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  • Changing the x-axis of seqlogo figures in matlab

    - by JudoWill
    I'm making a large number of seqlogos programatically. They are hundreds of columns wide and so running a seqlogo normally creates letters that are too thin to see. I've noticed that I only care about a few of these columns (not necessarily consecutive columns) ... most are noise but some are highly conserved. I use something like this snippet: conserve_cell = seqlogo(wide_seqs, 'displaylogo', false); high_bit_cols = any(conserve_cell{2}>1.0,1); [~, handle] = seqlogo(wide_seqs(:,high_bit_cols )); Although when I do this I lose the information about which columns the data came from. Normally I would just change the x-axis of the seqlogo. However, seqlogo's are some sort of crazy java-based object and calls like: set(handle, 'xticklabel', num2str(find(high_bit_cols))) don't work. Any help would be greatly appreciated. Thanks, Will

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  • Industry Reports on Source Control Tools

    - by Kent Boogaart
    Hi, I'm looking for independent industry reports that compare and contrast the various source control tools out there. In particular, I care about Clearcase vs Sourcesafe vs SVN, but if the report includes other SCM systems that's fine. I need this for a client who wants to get a feel on exactly what they stand to gain switching to SVN (yes, from Clearcase and VSS). In other words, something I can use to sell it to their business. I'm hoping some case studies have been done on developer productivity with these tools and resultant reports made freely available. Thanks, Kent

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  • How can I process command line arguments in Python?

    - by photographer
    What would be an easy expression to process command line arguments if I'm expecting anything like 001 or 999 (let's limit expectations to 001...999 range for this time), and few other arguments passed, and would like to ignore any unexpected? I understand if for example I need to find out if "debug" was passed among parameters it'll be something like that: if 'debug' in argv[1:]: print 'Will be running in debug mode.' How to find out if 009 or 575 was passed? All those are expected calls: python script.py python script.py 011 python script.py 256 debug python script.py 391 xls python script.py 999 debug pdf At this point I don't care about calls like that: python script.py 001 002 245 568 python script.py some unexpected argument python script.py 0001 python script.py 02 ...first one - because of more than one "numeric" argument; second - because of... well, unexpected arguments; third and fourth - because of non-3-digits arguments.

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  • JPA and MySQL transaction isolation level

    - by armandino
    I have a native query that does a batch insert into a MySQL database: String sql = "insert into t1 (a, b) select x, y from t2 where x = 'foo'"; EntityTransaction tx = entityManager.getTransaction(); try { tx.begin(); int rowCount = entityManager.createNativeQuery(sql).executeUpdate(); tx.commit(); return rowCount; } catch(Exception ex) { tx.rollback(); log.error(...); } This query causes a deadlock: while it reads from t2 with insert .. select, another process tries to insert a row into t2. I don't care about the consistency of reads from t2 when doing an insert .. select and want to set the transaction isolation level to READ_UNCOMMITTED. How do I go about setting it in JPA?

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  • Options for keeping models and the UI in sync (in a desktop application context)

    - by Benju
    In my experience I have only had 2 patterns work for large-scale desktop application development when trying to keep the model and UI in sync. 1-An eventbus approach via a shared eventbus command objects are fired (ie:UserDemographicsUpdatedEvent) and have various parts of the UI update if they are bound to the same user object updated in this event. 2-Attempt to bind the UI directly to the model adding listeners to the model itself as needed. I find this approach rather clunky as it pollutes the domain model. Does anybody have other suggestions? In a web application with something like JSP binding to the model is easy as you ussually only care about the state of the model at the time your request comes in, not so in a desktop type application. Any ideas?

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  • Project tracking/management tool

    - by Alvaro Rodriguez
    Which project tracking tool do you use? Does it allow programmers to bill hours worked to projects/tasks? Does it allow to track items promised vs. items delivered? Does it allow to forecast personnel needs when you have only a ballpark estimate of how many hours you are going to need for different task types? Does it integrate with your bug tracker? [Mantis] Does it integrate with your source control tool? [Subversion] Does it allow you to easily publish your schedule and current priorities to team members? Does it produce reports on any or all of the above? Am I even right in calling a tool that does those things a "Project tracking/management tool"? What does your tool have that makes you love it and use it every day? I don't really care about Gantt charts. I find Microsoft Project quite clunky for this needs (although I'm hardly an expert user).

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  • Cucumber/Webrat: follow link by CSS class?

    - by Joe
    Hello there, is it possible to follow a link by it's class name instead of the id, text or title? Given I have (haha, cucumber insider he?) the following html code: <div id="some_information_container"> <a href="edit" class="edit_button">Translation here</a> </div> I do not want to match by text because I'd have to care about the translation values in my tests I want to have my buttons look all the same style, so I will use the CSS class. I don't want to assign a id to every single link, because some of them are perfectly identified through the container and the link class Is there anything I missed in Cucumber/Webrat? Or do you have some advices to solve this in a better way? Thanks for your help and best regards, Joe edit: I found an interesting discussion going on about this topic right here - seems to remain an open issue for now. Do you have any other solutions for this?

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  • Cocoa - How to copy files to /usr/share?

    - by cyaconi
    Hi all. I'm developing an "installation" like cocoa application wich needs to take care of some http request, some file system reading, copying files to /usr/share, set up cron (not launchd) and ask some information to user. I discarded PackageMaker since I need more flexibility. Currently everything is going well, but on my last installation step, I need to: Delete my previously installed application folder (if exists). It's always the same path: /usr/share/MY_APP Create again the application folder at: /usr/share/MY_APP Copy application files to /usr/share/MY_APP Update a cron job It's very important that /usr/share/MY_APP keeps protected with administrative privileges, so a regular shouldn't delete it. What would be the best approach to implement those steps? BTW, I'm using Xcode 3.2. Thanks a lot! Carlos.

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  • batch update SharePoint data

    - by Faiz
    Hi, I need to import user profile information to a sharepoint list. Also, the user profile information will be periodically updated to the list , therefore i think i should use a timer job to update the information. Importing for the first time works without any issues. But can you suggest what can be the best way to update information. The update should take care of updating existing records in profile , mark as orphaned for the records that are deleted from user profile and add new records in user profile to the list. Thanks

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  • Low noise sites to keep track of news related to computers & programming?

    - by Sridhar Ratnakumar
    I am aware of sites like Slashdot and Ars Technica. Unfortunately they publish way too many articles per day. Ars Technical: 100 posts per week Slashdot: 179 posts per week And I prefer not to waste my attention over reading about 180 posts (even if I were to skim) every week. Is there a site that provides only important news - excluding not-so-important news items like top 6 iPad apps that someone is dying to try out (but haven't done yet; still thinks their readers/advertisers care about it)?

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  • How to authenticate WCF calls using forms authentication and secutity

    - by Fixer
    I'm planning a set up for a distributed application that spans serveral machines and will use WCF to send data in between. Machine A Front end website http://www.site.com Password protected site using Forms Authentication Machine B WCF Application Service http://service1.site.com/DoSomething.svc Machine C WCF Application Service http://service2.site.com/DoSomething.svc The WCF services on Machine B and Machine C should check that the request from Machine A has been authenticated. How can i check that the request is authenticated across the different machines? I only care that the request is authenticated and not concerned about securing the message body (because we are not sending any sensitive data across the wire), so SSL is not required. What authentication methods can i use for the above scenario?

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  • Android MediaPlayer crashing app

    - by user1555863
    I have an android app with a button that plays a sound. the code for playing the sound: if (mp != null) { mp.release(); } mp = MediaPlayer.create(this, R.raw.match); mp.start(); mp is a field in the activity: public class Game extends Activity implements OnClickListener { /** Called when the activity is first created. */ //variables: MediaPlayer mp; //... The app runs ok, but after clicking the button about 200 times on the emulator, app crashed and gave me this error https://dl.dropbox.com/u/5488790/error.txt (couldn't figure how to post it here so it will appear decently) i am assuming this is because the MediaPlayer object is consuming up too much memory, but isn't mp.release() supposed to take care of this? What am i doing wrong here?

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  • C String literals: Where do they go?

    - by Chris Cooper
    I have read a lot of posts about "string literals" on SO, most of which have been about best-practices, or where the literal is NOT located in memory. I am interested in where the string DOES get allocated/stored, etc. I did find one intriguing answer here, saying: Defining a string inline actually embeds the data in the program itself and cannot be changed (some compilers allow this by a smart trick, don't bother). but, it had to do with C++, not to mention that it says not to bother. I am bothering. =D So my question is, again, where and how is my string literal kept? Why should I not try to alter it? Does the implementation vary by platform? Does anyone care to elaborate on the "smart trick?" Thanks for any explanations.

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  • A tool to find and fix incomplete source code documentation

    - by Pekka
    I have several finished, older PHP projects with a lot of includes that I would like to document in javadoc/phpDocumentor style. While working through each file manually and being forced to do a code review alongside the documenting would be the best thing, I am, simply out of time constraints, interested in tools to help me automate the task as much as possible. The tool I am thinking about would ideally have the following features: Parse a PHP project tree and tell me where there are undocumented files, classes, and functions/methods (i.e. elements missing the appropriate docblock comment) Provide a method to half-way easily add the missing docblocks by creating the empty structures and, ideally, opening the file in an editor (internal or external I don't care) so I can put in the description. Optional: Automatic recognition of parameter types, return values and such. But that's not really required. The language in question is PHP, though I could imagine that a C/Java tool might be able to handle PHP files after some tweaking. Thanks for your great input!

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  • Mutating the expression tree of a predicate to target another type

    - by Jon
    Intro In the application I 'm currently working on, there are two kinds of each business object: the "ActiveRecord" type, and the "DataContract" type. So for example, we have: namespace ActiveRecord { class Widget { public int Id { get; set; } } } namespace DataContracts { class Widget { public int Id { get; set; } } } The database access layer takes care of "translating" between hierarchies: you can tell it to update a DataContracts.Widget, and it will magically create an ActiveRecord.Widget with the same property values and save that. The problem I have surfaced when attempting to refactor this database access layer. The Problem I want to add methods like the following to the database access layer: // Widget is DataContract.Widget interface DbAccessLayer { IEnumerable<Widget> GetMany(Expression<Func<Widget, bool>> predicate); } The above is a simple general-use "get" method with custom predicate. The only point of interest is that I 'm not passing in an anonymous function but rather an expression tree. This is done because inside DbAccessLayer we have to query ActiveRecord.Widget efficiently (LINQ to SQL) and not have the database return all ActiveRecord.Widget instances and then filter the enumerable collection. We need to pass in an expression tree, so we ask for one as the parameter for GetMany. The snag: the parameter we have needs to be magically transformed from an Expression<Func<DataContract.Widget, bool>> to an Expression<Func<ActiveRecord.Widget, bool>>. This is where I haven't managed to pull it off... Attempted Solution What we 'd like to do inside GetMany is: IEnumerable<DataContract.Widget> GetMany( Expression<Func<DataContract.Widget, bool>> predicate) { var lambda = Expression.Lambda<Func<ActiveRecord.Widget, bool>>( predicate.Body, predicate.Parameters); // use lambda to query ActiveRecord.Widget and return some value } This won't work because in a typical scenario, for example if: predicate == w => w.Id == 0; ...the expression tree contains a MemberAccessExpression instance which has a MemberInfo property (named Member) that point to members of DataContract.Widget. There are also ParameterExpression instances both in the expression tree and in its parameter expression collection (predicate.Parameters); After searching a bit, I found System.Linq.Expressions.ExpressionVisitor (its source can be found here in the context of a how-to, very helpful) which is a convenient way to modify an expression tree. Armed with this, I implemented a visitor. This simple visitor only takes care of changing the types in member access and parameter expressions. It may not be complete, but it's fine for the expression w => w.Id == 0. internal class Visitor : ExpressionVisitor { private readonly Func<Type, Type> dataContractToActiveRecordTypeConverter; public Visitor(Func<Type, Type> dataContractToActiveRecordTypeConverter) { this.dataContractToActiveRecordTypeConverter = dataContractToActiveRecordTypeConverter; } protected override Expression VisitMember(MemberExpression node) { var dataContractType = node.Member.ReflectedType; var activeRecordType = this.dataContractToActiveRecordTypeConverter(dataContractType); var converted = Expression.MakeMemberAccess( base.Visit(node.Expression), activeRecordType.GetProperty(node.Member.Name)); return converted; } protected override Expression VisitParameter(ParameterExpression node) { var dataContractType = node.Type; var activeRecordType = this.dataContractToActiveRecordTypeConverter(dataContractType); return Expression.Parameter(activeRecordType, node.Name); } } With this visitor, GetMany becomes: IEnumerable<DataContract.Widget> GetMany( Expression<Func<DataContract.Widget, bool>> predicate) { var visitor = new Visitor(...); var lambda = Expression.Lambda<Func<ActiveRecord.Widget, bool>>( visitor.Visit(predicate.Body), predicate.Parameters.Select(p => visitor.Visit(p)); var widgets = ActiveRecord.Widget.Repository().Where(lambda); // This is just for reference, see below Expression<Func<ActiveRecord.Widget, bool>> referenceLambda = w => w.Id == 0; // Here we 'd convert the widgets to instances of DataContract.Widget and // return them -- this has nothing to do with the question though. } Results The good news is that lambda is constructed just fine. The bad news is that it isn't working; it's blowing up on me when I try to use it (the exception messages are really not helpful at all). I have examined the lambda my code produces and a hardcoded lambda with the same expression; they look exactly the same. I spent hours in the debugger trying to find some difference, but I can't. When predicate is w => w.Id == 0, lambda looks exactly like referenceLambda. But the latter works with e.g. IQueryable<T>.Where, while the former does not (I have tried this in the immediate window of the debugger). I should also mention that when predicate is w => true, it all works just fine. Therefore I am assuming that I 'm not doing enough work in Visitor, but I can't find any more leads to follow on. Can someone point me in the right direction? Thanks in advance for your help!

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  • How to get query result even if JOIN hasn't found any results?

    - by user1734651
    I want select data for user, and join another info from other table that related to the user. The problem is that this extra data not always exist for any user, just for few. How can I write a query that will return NULL for not found data, instead just return null for the whole query? SELECT a.*, b.* FROM user AS a LEFT JOIN extra AS b ON (a.userid = b.userid) WHERE a.userid = {$userid} LIMIT 1 When extra data found for the user, I get the resource as expected. If not, I get NULL for the whole query. Bottom line, I don't care if "extra" exist for the user or not, if yes - select it as well, if not - ignore that.

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  • python duration of a file object in an argument list

    - by msw
    In the pickle module documentation there is a snippet of example code: reader = pickle.load(open('save.p', 'rb')) which upon first read looked like it would allocate a system file descriptor, read its contents and then "leak" the open descriptor for there isn't any handle accessible to call close() upon. This got me wondering if there was any hidden magic that takes care of this case. Diving into the source, I found in Modules/_fileio.c that file descriptors are closed by the fileio_dealloc() destructor which led to the real question. What is the duration of the file object returned by the example code above? After that statement executes does the object indeed become unreferenced and therefore will the fd be subject to a real close(2) call at some future garbage collection sweep? If so, is the example line good practice, or should one not count on the fd being released thus risking kernel per-process descriptor table exhaustion?

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  • Flex 4 - Using .pfm/.pfb fonts

    - by Zed-K
    Hi everyone, I just switched to Flash Builder 4 & Flex 4 SDK, and it seems it's no longer possible to use a .pfm/.pfb font, either by embedding it or using it as a system font. I keep getting error messages, and Google can't find anybody having the same issue. I tried several methods: - copy/pasting the [Embed] statement which was working using Flex 3 SDK - installing the font and then try to simply call it by its name in a CSS declaration without embedding it ; seems to work for every .ttf and .otf system fonts, but not for .pfm/.pfm ones - using a Flash-generated swf which embeds the font So far none of these seems to work. Has anybody got an idea on how to achieve this? I actually don't care using a system font without embedding it as long as it works. I'll be really grateful if somebody could help me on this, I'm totally stuck and cannot use another font instead.

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  • Is it possible to implement a GC.GetAliveInstancesOf<T>() (for use in debugging)?

    - by Omer Raviv
    Hi, I know this was answered before, but I'd like to pose a somewhat different question. Is there any conceivable way to implement GC.GetAliveInstancesOf(), that can be evaluated in Visual Studio Debug Watch window? Sasha Goldstein shows one solution in this article, but it requires every class you want to query inherit from a specific base class. I'll emphasize that I only want to use this method during debugging, so I don't care that the GC may change an object's address in memory during runtime. One idea might be to somehow harness the !dumpheap –type command of SOS, and do some magic trick to create a temporary variable and have it point out to the memory address printed by SOS. Does anyone have a solution that works?

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  • Changing text size on a ggplot bump plot

    - by Tom Liptrot
    Hi, I'm fairly new to ggplot. I have made a bumpplot using code posted below. I got the code from someones blog - i've lost the link.... I want to be able to increase the size of the lables (here letters which care very small on the left and right of the plot) without affecting the width of the lines (this will only really make sense after you have run the code) I have tried changing the size paramater but that always alter the line width as well. Any suggestion appreciated. Tom require(ggplot2) df<-matrix(rnorm(520), 5, 10) #makes a random example colnames(df) <- letters[1:10] Price.Rank<-t(apply(df, 1, rank)) dfm<-melt(Price.Rank) names(dfm)<-c( "Date","Brand", "value") p <- ggplot(dfm, aes(factor(Date), value, group = Brand, colour = Brand, label = Brand)) p1 <- p + geom_line(aes(size=2.2, alpha=0.7)) + geom_text(data = subset(dfm, Date == 1), aes(x = Date , size =2.2, hjust = 1, vjust=0)) + geom_text(data = subset(dfm, Date == 5), aes(x = Date , size =2.2, hjust = 0, vjust=0))+ theme_bw() + opts(legend.position = "none", panel.border = theme_blank()) p1 + theme_bw() + opts(legend.position = "none", panel.border = theme_blank())

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  • Should I worry about reigning in namespace number/length/scope?

    - by Jay
    I've recently reorganized a solution-in-progress from 24 projects to 4. To keep the copious files organized in the "main" project, things are in folders in folders in folders. I think I've preserved a logical, discoverable arrangement of the solution content. As a result, of course, I end up with namespaces like AppName.DataAccess.NHibernate.Fluent.Mappings. Is there any compelling reason that I should care about flattening out the namespace hierarchy when my project has a somewhat deeply nested folder structure? (I am not concerned about resolving or managing using directives; I let ReSharper do all the heavy lifting here.)

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  • How do I convert PDF to HTML programmatically?

    - by SoaperGEM
    Are there any classes, COM objects, command line utilities, or anything else that I can make an API for that can convert a PDF to an HTML document? Obviously the conversion might be a little rough since PDFs can contain a lot more than HTML can describe. I found a utility called pdftohtml on Source Forge, but quite honestly it does a horrible job with the conversion. I don't care if the software is free or commercial, but is there anything out there at all that I can incorporate with my own software to do this sort of conversion at least decently? I know Google's developed their own method of doing this, since you can click "View as HTML" on a PDF attached to an email through Gmail, but I was hoping there was something out available to the public. Remember, PDF to HTML. I'm NOT worried about HTML to PDF.

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  • Advantage of using a static member function instead of an equivalent non-static member function?

    - by jonathanasdf
    I was wondering whether there's any advantages to using a static member function when there is a non-static equivalent. Will it result in faster execution (because of not having to care about all of the member variables), or maybe less use of memory (because of not being included in all instances)? Basically, the function I'm looking at is an utility function to rotate an integer array representing pixel colours an arbitrary number of degrees around an arbitrary centre point. It is placed in my abstract Bullet base class, since only the bullets will be using it and I didn't want the overhead of calling it in some utility class. It's a bit too long and used in every single derived bullet class, making it probably not a good idea to inline. How would you suggest I define this function? As a static member function of Bullet, of a non-static member function of Bullet, or maybe not as a member of Bullet but defined outside of the class in Bullet.h? What are the advantages and disadvantages of each?

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  • Creating a Box Control over an area of the map with OpenLayers

    - by Bernie Perez
    I am using OpenLayers to create a box of interest with my program. I am using this code: var control = new OpenLayers.Control(); OpenLayers.Util.extend(control, { draw: function () { this.box = new OpenLayers.Handler.Box( control, {"done": this.notice}, {keyMask: OpenLayers.Handler.MOD_SHIFT}); this.box.activate(); }, notice: function (bounds) { areaSelected(bounds); } }); map.addControl(control); to capture the "Shift Create a Box" control and use the area selected as my area of interest. However the values come back as pixels. But I want Longitude and Latitude, not pixels. The Mouse Position control does show the correct long & lat. I really don't care how to box is created, I just want an easy way for the user to select a area of the map and I need to get the lat & longs of the area. (Box, Circle, doesn't matter)

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  • Sync Framework: SqlSyncProvider ItemConflicting vs ApplyChangeFailed

    - by Paul Smith
    I'm trying to use design a syncronisation application that syncs changes between different SQL Server databases. I came up with a design based around receiving the ItemConflicting event, storing the knowledge associated with the conflict, and resolving all conflicts off-line. However, it seems that I can only get the ApplyChangeFailed event to fire. Is there some reason why SqlSyncProvider does not use the ItemConflicting event? Am I just hooking up to the event wrongly? The reason I care is that the ItemConlficting event allows me to simply log the conflict and continue with the rest of the synchronisation in a way that I can't seem to achieve with the ApplychangeFailed event.

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