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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 use JComboBox using Enum in Dialog Box

    - by Edan
    Hi, I define enums: enum itemType {First, Second, Third}; public class Item { private itemType enmItemType; ... } How do I use it inside Dialog box using JComboBox? Means, inside the dialog box, the user will have combo box with (First, Second, Third). Also, is it better to use some sort of ID to each numerator? (Integer) thanks.

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  • how to reload the whole page through a button placed in a division in jsp

    - by ajeet singh
    when i tried to make web project, i placed the links on the left on one division and a bigger division on the right to load the jsp pages on clicking the links making the main page same... but when there is a need arises to load the whole page by clicking the button placed on the right division, i found that the only page is loaded on the right division jsp calling its action... please help me to sort out this problem..

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  • Python sorting problem

    - by matt
    I'm sure this is simple but I can't figure it out. I have a list of strings like this(after using sorted on it): Season 2, Episode 1: A Flight to Remember Season 2, Episode 20: Anthology of Interest I Season 2, Episode 2: Mars University Season 2, Episode 3: When Aliens Attack .... Season 3, Episode 10: The Luck of the Fryrish Season 3, Episode 11: The Cyber House Rules Season 3, Episode 12: Insane in the Mainframe Season 3, Episode 1: The Honking Season 3, Episode 2: War Is the H-Word How can I make them sort out properly? (by episode #, ascending)

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  • Managing dependencies with Hadoop Streaming?

    - by beagleguy
    hi all, had a quick hadoop streaming question.. If I'm using python streaming and I have python packages my mappers/reducers require that aren't installed by default do I need to install those on all the hadoop machines as well or is there some sort of serialization that sends them to the remote machines? thanks!

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  • Wierd typeloadexception "Bad flags on delegate constructor."

    - by Marcus
    Hi, Anybody seen this exception before, Google doesn't have a single post regarding the exception. The code that raises the error is a simple add. Items.Add(item); System.TypeLoadException: Bad flags on delegate constructor. at System.Windows.Forms.ListView.Sort() at System.Windows.Forms.ListView.InsertItems(Int32 displayIndex, ListViewItem[] items, Boolean checkHosting) at System.Windows.Forms.ListView.ListViewNativeItemCollection.Add(ListViewItem value) at System.Windows.Forms.ListView.ListViewItemCollection.Add(ListViewItem value)

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  • QueryString From Shared Function

    - by Kezzer
    I'm trying to get a query string from a shared function in a code-behind model using VB.NET. You have to use HttpContext.Current.Request.QueryString("Query") in order to get it from a shared function, however doing HttpContext.Current.Request.QueryString.Count gives back 0, which obviously isn't right in my case as there's many that exist. Is there some sort of issue with using this static call from a shared function?

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  • How to set a sorting mode in Open Dialog

    - by Serg
    A user can manually sort files in a standard Windows Open Dialog (in "Details" view mode) by Name, Date or Size by clicking on the corresponding column header. How to set a sorting mode in Open Dialog (TOpenDialog class in Delphi) programmatically in application so that the dialog opens with a preferred sorting?

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  • Function in JS returns undefined

    - by megapool020
    Hello there, I have the following problem. The alert allways returns undefined, but I know it has a value. What am I doing wrong. I'm out of solutions... I'm using JQUERY jquery-1.4.2.min.js Tnx in advance $(document).ready(function(){ $('#generateButton').click(createIBAN); }); function createIBAN(){ //---- First check if a bank has been selected, //---- if not, then show error if($('#selectBank').val()==''){ alert('Selecte a bank!'); }else{ var bankAccount = generateBankAccount(); alert(bankAccount); } return false; } function generateBankAccount(){ //---- Create "elfproef" bankaccount var bankAccount = ''; //---- Set the amount of digits in a bankaccount digitAmount = 9; //---- Make random digitstring for (var i = 0; i < digitAmount; i++) { bankAccount += Math.floor(Math.random() * digitAmount); } //---- validate the string, if not "elf-proef" if (elfProef(bankAccount)==false) { //---- regenerate the string generateBankAccount(); }else{ return bankAccount; } } function elfProef(bankAccount) { //---- set sum to 0 and start the for-loop for counting var sum = 0; for (var i = 0; i < digitAmount; i++) { //---- for every digit multiply it times 9 - number //---- of the digit and count it to the sum var sum += bankAccount.charAt(i) * (digitAmount - i); } //---- Check if sum can be devided by 11 without having ##,## if(sum % 11==0){ //---- return true means string is "elf-proef" return true; }else { //---- String is not "elf-proef", try again return false; } }

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  • stl priority queue based on lower value first

    - by russell
    I have a problem with stl priority queue.I want to have the priority queue in the increasing order,which is decreasing by default.Is there any way to do this in priority queue. And what is the complexity of building stl priority queue.If i use quick sort in an array which takes O(nlgn) is its complexity is similar to using priority queue??? Plz someone ans.Advanced thanx.

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  • who wrote 250k unit tests for webkit?

    - by amwinter
    assuming a yield of 3 per hour, that's 83000 hours. 8 hours a day makes 10,500 days, divide by thirty to get 342 mythical man months. I call them mythical because writing 125 tests per person per week is unreal. can any wise soul out there on SO shed some light on what sort of mythical men write unreal quantities of tests for large software projects? thank you.

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  • Wait function in Java

    - by user220755
    So I am writing a Java code to represent a heap sort and to represent the operation I need to have a waiting function which will wait between different operation but I am not sure if there is a function in Java that does that or do I need to write the function by myself and how would i do that. Representing heap sport is a homework but writing the waiting function isn't so I appreciate your help

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  • Rectangles Covering

    - by den bardadym
    I have N rectangles with sides parallel Ox and Oy. Exists another rectangele (model). I need create algorithm, which can tell: is model covered by N rectangles? and code him. I have some ideas. First I think need sort rectangles by left side (it can be done by O(n log n)). Then I think need use vertical sweeping line. Thanks.

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  • Sorting function/variables in an object by name

    - by sissonb
    I was wondering if PHPStorm by Jetbrains has a tool to sort the methods in my JavaScript object by name. If not are there any other tools that can do this for me? Ext.regController("dashboard", { goToShoppingCart:function() { Ext.dispatch({ controller:"shoppingCart", action:"loadCart" }); }, goToDashboard:function() {}, goToContact:function() {} } ); to Ext.regController("dashboard", { goToContact:function() {}, goToDashboard:function() {}, goToShoppingCart:function() { Ext.dispatch({ controller:"shoppingCart", action:"loadCart" }); } } ); This is only for organization. Thanks

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  • Django multiple many to many fields?

    - by Tom
    Hello everybody I am building a news app for my website. I want to use a sort of tag system. Each news article can have different and multiple tags. All tags are saved in a tag model, and i want to connect the tags to the newsarticle. Now is this possible with: tags = models.ForeignKey( TagsModel ) for one tag, but how i can do this with multiple of them? Thank you!

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  • JMS Topic message size

    - by jjoshi
    Our application uses a topic to push message to a small set of subscribers. what sort of things should i look for when modeling a jms message with respect to the size of the actual message to be pushed. Are there any known limits or is application server specific? Any best practices or suggestions on this topic (pun unintended)?

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  • Finding character in String in Vector.

    - by SoulBeaver
    Judging from the title, I kinda did my program in a fairly complicated way. BUT! I might as well ask anyway xD This is a simple program I did in response to question 3-3 of Accelerated C++, which is an awesome book in my opinion. I created a vector: vector<string> countEm; That accepts all valid strings. Therefore, I have a vector that contains elements of strings. Next, I created a function int toLowerWords( vector<string> &vec ) { for( int loop = 0; loop < vec.size(); loop++ ) transform( vec[loop].begin(), vec[loop].end(), vec[loop].begin(), ::tolower ); that splits the input into all lowercase characters for easier counting. So far, so good. I created a third and final function to actually count the words, and that's where I'm stuck. int counter( vector<string> &vec ) { for( int loop = 0; loop < vec.size(); loop++ ) for( int secLoop = 0; secLoop < vec[loop].size(); secLoop++ ) { if( vec[loop][secLoop] == ' ' ) That just looks ridiculous. Using a two-dimensional array to call on the characters of the vector until I find a space. Ridiculous. I don't believe that this is an elegant or even viable solution. If it was a viable solution, I would then backtrack from the space and copy all characters I've found in a separate vector and count those. My question then is. How can I dissect a vector of strings into separate words so that I can actually count them? I thought about using strchr, but it didn't give me any epiphanies.

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  • How do I accurately handle a batch seperator for SQL from C#

    - by Sam Saffron
    For Data Explorer I would like to add support for a Batch separator. So for example if users type in: select 'GO' go select 1 as go Go select 100 I would like to return the three result sets. Its clear that I need some sort of parser here, my hope is that this is a solved problem and I can just plug it in. (writing a full T-SQL parser is not something I would like to do) What component / demo code could achieve splitting this batch into its 3 parts?

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  • Qt Audio Recording Question

    - by Cenoc
    This is sort of a follow-up/branch off a previous question, which still stands unresolved. Are there other codecs besides pcm for qt QAudio class? I cant seem to find any... I want to have a way of playing stuff recorded by qt on vlc. Thanks in advance.

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