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  • Faster way to split a string and count characters using R?

    - by chrisamiller
    I'm looking for a faster way to calculate GC content for DNA strings read in from a FASTA file. This boils down to taking a string and counting the number of times that the letter 'G' or 'C' appears. I also want to specify the range of characters to consider. I have a working function that is fairly slow, and it's causing a bottleneck in my code. It looks like this: ## ## count the number of GCs in the characters between start and stop ## gcCount <- function(line, st, sp){ chars = strsplit(as.character(line),"")[[1]] numGC = 0 for(j in st:sp){ ##nested ifs faster than an OR (|) construction if(chars[[j]] == "g"){ numGC <- numGC + 1 }else if(chars[[j]] == "G"){ numGC <- numGC + 1 }else if(chars[[j]] == "c"){ numGC <- numGC + 1 }else if(chars[[j]] == "C"){ numGC <- numGC + 1 } } return(numGC) } Running Rprof gives me the following output: > a = "GCCCAAAATTTTCCGGatttaagcagacataaattcgagg" > Rprof(filename="Rprof.out") > for(i in 1:500000){gcCount(a,1,40)}; > Rprof(NULL) > summaryRprof(filename="Rprof.out") self.time self.pct total.time total.pct "gcCount" 77.36 76.8 100.74 100.0 "==" 18.30 18.2 18.30 18.2 "strsplit" 3.58 3.6 3.64 3.6 "+" 1.14 1.1 1.14 1.1 ":" 0.30 0.3 0.30 0.3 "as.logical" 0.04 0.0 0.04 0.0 "as.character" 0.02 0.0 0.02 0.0 $by.total total.time total.pct self.time self.pct "gcCount" 100.74 100.0 77.36 76.8 "==" 18.30 18.2 18.30 18.2 "strsplit" 3.64 3.6 3.58 3.6 "+" 1.14 1.1 1.14 1.1 ":" 0.30 0.3 0.30 0.3 "as.logical" 0.04 0.0 0.04 0.0 "as.character" 0.02 0.0 0.02 0.0 $sampling.time [1] 100.74 Any advice for making this code faster?

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  • how to number t-rows ,when table generated using nested forloop in django templates

    - by stackover
    Hi, This part is from views.py results=[(A,[stuObj1,stuObj2,stuObj3]),(B,[stuObj4,stuObj5,stuObj6]),(C,[stuObj7,stuObj8])] for tup in results: total = tot+len(tup[1]) render_to_response(url,{'results':res , 'total':str(tot),}) this is template code: <th class="name">Name</th> <th class="id">Student ID</th> <th class="grade">Grade</th> {% for tup in results %} {% for student in tup|last %} {% with forloop.parentloop.counter as parentid%} {% with forloop.counter as centerid%} <tbody class="results-body"> <tr> <td>{{student.fname|lower|capfirst}} {{student.lname|lower|capfirst}}</td> <td>{{student.id}}</td> <td>{{tup|first}}</td> </tr> {% endfor %} {% endfor %} Now the problems am having are 1. numbering the rows. Here my problem is am not sure if i can do things like total=total-1 in the templates to get the numbered rows like <td>{{total}}</td> 2.applying css to tr:ever or odd. Whats happening in this case is everytime the loop is running the odd/even ordering is lost. these seems related problems. Any ideas would be great :)

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  • JavaScript onchange, onblur, and focus weirdness in Firefox

    - by typoknig
    On my form I have a discount field that accepts a dollar amount to be taken off of the total bill (HTML generated in PHP): echo "<input id=\"discount\" class=\"text\" type=\"text\" name=\"discount\" onkeypress=\"return currency(this, event)\" onchange=\"currency_format(this)\" onfocus=\"on_focus(this)\" onblur=\"on_blur(this); calculate_bill()\"/><br/><br/>\n"; The JavaScript function calculate_bill calculates the bill and takes off the discount amount as long as the discount amount is less than the total bill: if(discount != ''){ if(discount - 0.01 > total_bill){ window.alert('Discount Cannot Be Greater Than Total Bill'); document.form.discount.focus(); } else{ total_bill -= discount; } } The problem is that even that when the discount is more than the total bill focus is not being returned to the discount field. I have tried calling the calculate_bill function with onchange but neither IE or Firefox will return focus to the discount field when I do it like that. When I call calculate_bill with onblur it works in IE, but still does not work in Firefox. I have attempted to use a confirmation box instead of an alert box as well, but that didn't work either (plus I don't want two buttons, I only an "OK" button). How can I ensure focus is returned to the discount field after a user has left that field by clicking on another field or tabbing IF the discount amount is larger than the total bill?

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  • Naive Bayesian classification (spam filtering) - Doubt in one calculation? Which one is right? Plz c

    - by Microkernel
    Hi guys, I am implementing Naive Bayesian classifier for spam filtering. I have doubt on some calculation. Please clarify me what to do. Here is my question. In this method, you have to calculate P(S|W) - Probability that Message is spam given word W occurs in it. P(W|S) - Probability that word W occurs in a spam message. P(W|H) - Probability that word W occurs in a Ham message. So to calculate P(W|S), should I do (1) (Number of times W occuring in spam)/(total number of times W occurs in all the messages) OR (2) (Number of times word W occurs in Spam)/(Total number of words in the spam message) So, to calculate P(W|S), should I do (1) or (2)? (I thought it to be (2), but I am not sure, so plz clarify me) I am refering http://en.wikipedia.org/wiki/Bayesian_spam_filtering for the info by the way. I got to complete the implementation by this weekend :( Thanks and regards, MicroKernel :) @sth: Hmm... Shouldn't repeated occurrence of word 'W' increase a message's spam score? In the your approach it wouldn't, right?. Lets take a scenario and discuss... Lets say, we have 100 training messages, out of which 50 are spam and 50 are Ham. and say word_count of each message = 100. And lets say, in spam messages word W occurs 5 times in each message and word W occurs 1 time in Ham message. So total number of times W occuring in all the spam message = 5*50 = 250 times. And total number of times W occuring in all Ham messages = 1*50 = 50 times. Total occurance of W in all of the training messages = (250+50) = 300 times. So, in this scenario, how do u calculate P(W|S) and P(W|H) ? Naturally we should expect, P(W|S) P(W|H)??? right. Please share your thought...

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  • functor returning 0

    - by Jon
    I've recently started teaching myself the standard template library. I was curious as to why the GetTotal() method in this class is returning 0? ... class Count { public: Count() : total(0){} void operator() (int val){ total += val;} int GetTotal() { return total;} private: int total; }; void main() { set<int> s; Count c; for(int i = 0; i < 10; i++) s.inset(i); for_each(s.begin(), s.end(), c); cout << c.GetTotal() << endl; }

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  • Find numbers that equals a sum in an array

    - by valli-R
    I want to find the first set of integers in an array X that the sum equals a given number N. For example: X = {5, 13, 24, 9, 3, 3} N = 28 Solution = {13, 9, 3, 3} Here what I have so far : WARNING, I know it uses global and it is bad,that's not the point of the question. <?php function s($index = 0, $total = 0, $solution = '') { global $numbers; global $sum; echo $index; if($total == 28) { echo '<br/>'.$solution.' = '.$sum.'<br/>'; } elseif($index < count($numbers) && $total != 28) { s($index + 1, $total, $solution); s($index + 1, $total + $numbers[$index], $solution.' '.$numbers[$index]); } } $numbers = array(5, 13, 24, 9, 3, 3); $sum = 28; s(); ?> I don't get how I can stop the process when it finds the solution.. I know I am not far from good solution.. Thanks in advance

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  • How to do Linq aggregates when there might be an empty set?

    - by Shaul
    I have a Linq collection of Things, where Thing has an Amount (decimal) property. I'm trying to do an aggregate on this for a certain subset of Things: var total = myThings.Sum(t => t.Amount); and that works nicely. But then I added a condition that left me with no Things in the result: var total = myThings.Where(t => t.OtherProperty == 123).Sum(t => t.Amount); And instead of getting total = 0 or null, I get an error: System.InvalidOperationException: The null value cannot be assigned to a member with type System.Decimal which is a non-nullable value type. That is really nasty, because I didn't expect that behavior. I would have expected total to be zero, maybe null - but certainly not to throw an exception! What am I doing wrong? What's the workaround/fix?

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  • SQL Server Update Group by

    - by Gerardo Abdo
    I'm trying to execute this on MS-SQL but returns me an error just at the Group by line update #temp Set Dos=Count(1) From Temp_Table2010 s where Id=s.Total and s.total in (Select Id from #temp) group by s.Total Do anyone knows how can I solve this problem having good performance.

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  • Implement loops for python 3

    - by Alex
    Implement this loop: total up the product of the numbers from 1 to x. Implement this loop: total up the product of the numbers from a to b. Implement this loop: total up the sum of the numbers from a to b. Implement this loop: total up the sum of the numbers from 1 to x. Implement this loop: count the number of characters in a string s. i'm very lost on implementing loops these are just some examples that i am having trouble with-- if someone could help me understand how to do them that would be awesome

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  • Efficiently display file status when using background thread

    - by schmoopy
    How can i efficiently display the status of a file when using a background thread? For instance, lets say i have a 100MB file: when i do the code below via a thread (just as an example) it runs in about 1 min: foreach(byte b in file.bytes) { WriteByte(b, xxx); } But... if i want to update the user i have to use a delegate to update the UI from the main thread, the code below takes - FOREVER - literally i don't know how long im still waiting, ive created this post and its not even 30% done. int total = file.length; int current = 0; foreach(byte b in file.bytes) { current++; UpdateCurrentFileStatus(current, total); WriteByte(b, xxx); } public delegate void UpdateCurrentFileStatus(int cur, int total); public void UpdateCurrentFileStatus(int cur, int total) { // Check if invoke required, if so create instance of delegate // the update the UI if(this.InvokeRequired) { } else { UpdateUI(...) } }

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  • Problem with variable inside gsp

    - by xain
    Hi, I have a loop inside a gsp page, and I want to do a calculation on the fly, so I set a variable: <g:set var="total" value="0" /> And in the loop: <g:each in="${mob}" var="m"> ... <g:set var="total" value="${total+(m.q*m.sts.uf)}"/> ... </g:each> The "total" value does not correspond to the expected calculation. m.q is an integer, and m.sts.uf is a float. Any hints ? Thanks.

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  • SQL Server Reporting Services Format Hours as Hours:Minutes

    - by Frank Schmitt
    I'm writing reports on SQL Server Reporting Server that have a number of hours grouped by, say, user, and a total calculated based on the sum of the values. Currently my query runs a stored proc that returns the hours as in HH:MM format, rather than decimal hours, as our users find that more intuitive. The problem occurs when I try and add up the column using an SSRS expression, because the SUM function isn't smart enough to handle adding up times in this format. Is there any way to: Display a time interval (in minutes or hours) in HH:MM format while having it calculated in decimal form? Or split up and calculate the total of the HH:MM text values to arrive at a total as an expression? I'd like to avoid having to write/run a second query just to get the total.

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  • Mysql query: count and distinct

    - by Azevedo
    I have this hypotetical MySQL table: TABLE cars: (year, color, brand) How do I count # of cars grouped by brand and year? I mean, how can I get to know how many colors are there grouped by brand like: brand "GM": total # of colors: 8. brand "GM": total # of years (grouped together): 14 (meaning there are count of 14 different years). brand "TOYOTA": total # of colors: 3. brand "TOYOTA": total # of years (grouped together): 10 (meaning there are count of 14 different years) I tried playing some queries with COUNT, DISTINCT, GROUP BY but I can't get to it. Actually I'm trying to get the 2 queries... +-------+---------------+ | brand | count(colors) | +-------+---------------+ +-------+--------------+ | brand | count(years) | +-------+--------------+ thanks a lot!

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  • g-wan - reproducing the performance claims

    - by user2603628
    Using gwan_linux64-bit.tar.bz2 under Ubuntu 12.04 LTS unpacking and running gwan then pointing wrk at it (using a null file null.html) wrk --timeout 10 -t 2 -c 100 -d20s http://127.0.0.1:8080/null.html Running 20s test @ http://127.0.0.1:8080/null.html 2 threads and 100 connections Thread Stats Avg Stdev Max +/- Stdev Latency 11.65s 5.10s 13.89s 83.91% Req/Sec 3.33k 3.65k 12.33k 75.19% 125067 requests in 20.01s, 32.08MB read Socket errors: connect 0, read 37, write 0, timeout 49 Requests/sec: 6251.46 Transfer/sec: 1.60MB .. very poor performance, in fact there seems to be some kind of huge latency issue. During the test gwan is 200% busy and wrk is 67% busy. Pointing at nginx, wrk is 200% busy and nginx is 45% busy: wrk --timeout 10 -t 2 -c 100 -d20s http://127.0.0.1/null.html Thread Stats Avg Stdev Max +/- Stdev Latency 371.81us 134.05us 24.04ms 91.26% Req/Sec 72.75k 7.38k 109.22k 68.21% 2740883 requests in 20.00s, 540.95MB read Requests/sec: 137046.70 Transfer/sec: 27.05MB Pointing weighttpd at nginx gives even faster results: /usr/local/bin/weighttp -k -n 2000000 -c 500 -t 3 http://127.0.0.1/null.html weighttp - a lightweight and simple webserver benchmarking tool starting benchmark... spawning thread #1: 167 concurrent requests, 666667 total requests spawning thread #2: 167 concurrent requests, 666667 total requests spawning thread #3: 166 concurrent requests, 666666 total requests progress: 9% done progress: 19% done progress: 29% done progress: 39% done progress: 49% done progress: 59% done progress: 69% done progress: 79% done progress: 89% done progress: 99% done finished in 7 sec, 13 millisec and 293 microsec, 285172 req/s, 57633 kbyte/s requests: 2000000 total, 2000000 started, 2000000 done, 2000000 succeeded, 0 failed, 0 errored status codes: 2000000 2xx, 0 3xx, 0 4xx, 0 5xx traffic: 413901205 bytes total, 413901205 bytes http, 0 bytes data The server is a virtual 8 core dedicated server (bare metal), under KVM Where do I start looking to identify the problem gwan is having on this platform ? I have tested lighttpd, nginx and node.js on this same OS, and the results are all as one would expect. The server has been tuned in the usual way with expanded ephemeral ports, increased ulimits, adjusted time wait recycling etc.

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  • how to get value from an array

    - by hwd
    how to get the value 4500 to a variable stdClass Object ( [total] => 4500 ) i tried like these $abc['total'] $abc->total but get error when i tried to echo the variable A PHP Error was encountered Severity: 4096 Message: Object of class stdClass could not be converted to string Filename: controllers/home.php Line Number: 144 please help me

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  • Help with a query

    - by stackoverflowuser
    Hi Based on the following table ID Effort Name ------------------------- 1 1 A 2 1 A 3 8 A 4 10 B 5 4 B 6 1 B 7 10 C 8 3 C 9 30 C I want to check if the total effort against a name is less than 40 then add a row with effort = 40 - (Total Effort) for the name. The ID of the new row can be anything. If the total effort is greater than 40 then trucate the data for one of the rows to make it 40. So after applying the logic above table will be ID Effort Name ------------------------- 1 1 A 2 1 A 3 8 A 10 30 A 4 10 B 5 4 B 6 1 B 11 25 B 7 10 C 8 3 C 9 27 C I was thinking of opening a cursor, keeping a counter of the total effort, and based on the logic insert existing and new rows in another temporary table. I am not sure if this is an efficient way to deal with this. I would like to learn if there is a better way.

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  • Modifying bundled properties from visitor

    - by ravenspoint
    How should I modify the bundled properties of a vertex from inside a visitor? I would like to use the simple method of sub-scripting the graph, but the graph parameter passed into the visitor is const, so compiler disallows changes. I can store a reference to the graph in the visitor, but this seems weird. /** A visitor which identifies vertices as leafs or trees */ class bfs_vis_leaf_finder:public default_bfs_visitor { public: /** Constructor @param[in] total reference to int variable to store total number of leaves @param[in] g reference to graph ( used to modify bundled properties ) */ bfs_vis_leaf_finder( int& total, graph_t& g ) : myTotal( total ), myGraph( g ) { myTotal = 0; } /** Called when the search finds a new vertex If the vertex has no children, it is a leaf and the total leaf count is incremented */ template <typename Vertex, typename Graph> void discover_vertex( Vertex u, Graph& g) { if( out_edges( u, g ).first == out_edges( u, g ).second ) { myTotal++; //g[u].myLevel = s3d::cV::leaf; myGraph[u].myLevel = s3d::cV::leaf; } else { //g[u].myLevel = s3d::cV::tree; myGraph[u].myLevel = s3d::cV::tree; } } int& myTotal; graph_t& myGraph; };

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  • Transaction within a Transaction in C#

    - by Rosco
    I'm importing a flat file of invoices into a database using C#. I'm using the TransactionScope to roll back the entire operation if a problem is encountered. It is a tricky input file, in that one row does not necessary equal one record. It also includes linked records. An invoice would have a header line, line items, and then a total line. Some of the invoices will need to be skipped, but I may not know it needs to be skipped until I reach the total line. One strategy is to store the header, line items, and total line in memory, and save everything once the total line is reached. I'm pursuing that now. However, I was wondering if it could be done a different way. Creating a "nested" transaction around the invoice, inserting the header row, and line items, then updating the invoice when the total line is reached. This "nested" transaction would roll back if it is determined the invoice needs to be skipped, but the overall transaction would continue. Is this possible, practical, and how would you set this up?

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  • Simple iPhone tally method question

    - by Rob
    Just trying to create a simple method that counts up 1 on the tally when the button is pressed. My knowledge is extremely limited and I am pretty sure that my problem is somewhere in the method implementation: -(IBAction) updateTally:(id) sender { NSString *text; int total = 0; total = total + 1; text=[[NSString alloc] initWithFormat: @"%i", total]; lblTally.text = text; } I have done the necessary interface declarations for the lblTally UILabel and the updateTally method. I suspect that there is some sort of an NSString/int/%i/%@ mixup that I am making but I'm not sure how to fix it. When I run the program as it currently is it displays a 0 in the lblTally label field on the iphone. When I press the button it then displays a 1 in that field. However, if I continue to press the button - nothing happens.

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  • Either .each do or .all isn't working how I think it should

    - by user1299656
    So whenever someone rates a shop, I want the Shop model to calculate its new average rating and store that in the database (instead of calculating the average every time someone looks at it). So I wrote the segment of code that follows, and it doesn't work. The loop always iterates exactly once, no matter how many shop_ratings in the database exist that have the shop's id as their shop_id. I played around with it a bit and found that every time a new rating is submitted the function is called successfully, but it only runs the loop once and sets the average to what the first rating was. I don't know if the "query" that sets the ratings variable is wrong or if it's the loop that's wrong. class Shop < ActiveRecord::Base has_many :shop_ratings attr_accessible :name, :latitude, :longitude validates_presence_of :name validates_presence_of :latitude validates_presence_of :longitude def distance_to(lat, long) return (self.longitude - long) + (self.latitude - lat) end def find_average total = 0 count = 0 ratings = ShopRating.all(:conditions => {:shop_id => id}) ratings.each do |submission| total = total + submission.rating count = count + 1 end update_attribute :average_rating, total/count end end

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  • Duplicate file descriptor after popen

    - by alaamh
    I am using popen to execute a command under linux, then 4 process wile use the same output. I am trying to duplicate the file descriptor again to pass it to each process. here is my code: FILE* file_source = (FILE*) popen(source_command, "r"); int fd = fileno(file_source); fdatasync(fd); int fd[4],y, total = 4 ; for (y = 0; y < total; y++) { dest_fd[y] = dup(fd); } actually if total set to 1 it work fin, after changing total = 4 it does not work anymore.

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  • show count of only configurable products of current category

    - by hs19
    hello, i want to show count of only configurable products of current category on category page. for that I have written following code... <?php $cate = Mage::registry('current_category')->getName(); $total=0; $category = Mage::registry('current_category'); $products = $category->getProductCollection(); foreach ( $products as $_product ) if ($_product->isConfigurable()) { $total++; } echo $cate."(".$total.")"; ?> my problem is the code is showing the total count of configurable products of all child categories... can anyone help me with this?

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  • While Loop in TSQL with Sum totals

    - by RPS
    I have the following TSQL Statement, I am trying to figure out how I can keep getting the results (100 rows at a time), store them in a variable (as I will have to add the totals after each select) and continue to select in a while loop until no more records are found and then return the variable totals to the calling function. SELECT [OrderUser].OrderUserId, ISNULL(SUM(total.FileSize), 0), ISNULL(SUM(total.CompressedFileSize), 0) FROM ( SELECT DISTINCT TOP(100) ProductSize.OrderUserId, ProductSize.FileInfoId, CAST(ProductSize.FileSize AS BIGINT) AS FileSize, CAST(ProductSize.CompressedFileSize AS BIGINT) AS CompressedFileSize FROM ProductSize WITH (NOLOCK) INNER JOIN [Version] ON ProductSize.VersionId = [Version].VersionId ) AS total RIGHT OUTER JOIN [OrderUser] WITH (NOLOCK) ON total.OrderUserId = [OrderUser].OrderUserId WHERE NOT ([OrderUser].isCustomer = 1 AND [OrderUser].isEndOrderUser = 0 OR [OrderUser].isLocation = 1) AND [OrderUser].OrderUserId = 1 GROUP BY [OrderUser].OrderUserId

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