn’t need to assume a molecular clock like UPGMA. Its output is an unrooted tree. One difference between UPGMA and NJ is how to update the distance matrix after merging two clusters. The formula when computing the distance between a new cluster and one merged cluster is different(Look at figure 3.21). In UPGMA, the last term “\(-d(C_{i},C_{j})\)” is not needed.
Another significant difference between UPGMA and NJ is how the length of edges are set, formula in terms os computing the distance between a leave and merged node is in following figure 3.22. In summary, based on these formula, we could recalculate the length of each branch in model tree, the direct difference when looking at UPGMA and NJ trees is the giant different in each branch length.
However, we need to note that one disadvantage using NJ algorithm is that it may produce negative branch length, which happens quite frequently.
A new and faster algorithm called FastME is proposed recently based on balanced minimum evolution(BME) framework, which could provide more accurate trees than NJ and never produce negative edge lengths.
Given a distance matrix and an unrooted bifurcating tree topology, we could calculate the leave edge and internal edge length based on clear formulas and total tree length is given as well, in other words, calculating BME tree is a statistically consistent tree construction method, however, finding the optimal BME tree is NP hard, so we turn to heuristics, more precise, FastME heuristic. It has two phases. First step is an initial tree is constructed , next step is to iteratively update the tree topology using NNI until no further improvement in the score of total tree length. Since it doesn’t need to explicitly point out each branch length, that’s why it is significantly faster than NJ in practice.
BME could be viewed as an improvement of classic minimum evolution problem. Moreover, it also consider the pairwise distance variance. In OLS method when constructing a tree, all distance have the same variance. But in general, it is not true, the variance of larger distance tend to be larger. Actually, based on the formula of total length tree length, longer distance implies a smaller weight, therefore, BME can also be interpreted as a weighted least square method. FastME runs much faster than all previous weighted least square approaches.
When comparing the distance between two phylogenetic trees, generally the trees are unrooted ones. Robinson-Foulds distance and quartet distance is used when measuring the similarity for a pair of trees. Even though there are so-called NNI, SPR and TBR distances which determine the minimal number of related operations from one topology to another, computation is NP hard and is rarely used in practice.
In general, when facing with a collection of different phylogenetic trees, producing from different methods given the same multiple sequence alignment like MLE , MP and so forth, or from Bayesian inference, consensus method is necessary used to obtain consensus tree that represents evolutionary history which different phylogenetic trees agree, in some sense.
Here we introduce two kinds of consensus trees: strict consensus and majority consensus. Let \(S_{strict}(T)\) denotes the set of all splits that occur in every tree in tree set. \(S_{majority}(T)\) denotes the set of splits that occur in more than half of all trees in tree set. Here is an example figure to explain the strict and majority tree. In practice, majority consensus tree is more informative than strict consensus tree since the latter tends to be a star tree easily.
Newick format is used to describe a rooted phylogenetic tree, of course it is also used to describe unrooted tree by erasing the root. example is here: text=“((t4:0.104381,(t2:0.075411,t1:0.075411):0.5):0.065840,t3:0.170221);”
If possible, you could try this R code to plot a tree and check whether it is consistent with mine as shown beside the code:
library(ape)
tr1 <- read.tree(text= "((t5:0.161175,t6:0.161175):0.392293,((t4:0.104381,(t2:0.075411,t1:0.075411):0.028969):0.065840,t3:0.170221):0.383247);")
tr2 <- read.tree(text= "((t5:2.161175,t6:0.161175):0.392293,((t4:0.104381,(t2:0.075411,t1:0.075411):1):0.065840,t3:0.170221):0.383247);")
plot(tr1,font=1)
plot(tr2,font=1)
An overview of phylogenetic network is here
Phylogenetic networks can be computed from wide range of datasets, including multiple sequence alignments, splits, distance matrices, set of trees, clusters, rooted triplets or unrooted quartets.
Newick string could be extended to describe a rooted phylogenetic network. The method is to to assign formal labels \(Hi\) to reticulate nodes, details could be in the following Figure 4.7. Conversely, if we are given a this kind of Newick format to construct a network, first step is to construct a rooted phylogenetic tree, then merge the same formal taxon \(H\).
Since my PhD project is related with recombination network. Let’s introduce this type.
Recombination network is a rooted network that describe the evolution of a set of sequences(usually come from different individuals) in terms of mutation(along the edges of branch), speciation events (at tree nodes) and recombination events (at reticulate nodes).
Here is a formal definition of recombination network:
Let \(M\) be a multiple alignment of binary sequences of length L, on \(\chi\). A recombination network \(N\) representing \(M\) is given by a combining of rooted phylogenetic network on \(\chi\), together with two additional labelings:
(i)each node \(v\) of \(N\) is labeled by a binary sequence \(\delta(v)\) of length L.
(ii)each tree edge \(e\) is labeled by a set of positions \(\delta(e) \subseteq \left\{1, 2,...L \right\}\).
These two labelings must fulfill the following compatibility conditions:
For computational reasons, the following condition is usually also required:
Here we can verify this simple recombination network example, can the node \(r\) be obtained by a single-crossover recombination from parental sequences?
Evolution in the presence of recombination is usually studied in population genetics, rather than in phylogeny, focusing a statistical method , under the ``coalescent with recombination" model, a description of history from \(n\) sampled sequences give rise to a graph called ancestral recombination graph(ARG).
In fact, evolutionary history of any sufficiently short segment of sequence is a rooted phylogenetic tree. Therefore, one natural and direct way is to construct a suitable rooted phylogenetic tree \(T_i\) for each position \(i\) in the alignment \(M\), we call any such tree \(T_i\) as , then combine all trees into a suitable phylogenetic network \(N\).
Currently, there are two ways to construct phylogenetic network by these local trees:
First in the local-tree parsimony approach, in the local-tree graph \(G\) any path \(P\) is defined as :
\[\begin{equation} P=( v(1,T_{1}), v(2,T_{2}),... v(L,T_{L})) \end{equation}\]The total weight of such path is the summation of node weight and edge weight. node weight means the minimum number of substitutions required for the i-th character on the rooted phylogenetic tree, edge weight is the minimum number of reticulate nodes which links tree \(T\) and \(T'\), reflecting the recombination distance. Any two nodes \(v(i,T)\) and \(v(i+1,T')\) at adjacent positions in the alignment are corrected by a directed edge \(e=(v(i,T), v(i+1,T'))\).
A most parsimony set of trees for \(M\) is given by a path P of minimum weight, then recursion method could be used, see below:
\[\begin{equation} W(i,T)= \begin{cases} min_{T'}{W(i-1,T')+w(v(i-1,T'), v(i,T))+w(v(i,T))}& \text{if i $>$1}\\ w(v(1,T))& \text{else} \end{cases} \end{equation}\]An example is shown in the figure. Unfortunately, this method is not practical, since computing a suitable phylogenetic network representing all rooted trees in second part is an NP-hard problem, besides that, computation of edges weight is also NP-hard.
Next is the heuristic for the local tree approach.The first simplification is to use unrooted phylogenetic trees rather than rooted trees, main simplification is to consider a small part of full local tree graph.
The heuristic starts by computing a phylogenetic tree for \(M\) using maximum parsimony method. Then we compute the SPR-neighborhood S of T that only one SPR modification of T, the main recursion is the same as previous section. The resulting set of trees might depend quite strongly on the initial tree, so once completing the first pass of this algorithm, a second pass is needed, start tree will be replaced by the tree from last position. However, this step is still challenging in practice.
Actually, in paper “Computing recombination networks from binary sequences” Daniel H.Huson 2005, researchers proposed a method to draw recombination network from aligned binary sequences. There are some important and meaningful concepts before the description of core algorithm. Let’s first introduce these concepts.
Splits can be compatible, circular, and weakly compatible. The last one is of interest because these splits can be efficiently computed using split decomposition algorithm.
Here the term compatible, incompatible and split network all occur in above mentioned paper.
Given the following unrooted phylogenetic tree, there are seven edges in this tree, it gives rise to seven split, called split encoding of \(T\). Suppose we are given an arbitrary set of splits S, we would like to know whether S can be represented by some unrooted phylogenetic tree T with \(S=S(T)\). The answer is given by compatibility theorem.
It is also useful to represent the incompatibilities among a set of splits S by a graph called Incompatibility graph, the formal definition is here:
Incompatibility graph: The Incompatibility graph IG(S) of a set of splits S is the graph \((V,E)\) that has node \(V= S\) and edge set \(E=\left\{(s_{1},s_{2}) | s_{1} and s_{2} are compatible\right\}\) , one example is shown in figure 5.3.
From the definition of incompatibility graph, we could know that if one split in S is compatible with other splits in S, then this split will be isolated node in incompatibility graph.The formal definition of split network is shown below.
If we want to compare two split network \(N_{1}\) and \(N_{2}\), we compare the corresponding set of splits \(S_{1}\) and \(S_{2}\), using the Robinson-Foulds distance: \[\begin{equation} d_{RF}(S_{1},S_{2})=\frac{|S_{1} \Delta S_{2}|}{2} \end{equation}\]
Robinson-Foulds distance is also a proper metric for comparing tree distance.
Actually, there could be a tree or other graph to represent a same set of splits. There is also an important lemma: a set of splits are compatible if and only if there exists a split network N representing S that is a tree. Hence, given our input is a set of splits, how to construct a split network N as output is our first challenge. Below are two available approaches.
The first is the convex hull algorithm that computes the Buneman graph and can be applied to any set of splits, using an exponential number of nodes and edges in the worst case; the second is the circular network algorithm , which can be applied to any set of circular splits and produces an outer-labeled planar network with only a quadratic number of nodes and edges.
Both algorithms proceed in two steps. In the first step, all trivial splits in \(S =\left\{ S_{1} , . . . , S_{m} \right\}\) are processed to obtain a star network consisting of a central node and one leaf per taxon, noted \(S^{O}\) (outer). Then, in the second step, the remaining splits are inserted one by one , noted \(S^{I}\) (inner) so as to obtain the final network.
This R Markdown site was created with workflowr


--- layout: newsstory title: I DON'T BELIEVE IT! 5IVE! match: Atherstone 4 Yeltz 5 ---
All very strange - a team of defenders, Andy Crannage in goal (oh yes, the 45-year-old local celebrity) but it really was Atherstone 4 Yeltz 5 .
Ross Collins played in centre-midfield and Ralphy Crisp played up front but we doubled the season's meagre goal tally in one game, the scorers being Ashley Brown (2), Crispy (2) and another from Ada Cooper .
We went behind to an early Atherstone goal, took a 3-1 lead but then conceded another before half-time. We then twice went two ahead, were twice pulled back to a single goal lead and eventually were very pleased to take all 3 points. Hu-bloody-rrah!!
FA Cup News: the 3rd Qualifying Round draw has been made, giving us the truly memorable:
REVISED: Stafford Rangers or Eastwood Town v Oadby Town or Halesowen Town
The full draw can be found on http://www.canvey.org.uk/football/1999/cups/facupQ3.htm


Joan Marie Verba, author of Countdown to Action and other Thunderbirds novels
Anthony Taylor brings an intriguing perspective to International Rescue, which feels very much in the tradition of the best episodes of the series, making effective use of both drama and humor to tell the story. In Arctic Adventure, an experimental plane crashes in the Arctic, with Brains and the pilot inside. ... All of it is woven together in a suspenseful tale, where the team must put all their resources into play to meet a variety of dangers, expected and unexpected.
Brains is the genius behind International Rescue’s technology. Besides designing and upgrading all of their equipment, he constantly develops and tests new products and processes, sometimes in partnership with outside interests. Eager to try out a new stealth system of his invention, Brains teams up with Humboldt Aviation to install his system on their new aircraft, the V-17. On the first test flight, the V-17 is shot down over the arctic by agents of the outlaw state of Reznia. With the aircraft shattered and partly buried in the ice, Brains and the V-17’s pilot are injured and unable to free themselves. Although Brains is able to contact International Rescue for recovery, the Reznians are also converging on the crash site in order to claim the wreckage for their research. Can the rest of International Rescue find and retrieve Brains and the V-17 pilot before the Reznians can capture them and the crashed plane?


Android Application Development
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We layer down your application like a book reading or navigation through is made faster and easier.


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@* * Copyright 2019 HM Revenue & Customs * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. *@ @import config.AppConfig @import controllers.declaration.routes @import forms.declaration.destinationCountries.DestinationCountries @import models.requests.JourneyRequest @import services.Countries @import services.view.AutoCompleteItem @import uk.gov.hmrc.play.views.html._ @this(main_template: views.html.main_template) @(form: Form[DestinationCountries])(implicit request: JourneyRequest[_], messages: Messages, appConfig: AppConfig) @main_template( title = messages("declaration.destinationCountries.title"), appConfig = appConfig ) { @helper.form(routes.DestinationCountriesController.saveCountries(), 'autoComplete -> "off") { @helper.CSRF.formField @components.back_link("/customs-declare-exports/declaration/holder-of-authorisation") @components.error_summary(form.errors) @components.section_header(messages("declaration.summary.locations.header")) @components.page_title(Some("declaration.destinationCountries.title"))


--- layout: post status: publish published: true title: 'Magento 1.9.2: 5-cents Price Rounding' author: display_name: aditya login: aditya email<EMAIL_ADDRESS>url: '' author_login: aditya author_email<EMAIL_ADDRESS>wordpress_id: 642 wordpress_url: http://adityaputra.com/?p=642 date: '2016-08-25 21:08:35 +0800' date_gmt: '2016-08-25 14:08:35 +0800' categories: - Tutorial tags: - magento - rappen rounding - 5-cents rounding comments: - id: 1035 author: HappyDev author_email<EMAIL_ADDRESS>author_url: '' date: '2017-02-13 23:40:08 +0800' date_gmt: '2017-02-13 16:40:08 +0800' content: Thank you! This was exactly what I had to do for a Swiss online shop that I'm developing for in my job. The client will be happy that you saved me so much time - because he pays per hour. You saved me so many headaches because I'm not yet a Magento expert. - id: 1036 author: aditya author_email<EMAIL_ADDRESS>author_url: '' date: '2017-02-14 07:40:36 +0800' date_gmt: '2017-02-14 00:40:36 +0800' content: Glad it helped you. Thanks for leaving your comment! - id: 1042 author: Raffaele Capasso author_email<EMAIL_ADDRESS>author_url: '' date: '2017-11-20 17:18:28 +0800' date_gmt: '2017-11-20 10:18:28 +0800' content: "Hi! Thanks for your article. \r\nIt don't works on configurable product. How can I fix it?\r\n\r\nHave a nice day!" - id: 1043 author: aditya author_email<EMAIL_ADDRESS>author_url: '' date: '2017-11-22 11:22:56 +0800' date_gmt: '2017-11-22 04:22:56 +0800' content: |- Hi, thanks for coming in! In my case, it was working well both for simple and configurable products. Do you have the product URL? ---
Today I am working on a Magento site for a Switzerland client which requires the implementation of Rappen Rounding, a 5-cents rounding for the total price for every transaction.
I actually found an extension on GitHub for that, but it was not compatible with my Magento install. I am not sure if it is not compatible with Magento 1.9.2 or conflicting with any other extensions, it just didn't work.
After digging into Magento core codes, I found that there is a simple workaround for this functionality, though we have to override Magento's core. Please be advised that this is not the best practice, it is just a simple workaround. If you want a better functionality and compatibility with future Magento updates, you'd better build a custom module / extension for that.
Here's what I did as a workaround:
app/code/core/Mage/Core/Model/store.php
app/code/local/Mage/Core/Model/store.php
function roundPrice($price){}
return round ($ price, 2);
return round($price * 2, 1)/2;
Let me know if it helps!


editable_view.js |
|
|---|---|
Duckbone.EditableViewThis module can be added to any view that contains form elements. It will take over the form found in its template and all of its fields, providing most of the functionality that is needed for taking and saving user input. UsageTo use EditableView, take the following steps:
Defining FieldsThe There are some standard attributes that can be added to all fields:
Additionally, some fields take special options. Select and Radio Set fields accept:
A Submit Button accepts:
The Form ManagerThe EditableView’s default initializer calls Form Binding BehaviorEach form field will automatically bind changes on itself to its model. This behavior is defined by each form field type, and implemented by Duckbone.BindableField. Each field will also bind its validation check, if defined. This behavior is defined on all form field types, and implemented by Duckbone.ValidateableField. Form submission events are captured by the EditableView’s FormManager,
and To define alternate behavior on form submission, it is simplest to simply omit any submit buttons inside the form itself, and bind form submission to another button defined outside of the form itself. Default Model Sync BehaviorBe default, the following events trigger these behaviors on the form:
Defining Additional Model Sync BehaviorCreate a If you wish to redefine default behavior, the easiest approach is to
override Cloning ModelsEditable view clones the given model to create a scratch model to work with in the form. When the model is saved, then all attributes from the scratch model are copied back to the original model. The approach has a number of advantages:
This clone is created by If a model has additional properties or associations that are necessary for the form to function,
then the developer should override the model’s After Save DestinationWhen the EditableView’s model is successfully saved, the original model can be assigned to
an afterSaveDestination. The model can be added to a collection, or set as a property on another model.
Define the view’s Usage examples:
|
(function() { |
helper {{base_errors}}This helper creates a ul containing each base error on the form’s model. |
Handlebars.registerHelper('base_errors', function() {
return Handlebars.helpers.child("_baseErrors");
});
Duckbone.EditableView = { |
Mixin |
|
property isEditableViewIndicates a view that includes EditableView |
isEditableView: true, |
function includedAlso includes ViewLifecycleExtensions, which automatically calls several of these methods during the view’s initialize and remove |
included: function() {
if (!this.hasViewLifecycleExtensions) {
Duckbone.include(this, Duckbone.ViewLifecycleExtensions);
}
}, |
Form Set Up |
|
function createFormAccepts the following options:
This method creates the view’s FormManager which builds all of the form field views. |
createForm: function(options) {
options = options || {};
var formElement = options.el || $(this.el).find('form').get(0) || $(this.el).get(0);
var fieldOptions = options.fields || this.options.fields || this.fields;
var model = options.model || this.model;
var form = new Duckbone.FormManager({
el: formElement,
fields: fieldOptions,
model: model || new Backbone.Model(),
view: this
});
this.form = this.form || form;
return form;
}, |
|
Override NestableView.setupNestedViews to include base errors |
setupNestedViews: function() {
this.children = this.createChildren();
this.children._baseErrors = new Duckbone.BaseErrorsView({ model: new Duckbone.ErrorList(this.model) });
}, |
function bindModelSyncEventsBinds the events triggered by a Syncable-enhanced Model to those default
behaviors defined below. Additionally binds user defined model sync events,
defined on the view’s |
bindModelSyncEvents: function() {
bindEvents(this, defaultModelSyncEvents);
if (this.modelSyncEvents) bindEvents(this, this.modelSyncEvents);
}, |
Model cloning |
|
function cloneModelForEditingThis function clones the model for the workspace, and binds a handler to copy back
attributes to the original model when saved. It also sets up the model’s after save destination.
After this method has been called, |
cloneModelForEditing: function() {
if (!this.model) throw("Found not, has your model been. Cloned, it can not be.");
this.originalModel = this.model;
this.model = this.originalModel.clone();
this.weakBindToModel('sync:success', this.saveClone, this);
}, |
function saveCloneAutomatically called when the model is successfully synced, or |
saveClone: function() {
var attrs = _.clone(this.model.attributes);
_(this.form.fields).each(function(field) {
if (field.options.temporary) {
delete attrs[field.modelAttribute];
}
});
this.originalModel.set(attrs);
copyToDestination.call(this);
}, |
function expireCloneThe function is called by the ViewLifecycleExtensions when the view’s |
expireClone: function() {
if (!this.originalModel) return;
this.model.clear({silent: true});
var explode = function() {
throw('Attempted get/set on expired clone from Duckbone.EditableView. Use original model instead.');
}
this.model.set = explode;
this.model.get = explode;
this.model = this.originalModel;
delete this.originalModel;
}, |
function resetModelDiscards any edits to the clone, and restore its attributes from the original model. |
resetModel: function() {
if (!this.originalModel) throw("Cloned not, has your model been. Reset, we can not do.")
this.model.set(this.originalModel.attributes);
}, |
Default Model Sync HandlersThese handlers are automatically bound to the model’s sync events. |
|
function defaultModelSyncSavingHandlerCalled on either a sync:create or sync:update event. The default behavior is to clear all of the validation error notices on the form. |
defaultModelSyncSavingHandler: function(response) {
$(this.el).find('div.error_banner').hide();
_.each(this.form.fields, function(field) {
if (field.isValidateableField) {
field.clearErrors();
}
}, this);
}, |
function defaultModelSyncInvalidHandlerCalled on a sync:invalid event. The default behavior is to inspect the validation errors on the model, and add error notices to all invalid fields. It also scrolls the page so that the top of the form is visibile, in the event that it contains an error notice bar. |
defaultModelSyncInvalidHandler: function(response) {
$(this.el).find('div.error_banner').show();
_.each(this.model.errors, function(error, modelAttribute) {
var field = this.form.getFieldForModelAttribute(modelAttribute);
_.each(this.model.errors[modelAttribute], function(error) {
if (field && field.isValidateableField) {
field.addError(error);
field.form.trigger('fieldValidityChanged', field);
} else {
_.log("Cannot add error for field " + modelAttribute + ": " + error);
}
}, this);
}, this);
this.form.showErrorBanner();
}, |
function defaultModelSyncSuccessHandlerCalled on a sync:success event. No operation. Reserved for future use. |
defaultModelSyncSuccessHandler: function(response) {}, |
function defaultModelSyncErrorHandlerCalled on a sync:error event. No operation. Reserved for future use. Note that SyncableModel will also trigger sync error events on the top level Duckbone object so that the entire application may respond to fatal server errors. |
defaultModelSyncErrorHandler: function(response) {}, |
function defaultModelSyncCompleteHandlerCalled on a sync:complete event. No operation. Reserved for future use. |
defaultModelSyncCompleteHandler: function(response) {}
}; |
FormManagerThe Form Manager creates all of the subviews for each form field and manages their state and validation.
Normally this object is not used much in practice, but in a view one can
access individual form fields with it like: |
|
ConstructorAccepts the following options:
|
Duckbone.FormManager = function(options) {
this.el = options.el || $('<form action="#"></form>').get(0);
this.fieldOptions = _.clone(options.fields) || {};
this.model = options.model || new Backbone.Model({});
this.view = options.view;
this.name = $(this.el).attr('name') || 'untitled_form';
this.createFields();
}; |
|
Mix in Backbone.Events |
_.extend(Duckbone.FormManager.prototype, Backbone.Events);
_.extend(Duckbone.FormManager.prototype, { |
function createFieldsCreate form field views for all those defined in the fields object on the view. |
createFields: function() { |
|
Create all of the model fields |
var field, form = this, name;
for (name in this.fieldOptions) {
field = this.createField(name, this.fieldOptions[name]);
} |
|
Create the submit button fields |
$(this.el).find('button.form_submit').each(function() {
name = $(this).attr('name');
if (!form.fields[name]) {
field = new Duckbone.forms.fieldTypes['submit']({
name: name, el: this, form: form
});
form.fields[field.name] = field;
}
}); |
|
Assign ids and names to form labels |
$(this.el).find('label').each(function() {
var name = $(this).attr('data-field-name');
if (name && form.fields[name]) $(this).attr('for', idFor(form, form.fields[name]));
});
}, |
function createField
Create an individual form field view for the given field name and options. The field type is either determined by the “type” attribute in options, or by a heuristic in looking at the form field class attribute. Fields defined by Duckbone are classed “form_[type]” by the form helpers. |
createField: function(name, fieldOptions) {
this.fields = this.fields || {};
var el, formFieldClass, field;
el = $(this.el).find(selectorFor(name)).get(0);
if (el) {
formFieldClass = (fieldOptions['type']) ? Duckbone.forms.fieldTypes[fieldOptions['type']] : getFormFieldClass(el);
if (formFieldClass) {
field = new formFieldClass(_.extend(fieldOptions, {el: el, model: this.model, form: this, name: name} ));
field.name = name;
$(field.el).attr('id', idFor(this, field));
} else {
throw ("Bad form field type " + name);
}
} else {
throw ("Form field " + name + " defined in view, missing in template")
}
this.fields[name] = field;
return field;
}, |
function getField
Return a field view from the form for the given name. The developer may then use get() and set() on this field to manipulate its value. |
getField: function(name) {
return this.fields[name];
}, |
function getFieldForModelAttribute
Return the field view that corresponds to the given model attribute. |
getFieldForModelAttribute: function(modelAttribute) {
return _.detect(this.fields, function (field) {
return field.modelAttribute == modelAttribute;
}, this);
}, |
function validate
Validate all fields in the form according to their validation rules. After this is called, the view will have a boolean property “isValid” |
validate: function() {
this.isValid = true
var fieldValid;
for (var field in this.fields) {
fieldValid = this.fields[field].validate ? this.fields[field].validate() : true;
if (!fieldValid) this.isValid = false;
}
return this.isValid;
}, |
function finishEditingValidates the model locally. If valid, saves the clone back to the originalModel. Otherwise displays errors and returns false. |
finishEditing: function() {
if (this.validate()) {
this.view.saveClone();
return true;
} else {
this.showErrorBanner();
return false;
}
},
showErrorBanner: function() {
$(this.el).find('div.error_banner').show();
scrollToTop(this.el);
}, |
function submit
Submits the form. First validate() is called on all fields,
and then if the form is valid, then the model is saved to the server.
The given options object is passed directly to |
submit: function(options) {
if (this.validate()) {
options = _.clone(options) || {};
_.each(['success','error'], function(callbackName) {
if (typeof options[callbackName] == 'function') {
var originalCallback = options[callbackName];
options[callbackName] = function(model, response) {
_.defer(_.bind(originalCallback, model, model, response));
}
}
}, this);
this.model.save(null, options);
} else {
this.showErrorBanner();
}
}
}); |
Internal Functions |
|
|
Copys the model to the final place it should arrive at once it is saved,
as defined by the view’s ‘afterSaveDestination’ property.
Called by |
var copyToDestination = function() {
var dests = this.options.afterSaveDestination || this.afterSaveDestination;
if (!dests) return;
if (!(dests instanceof Array)) {
dests = [dests];
}
_.each(dests, function(dest) {
if (dest.collection) {
dest.collection.add(this.originalModel);
} else {
var setterName = 'set' + dest.association.slice(0, 1).toUpperCase() + dest.association.slice(1);
dest.model[setterName].call(dest.model, this.originalModel);
}
}, this);
}; |
|
Default model sync events that are bound when bindModelSyncEvents() is called |
var defaultModelSyncEvents = {
'sync:create': 'defaultModelSyncSavingHandler',
'sync:update': 'defaultModelSyncSavingHandler',
'sync:success': 'defaultModelSyncSuccessHandler',
'sync:invalid': 'defaultModelSyncInvalidHandler',
'sync:error': 'defaultModelSyncErrorHandler',
'sync:complete': 'defaultModelSyncCompleteHandler'
}; |
|
Binds default events to the model |
function bindEvents(view, events) {
for (var event in events) {
var method = view[events[event]];
if (typeof method == 'function') view.weakBindToModel(event, method, view);
}
}; |
|
Concatenates the form and field names into an id for each form field DOM element |
function idFor(formManager, field) {
return formManager.name + '_' + field.name;
}; |
|
Returns a jQuery selector for the given form field name |
function selectorFor(name) {
return '[name=' + name + ']';
}; |
|
Inspects a DOM element and determines the form field type based upon its class name. The handlebars form helpers insert a class name, ie “formtext” or “formselect” |
function getFormFieldClass(el) {
var type = /^form_(.*)/.exec($(el).attr('class'))[1];
return Duckbone.forms.fieldTypes[type];
} |
Scrolling |
|
|
Time to scroll to the top of the form in milliseconds |
var SCROLL_TIME = 400; |
|
Easing function to use |
var SCROLL_EASING = 'swing'; |
|
Number of pixels above the top of the form element we scroll to |
var SCROLL_BREATHING_ROOM = 100; |
|
Smooth scrolls the browser window so that the top of the form is visible. Called when a form is invalid and all errors should be shown. |
function scrollToTop(el) {
var offset = $(el).offset().top;
offset = (offset > SCROLL_BREATHING_ROOM) ? offset - SCROLL_BREATHING_ROOM : 0;
$('html body').animate({ scrollTop: offset }, SCROLL_TIME, SCROLL_EASING);
}
})(); |


58 tweets from the party may not appear in this replay feed because they have been deleted by the author


--- title: 'Contributions / Fees' contacts: - name: 'Peter' image: 'what-we-do/peter_ny-300x197.jpg' - name: 'Suna' image: 'what-we-do/board4-200x300.jpg' ---
The Alumni Board’s efforts to establish the association as a self-sufficient and financially independent institution has received strong support from within the association. With almost 30 alumni from various majors and graduating classes, the Alumni Fees Initiative (AFI) aims at designing a sustainable membership model for alumni contributions.
We are currently evaluating our crowdsourced feedback and will share the results for further discussion and fine-tuning. Should you be interested in partaking in the process or have any questions, please get in touch with Peter or Suna from the Alumni Board. Expect further news on Alumni Fees soon!


Over at The Dabbler this week, the muffin dilemma of De Quincey's lieutenant-colonel, one of the greatest of all breakfast anecdotes.
Elsewhere, global dominion continues apace with my diverse and vibrant wittering on Episode 72 of The Pod Delusion.


05 March 2002
Disease Outbreak Reported
As of 5 March the Ministry of Health, Democratic Republic of the Congo has reported 5021 cases of cholera and 407 deaths in Katanga province, since the outbreak began in November 2001. A total of 8 health zones in Katanga province, including the city of Lubumbashi, have been affected, including Ankoro, Kabolo, Kongolo and Kalemie in the northern part of the province.
The Minister of Public Health and health workers from Médecins sans frontières (MSF Belgium, MSF France, MSF Spain) and WHO have traveled to the affected province. An interagency committee was set up and has set in place outbreak control measures including case management, preventive measures, social mobilization and training, surveillance and operational training activities.


Public Member Functions | |
| Character (final String name) | |
| Constructor for Character with name only. More... | |
| Character (final String name, final String dialog) | |
| Constructor for Character with name and dialog only. More... | |
| Character (final String name, final String dialog, Item wantedItem, final String successAction, final String failureAction) | |
| Constructor for Character. More... | |
| void | addDialog (final String dialog) |
| Add a possible dialog. More... | |
| String | talk () |
| A dialog to be displayed. More... | |
| String | takeItem (Item item) |
| Try to give him an Item. More... | |
| boolean | wantsItem (Item item) |
| Returns true if the given Item is wanted by the creature/character. More... | |
| String | getName () |
| Name field getter. More... | |
| boolean | isSatisfied () |
class Character
Definition at line 17 of file Character.java.
| pkg_world.pkg_characters.Character.Character | ( | final String | name | ) |
Constructor for Character with name only.
When using this constructor only, the creature/character says nothing and wants nothing.
| name | The name of the creature/character |
Definition at line 62 of file Character.java.
| pkg_world.pkg_characters.Character.Character | ( | final String | name, |
| final String | dialog | ||
| ) |
Constructor for Character with name and dialog only.
When using this constructor only, the creature/character wants nothing.
| name | The name of the creature/character |
| dialog | The dialog displayed when talking to it/him/her |
Definition at line 75 of file Character.java.
| pkg_world.pkg_characters.Character.Character | ( | final String | name, |
| final String | dialog, | ||
| Item | wantedItem, | ||
| final String | successAction, | ||
| final String | failureAction | ||
| ) |
Constructor for Character.
| name | The name of the creature/character |
| dialog | The dialog displayed when talking to it/him/her |
| wantedItem | Item wanted by the creature/character |
Definition at line 86 of file Character.java.
| void pkg_world.pkg_characters.Character.addDialog | ( | final String | dialog | ) |
Add a possible dialog.
| dialog | The dialog to add |
Definition at line 97 of file Character.java.
| String pkg_world.pkg_characters.Character.getName | ( | ) |
Name field getter.
Definition at line 132 of file Character.java.
Referenced by pkg_world.pkg_characters.MovingCharacter.move().
| boolean pkg_world.pkg_characters.Character.isSatisfied | ( | ) |
Definition at line 136 of file Character.java.
Referenced by pkg_commands.GiveCommand.execute().
| String pkg_world.pkg_characters.Character.takeItem | ( | Item | item | ) |
Try to give him an Item.
Definition at line 113 of file Character.java.
Referenced by pkg_commands.GiveCommand.execute().
| String pkg_world.pkg_characters.Character.talk | ( | ) |
A dialog to be displayed.
Definition at line 105 of file Character.java.
| boolean pkg_world.pkg_characters.Character.wantsItem | ( | Item | item | ) |
Returns true if the given Item is wanted by the creature/character.
| item | The Item to check |
Definition at line 124 of file Character.java.
Referenced by pkg_commands.GiveCommand.execute().


home
about
portfolio
resume
*ann tran*
A Boston-based creative professional.
I like to make things expressive and functional.


More Information about the FNEXRAD Feed
Estimated hourly volume: about 3 Mbytes in 225 products
How to access NEXRAD data via the LDM
(including FNEXRAD data)


GSoC Project
May 20, 2017
The project I will be working this (G) summer (oC)
Overview
The motivation, here, is to extend the functionality of vulture as a library,
and to pass on all metadata through the API and then to harness this utility in
VultureBear for auto removing dead code, which would greatly optimise the bear.
The second part of this project focuses on offering the source range of the dead
code which would make auto-removal much easier. As of now, vulture only supplies
the beginning of the dead code. Also, it proposes to enhance vulture in order to
detect unreachable code (like if False
, if True else
, any code written after
return statements, etc). - this shall help the user in trimming down their
codebase without affecting usability. Also, the third part would be to implement
a confidence value for every result, this shall be helpful when tackling false
positives.
Goals
- Modify vulture, such as to extend its core functionality as a library.
- Refactor VultureBear accordingly for ensuring optimal performance.
- Implement a method to acquire the source range of dead code and make suitable changes in the API and Bear.
- Detect the instances of unreachable code, like `if False** statements
- Analyse and implement a confidence value for results.
Specifications
1.) Realise vulture’s API in VultureBear*
Extending vulture’s API: This would allow the user to find all the unused
code through a single abstract layer: get_unused_code
. Strategy here
would be to:
Parse all files straight away from dict(filename: filecontent) - This
would highly improve the performance of the bear later due to the time we
save of memory copying.
Return a sorted list of tuples [(item.filename, item.lineno, item.typ,
item)...]
- which would be easily configurable. This can be easily implemented,
given the already existing Vulture.scan(), Vulture.report(),
Vulture.unused_funcs()
, etc.
Enhance VultureBear
Refactor VultureBear to directly fetch results through get_unused_code
(API), thus making it more efficient- we would have memory files passing
(An extra layer of parsing would then be removed)
Further enhancements in vulture (detect unreachable code and reporting ranges of dead code** would influence the API, which would also need refactoring of the Bear.
2.) Making whitelist default and extending it further
The first step here would be to make the whitelist default. The important thing would be to identify possible cases which might cause vulture to report a false positive. This can be achieved through extensive testing with major projects - trending python projects on github would cater to our need for the purpose. This approach would serve us many benefits:
We can identify instances of what should ideally be in our whitelist file - as we may find any lesser known constructs.
We can test vulture for any unreported bugs.
We can find many projects which use/might want to use vulture - they may further collaborate with us in making the whitelists together. (As proposed by @jendrikseipp**
3.) Acquiring source range and implementing auto-removal
Analyse and discuss with the community the utilities of ast or enhanced pyflake ast for what would better cater to our problem and would offer simplicity for source-range acquisition and arrive at a concrete conclusion. Also, there was another proposal by @m0hawk to get everything until the next node starts. Dialogue here - #25
Also, if able to fetch the source range successfully, implement the pathway through which the metadata flows in and out of API, this would not require much work because we can easily change item.lineno (int) to item.dead_range (tuple of ints** and can parse them over in the VultureBear.
4.) Detecting unreachable code
We would first need to identify cases where code cannot be reached. Some of the common ones are:
If False
If True; else
- Any code after
return
statement in the block containing return itself. raise
statement in `try** block.
Similar constructs would have to be looked onto. The crude form of this would be:
- Analyse the ast’s
- Look for the if nodes
- Check the boolean affiliated to it, tracking previous arguments.
5.) Implementing a confidence value for results
We would need to analyse every construct individually on a case by case basis. For example, we already know that import statements can be predicted with 100% surety (except for * imports, where it would be 0%), but functions often have false-positives.
The confidence value will be alike the ones given below: (The finer grained distinctions will need further discussion)
Table 1: A table with default style formatting
| Construct | Confidence Value |
|---|---|
| import | 100% |
| from foo import * | 0% |
| variable | <100% |
| function | <100% |
| class | <100% |
| if False | 100% |
References:
Milestones
PREPARATION/BONDING
- A concept for the source range acquisition is finalized.
- Use vulture to report dead code for popular Python projects on Github
CODING PHASE 1
- Vulture offers its functionality as a library
- The VultureBear uses the new vulture library
- Confidence values are implemented for vulture results
CODING PHASE 2
- Create whitelist files for popular Python frameworks like Django
- Refine default whitelists for vulture
- If a way was found to offer source ranges, the removal of dead code is implemented for the VultureBear using a confidence value as threshold.
CODING PHASE 3
- Implement additional detection cases for unreachable code
- Update the API to easily transmit newly created data (confidence values, unreachable code, source range, etc.)
- Integrate the resulting API with the VultureBear
- All implemented code is fully tested and documented.
Thank You for reading along, please feel free to tweet to @rahul722j or reach out to me at<EMAIL_ADDRESS>or just comment below for any queries.


- NAME
- Tcl_CreateChannelHandler, Tcl_DeleteChannelHandler - call a procedure when a channel becomes readable or writable
- SYNOPSIS
- #include <tcl.h>
- void
- Tcl_CreateChannelHandler(channel, mask, proc, clientData)
- void
- Tcl_DeleteChannelHandler(channel, proc, clientData)
- ARGUMENTS
- DESCRIPTION
- SEE ALSO
- KEYWORDS
Tcl_CreateChannelHandler, Tcl_DeleteChannelHandler - call a procedure when a channel becomes readable or writable
#include <tcl.h>
void
Tcl_CreateChannelHandler(channel, mask, proc, clientData)
void
Tcl_DeleteChannelHandler(channel, proc, clientData)
- Tcl_Channel channel (in)
-
Tcl channel such as returned by Tcl_CreateChannel.
- int mask (in)
-
Conditions under which proc should be called: OR-ed combination of
TCL_READABLE, TCL_WRITABLE and TCL_EXCEPTION. Specify
a zero value to temporarily disable an existing handler.
- Tcl_FileProc *proc (in)
-
Procedure to invoke whenever the channel indicated by channel meets
the conditions specified by mask.
- ClientData clientData (in)
-
Arbitrary one-word value to pass to proc.
Tcl_CreateChannelHandler arranges for proc to be called in the
future whenever input or output becomes possible on the channel identified
by channel, or whenever an exceptional condition exists for
channel. The conditions of interest under which proc will be
invoked are specified by the mask argument.
See the manual entry for fileevent for a precise description of
what it means for a channel to be readable or writable.
Proc must conform to the following prototype:
typedef void Tcl_ChannelProc(
ClientData clientData,
int mask);
The clientData argument is the same as the value passed to
Tcl_CreateChannelHandler when the handler was created. Typically,
clientData points to a data structure containing application-specific
information about the channel. Mask is an integer mask indicating
which of the requested conditions actually exists for the channel; it will
contain a subset of the bits from the mask argument to
Tcl_CreateChannelHandler when the handler was created.
Each channel handler is identified by a unique combination of channel,
proc and clientData.
There may be many handlers for a given channel as long as they do not
have the same channel, proc, and clientData.
If Tcl_CreateChannelHandler is invoked when there is already a handler
for channel, proc, and clientData, then no new
handler is created; instead, the mask is changed for the
existing handler.
Tcl_DeleteChannelHandler deletes a channel handler identified by
channel, proc and clientData; if no such handler exists,
the call has no effect.
Channel handlers are invoked via the Tcl event mechanism, so they
are only useful in applications that are event-driven.
Note also that the conditions specified in the mask argument
to proc may no longer exist when proc is invoked: for
example, if there are two handlers for TCL_READABLE on the same
channel, the first handler could consume all of the available input
so that the channel is no longer readable when the second handler
is invoked.
For this reason it may be useful to use nonblocking I/O on channels
for which there are event handlers.
Notifier, Tcl_CreateChannel, Tcl_OpenFileChannel, vwait(n).
blocking, callback, channel, events, handler, nonblocking.
Copyright © 1995-1997 Roger E. Critchlow Jr.
Copyright © 1996 Sun Microsystems, Inc.


Stephen A. Smith Fires Back At NFL Player’s Colin Kaepernick Comment
by Andrew HolleranESPN’s Stephen A. Smith posted his thoughts on Twitter regarding Colin Kaepernick’s NFL workout drama on Saturday night. The former NFL quarterback ended up moving his workout from the Atlanta Falcons facility to a high school about 60 miles away against the league’s wishes.
Kaepernick, who was scheduled to work out in front of 24-plus teams at the Falcons facility, worked out for much fewer teams at the high school. He allowed all media and some fans to watch him throw, too.
Smith does not believe Kaepernick truly wants to play in the NFL.
“He don’t want to play,” Smith said. “He wants to be a martyr.”
Eric Reid, who knelt with Kaepernick, called out Smith on Twitter.
“Tap dancing for the NFL,” he wrote. “Damn straight Colin wants to control the narrative! He supposed to trust the organization that blackballed him and has done absolutely nothing in good faith??? Born on Tuesday, just not last Tuesday.”
Smith then fired back on Twitter. He did not hold back.
OK then.
The Colin Kaepernick storyline had mostly gone away from NFL discussions over the last year or so, but it’s back in a big way now.


Match Play. Red leads 3-2 to 5. How should Red play 31?
pips Red=126 White=158
(CorrectAnswer= 0/0, ErrorScore= 0)
To quote Joe Sylvester (former world number one), “When on offence play offence, when on defence play defence”.
A gammon here is precisely what Red wants and so he should play 13/10, 7/6.
23/22, 13/10 is a reasonable play but I always adhere to Joe’s principle when I can.
A gammon here is precisely what Red wants and so he should play 13/10, 7/6.
23/22, 13/10 is a reasonable play but I always adhere to Joe’s principle when I can.
1. Cubeful 2-ply 13/10 7/6 Eq.: +0.663 0.650 0.391 0.008 - 0.350 0.083 0.005 2. Cubeful 2-ply 23/22 13/10 Eq.: +0.645 (-0.018) 0.650 0.358 0.006 - 0.350 0.077 0.004 3. Cubeful 2-ply 24/21 23/22 Eq.: +0.593 (-0.071) 0.645 0.311 0.006 - 0.355 0.077 0.003 4. Cubeful 2-ply 23/20 7/6 Eq.: +0.591 (-0.072) 0.641 0.341 0.006 - 0.359 0.079 0.003 5. Cubeful 2-ply 13/9 Eq.: +0.581 (-0.082) 0.634 0.358 0.007 - 0.366 0.082 0.004


|
OpenCV <IP_ADDRESS> | |||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object org.opencv.ml.CvStatModel org.opencv.ml.CvKNearest
public class CvKNearest
The class implements K-Nearest Neighbors model as described in the beginning of this section.
| Constructor Summary | |
|---|---|
CvKNearest()
Default and training constructors. |
|
CvKNearest(Mat trainData,
Mat responses)
Default and training constructors. |
|
CvKNearest(Mat trainData,
Mat responses,
Mat sampleIdx,
boolean isRegression,
int max_k)
Default and training constructors. |
| Method Summary | |
|---|---|
float |
find_nearest(Mat samples,
int k,
Mat results,
Mat neighborResponses,
Mat dists)
Finds the neighbors and predicts responses for input vectors. |
boolean |
train(Mat trainData,
Mat responses)
Trains the model. |
boolean |
train(Mat trainData,
Mat responses,
Mat sampleIdx,
boolean isRegression,
int maxK,
boolean updateBase)
Trains the model. |
| Methods inherited from class org.opencv.ml.CvStatModel |
|---|
load, load, save, save |
| Methods inherited from class java.lang.Object |
|---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Constructor Detail |
|---|
public CvKNearest()
Default and training constructors.
See "CvKNearest.train" for additional parameters descriptions.
public CvKNearest(Mat trainData, Mat responses)
Default and training constructors.
See "CvKNearest.train" for additional parameters descriptions.
trainData
- a trainDataresponses
- a responsespublic CvKNearest(Mat trainData, Mat responses, Mat sampleIdx, boolean isRegression, int max_k)
Default and training constructors.
See "CvKNearest.train" for additional parameters descriptions.
trainData
- a trainDataresponses
- a responsessampleIdx
- a sampleIdxisRegression
- a isRegressionmax_k
- a max_k| Method Detail |
|---|
public float find_nearest(Mat samples, int k, Mat results, Mat neighborResponses, Mat dists)
Finds the neighbors and predicts responses for input vectors.
For each input vector (a row of the matrix samples
), the method
finds the k
nearest neighbors. In case of regression, the
predicted result is a mean value of the particular vector's neighbor
responses. In case of classification, the class is determined by voting.
For each input vector, the neighbors are sorted by their distances to the vector.
In case of C++ interface you can use output pointers to empty matrices and the function will allocate memory itself.
If only a single input vector is passed, all output matrices are optional and the predicted value is returned by the method.
The function is parallelized with the TBB library.
samples
- Input samples stored by rows. It is a single-precision
floating-point matrix of number_of_samples x number_of_features
size.k
- Number of used nearest neighbors. It must satisfy constraint: k
<= "CvKNearest.get_max_k".results
- Vector with results of prediction (regression or
classification) for each input sample. It is a single-precision
floating-point vector with number_of_samples
elements.neighborResponses
- Optional output values for corresponding
neighbors
. It is a single-precision floating-point matrix of
number_of_samples x k size.dists
- a distspublic boolean train(Mat trainData, Mat responses)
Trains the model.
The method trains the K-Nearest model. It follows the conventions of the generic "CvStatModel.train" approach with the following limitations:
CV_ROW_SAMPLE
data layout is supported.
is_regression=false
)
or ordered (is_regression=true
).
var_idx
) and missing measurements are
not supported.
trainData
- a trainDataresponses
- a responsespublic boolean train(Mat trainData, Mat responses, Mat sampleIdx, boolean isRegression, int maxK, boolean updateBase)
Trains the model.
The method trains the K-Nearest model. It follows the conventions of the generic "CvStatModel.train" approach with the following limitations:
CV_ROW_SAMPLE
data layout is supported.
is_regression=false
)
or ordered (is_regression=true
).
var_idx
) and missing measurements are
not supported.
trainData
- a trainDataresponses
- a responsessampleIdx
- a sampleIdxisRegression
- Type of the problem: true
for regression and
false
for classification.maxK
- Number of maximum neighbors that may be passed to the method
"CvKNearest.find_nearest".updateBase
- Specifies whether the model is trained from scratch
(update_base=false
), or it is updated using the new training
data (update_base=true
). In the latter case, the parameter
maxK
must not be larger than the original value.
|
OpenCV <IP_ADDRESS> Documentation | |||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |


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flexible GMRES from ITSOL developed by Yousef Saad.
More...
|
| void | cdotc_ (complex *, int *, complex [], int *, complex [], int *) |
| |
| float | scnrm2_ (int *, complex [], int *) |
| |
| int | cfgmr (int n, void(*cmatvec)(complex, complex[], complex, complex[]), void(*cpsolve)(int, complex[], complex[]), complex *rhs, complex *sol, double tol, int im, int *itmax, FILE *fits) |
| |
◆ epsmac
◆ cdotc_()
◆ cfgmr()
| int cfgmr |
( |
int |
n, |
|
|
void(*)(complex, complex[], complex, complex[]) |
cmatvec, |
|
|
void(*)(int, complex[], complex[]) |
cpsolve, |
|
|
complex * |
rhs, |
|
|
complex * |
sol, |
|
|
double |
tol, |
|
|
int |
im, |
|
|
int * |
itmax, |
|
|
FILE * |
fits |
|
) |
| |
◆ scnrm2_()
| float scnrm2_ |
( |
int * |
, |
|
|
complex |
[], |
|
|
int * |
|
|
) |
| |


Success Tips for Cucumber Developers
Thoughtful step structuring will reduce step definitions
Review the underlying scenario steps and definitions
Consider the following feature file "attack-of-the-clones.feature"
Feature: Attack of the Clones
Scenario: Clone, Attack Anakin
Given I am a clone
When I am ordered to use my fists against Anakin
Then I should inflict some damage
Scenario: Stormtrooper, Attack Padme
Given I am a stormtrooper
When I am ordered to use my blaster against Padme
Then I should kill her
Scenario: Sith, Attack Obi-Wan
Given I am a sith
When I am ordered to use my lightsaber against Obi-Wan
Then I expect to have a 15 minute fight sequence
// File: /features/step_definitions/attack_steps.js
import { defineSupportCode } from 'cucumber'
defineSupportCode(function ({ Given, When, Then }) {
Given('I am a clone', function () {})
When('I am ordered to use my fists against Anakin', function () {})
Then('I should inflict some damage', function () {})
Given('I am a stormtrooper', function () {})
When('I am ordered to use my blaster against Padme', function () {})
Then('I should kill her', function () {})
Given('I am a sith', function () {})
When('I am ordered to use my lightsaber against Obi-Wan', function () {})
Then('I expect to have a 15 minute fight sequence', function () {})
})
Problem? We have a lot of steps to maintain
Reduce common steps into strings with data types and contextually named parameters
// File: /features/step_definitions/attack_steps.js
import { defineSupportCode } from 'cucumber'
defineSupportCode(function ({ Given, When, Then }) {
Given('I am a {word}', function (person) {})
When('I am ordered to use my {word} against {word}', function (weapon, person) {})
Then('I should inflict some damage', function () {})
Then('I should kill her', function () {})
Then('I expect to have a 15 minute fight sequence', function () {})
})
Can it be improved?
There are a few nuances with languages we might want to address which requires altering the feature file
Consider addressing proper article and gender identifiers that may be introduced later
Scenario: Enemy, Attack Androgeny
Given I am a enemy
But I am an enemy
Then I should kill her
But I should kill him
But I should kill it
Consider quoted words to address possible string types
Scenario: Darth Vader, Attack Obi-Wan
Given I am "Darth Vader"
When I am ordered to use my "red lightsaber" against "Obi-Wan Kenobi"
Replacing our words with strings
// File: /features/step_definitions/attack_steps.js
import { defineSupportCode } from 'cucumber'
defineSupportCode(function ({ Given, When, Then }) {
// A possible reusable definition for using a preceding article (a, an, the)
Given('I am {word} {word}', function (article, person) {})
// Quotes in feature steps are stripped in favor of the {string} type replacement
Given('I am {string}', function (person) {})
When('I am ordered to use my {string} against {string}', function (weapon, person) {})
Then('I should inflict some damage', function () {})
Then('I should kill {word}', function (thing_attacked) {})
Then('I expect to have a 15 minute fight sequence', function () {})
})
Any alternatives?
We can outline the scenarios with examples
Feature: Attack of the Clones
Scenario Outline: Attack!
Given I am --an enemy--
When I am ordered to use my --weapon-- against --a good guy--
Then I should --show result--
Examples:
| an enemy | a good guy | weapon | show result |
| a clone | Anakin | fists | inflict some damage |
| a stormtrooper | Padme | blaster | kill her |
| a sith | Obi-Wan Kenobi | blaster | expect a 15 minute fight sequence |
The 'Then' assertion would be a vague implementation, could be difficult to implement and may take away other phrasing options in outside features
Selenium Chemistry


Source Serif Pro¶
Source Serif Pro is a set of OpenType fonts to complement the Source Sans Pro family. In addition to a functional OpenType font, this open source project provides all of the source files that were used to build this OpenType font by using the AFDKO makeotf tool.
Installation instructions¶
Getting Involved¶
Send suggestions for changes to the Source Serif OpenType font project maintainer, Frank Grießhammer, for consideration.
Further information¶
For information about the design and background of Source Serif, please refer to the official font readme file.


_The_Art_of_War_ (R) ** 1/2 (out of ****)
Sneaking onto screens relatively unheralded by its distributor during the dog days of summer, _The_Art_of_War_ would appear to be one of those dumpers/writeoffs with which the studios traditionally clog late August. But for a good portion of its running time, director Christian Duguay's spy thriller is slickly, efficiently put together, featuring more than a few effective action sequences. Which makes it all the more unfortunate that, in the end, the film slips off the rails.
Wesley Snipes lends his usual blend of charisma and conviction to the role of Shaw, a deep cover United Nations operative who is introduced as he engages in some Bond-like derring-do at a millennium party in China. Little does he know this will be his introduction to some of the key players in a conspiracy in which he later finds himself entangled.  Accused of the latter, Shaw goes underground and, with the help of a U.N. translator (Marie Matiko), sets out to find the truth, which turns out to be more complex and far-reaching than he imagined.
As can be easily gleaned from the plot synopsis, Wayne Beach and Simon Davis Barry's script for _The_Art_of_War_ is hardly groundbreaking, and, in all honesty, neither is Duguay's direction of it. But he does make the material quite watchable. The action scenes, many of which are designed to showcase Snipes' martial arts skills, are decently handled, and he comes up with some interesting stylistic flourishes, particularly in one scene where Shaw studies the apartment of a murdered colleague; the use of flashbacks proves to be an economical storytelling device--in this instance, at least.
While Snipes remains convincing throughout the entire film, the film itself doesn't. As is the case with these conspiracy thrillers, there are late-inning twists abound, but the logistics render the already cloudy plot even murkier. The sense of overkill that ultimately does in the script spreads to other areas in the film, including some of the actors (whose names I won't divulge in the interest of protecting plot points). But no one gets infected more than Duguay. His kinetic visuals soon get out of control; the flashback device that had been employed well in the early going gets overused, and for no apparent purpose.other than to show off.
Even if _The_Art_of_War_ didn't lose its way in the end, it still wouldn't be a great film; it's much too standard a genre picture to be something truly special. But considering how right the film feels most of the way, it wouldn't have been too hard for Duguay to make a reasonably satisfying formula film. Instead, _The_Art_of_War_ illustrates how easily one can drop the ball down the stretch.
Michael Dequina<EMAIL_ADDRESS>|<EMAIL_ADDRESS>|<EMAIL_ADDRESS>Mr. Brown's Movie Site: http://www.moviereportsite.com CinemaReview Magazine: http://www.CinemaReview.com on ICQ: #25289934 | on AOL Instant Messenger: MrBrown23
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rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
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