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  • How can I save BioPerl sequence nested features in genbank or embl format?

    - by Ryan Thompson
    In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

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  • Nasty redirect loop in WordPress (trailing slash, no trailing slash, and so on)

    - by Brett W. Thompson
    Hi, I read a ton of pages and tried lots of solutions but none have worked yet! My problem is that: test.asifa.net/asifa-wp Redirects to: test.asifa.net/asifa-wp/ Which redirects to the first page. What's a little bizarre is asifa-wp produces: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>301 Moved Permanently</title> </head><body> <h1>Moved Permanently</h1> <p>The document has moved <a href="http://test.asifa.net/asifa-wp/">here</a>.</p> </body></html> Whereas asifa-wp/ produces an empty page but the following headers (curl -v output): * About to connect() to test.asifa.net port 80 (#0) * Trying 69.163.203.138... connected * Connected to test.asifa.net (69.163.203.138) port 80 (#0) > GET /asifa-wp/ HTTP/1.1 > User-Agent: curl/7.18.2 (i386-redhat-linux-gnu) libcurl/7.18.2 NSS/3.12.0.3 zlib/1.2.3 libidn/0.6.14 libssh2/0.18 > Host: test.asifa.net > Accept: */* > < HTTP/1.1 301 Moved Permanently < Date: Sun, 13 Jun 2010 05:40:12 GMT < Server: Apache < X-Powered-By: PHP/5.2.13 < X-Pingback: http://test.asifa.net/asifa-wp/xmlrpc.php < Set-Cookie: _icl_current_language=en; expires=Mon, 14-Jun-2010 05:40:12 GMT; path=/asifa-wp/ < Location: http://test.asifa.net/asifa-wp < Vary: Accept-Encoding < Content-Length: 0 < Content-Type: text/html; charset=UTF-8 .htaccess looks like: # BEGIN WordPress <IfModule mod_rewrite.c> RewriteEngine On RewriteBase /asifa-wp/ RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteRule . /asifa-wp/index.php [L] </IfModule> # END WordPress Any help at all would be tremendously appreciated!!!

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  • Using C preprocessor to construct a string literal for scanf?

    - by Brett
    I'm attempting to create an sscanf string literal to aid in buffer overrun prevention in C99. The goal is something like: #define MAX_ARG_LEN 16 char arg[MAX_ARG_LEN] = ""; if (sscanf(arg, "%"(MAX_ARG_LEN-1)"X", &input) > 0) The obvious "manual" solution is something like: #define MAX_ARG_LEN 16 #define MAX_ARG_CHARS "15" char arg[MAX_ARG_LEN] = ""; if (sscanf(arg, "%"MAX_ARG_CHARS"X", &input) > 0) However, I would prefer something to automatically generate "%15X" given a buffer size of 16. This link is almost works for my application: http://stackoverflow.com/questions/240353/convert-a-preprocessor-token-to-a-string but it does not handle the -1. Suggestions?

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  • Apache rewrite to add a directory to REQUEST_URI not working on localhost running wamp.

    - by Brett Pontarelli
    I'm running wamp on Vista (Apache v2.2.11) and have projects setup such that http://localhost/projectx is the base directory for projectx. Now, I want that requests for http://localhost/projectx/somepage/extra will rewrite to http://localhost/projectx/PUBLIC/somepage/extra To that end I have a file in C:\wamp\www\projectx\.htacces that is this simple: RewriteEngine On RewriteBase /projectx RewriteCond %{REQUEST_URI} !^/PUBLIC RewriteRule ^(.*)$ /PUBLIC$1 [L] I can't for the life of me figure out why this doesn't work. The error I'm getting is "The requested URL /PUBLIC was not found on this server". Thanks.

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  • Access to Perl's empty angle "<>" operator from an actual filehandle?

    - by Ryan Thompson
    I like to use the nifty perl feature where reading from the empty angle operator <> magically gives your program UNIX filter semantics, but I'd like to be able to access this feature through an actual filehandle (or IO::Handle object, or similar), so that I can do things like pass it into subroutines and such. Is there any way to do this? This question is particularly hard to google, because searching for "angle operator" and "filehandle" just tells me how to read from filehandles using the angle operator.

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  • NoSql Crash Course/Tutorial

    - by Chris Thompson
    Hi all, I've seen NoSQL pop up quite a bit on SO and I have a solid understanding of why you would use it (from here, Wikipedia, etc). This could be due to the lack of concrete and uniform definition of what it is (more of a paradigm than concrete implementation), but I'm struggling to wrap my head around how I would go about designing a system that would use it or how I would implement it in my system. I'm really stuck in a relational-db mindset thinking of things in terms of tables and joins... At any rate, does anybody know of a crash course/tutorial on a system that would use it (kind of a "hello world" for a NoSQL-based system) or a tutorial that takes an existing "Hello World" app based on SQL and converts it to NoSQL (not necessarily in code, but just a high-level explanation). I see this having one solid answer, but if you guys feel like it should be community wiki, I'll be happy to change it. Thanks! Chris

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  • When to use or not use symbols in PHP

    - by brett
    I'm reading a PHP book where the author says that symbols should be avoided except when it's valid to use them. Very informative stuff, if he could only elaborate or give code examples but he doesn't. Can someone from the experienced PHP bunch give me an example of what these symbols are, and when it makes sense to use them or not. I'm looking for a code example that I can wrap my head around since I don't quite get it in plain English. Code is more plain English to me.

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  • Showing renames in hg status?

    - by Ryan Thompson
    I know that Mercurial can track renames of files, but how do I get it to show me renames instead of adds/removes when I do hg status? For instance, instead of: A bin/extract-csv-column.pl A bin/find-mirna-binding.pl A bin/xls2csv-separate-sheets.pl A lib/Text/CSV/Euclid.pm R src/extract-csv-column.pl R src/find-mirna-binding.pl R src/modules/Text/CSV/Euclid.pm R src/xls2csv-separate-sheets.pl I want some indication that four files have been moved. I think I read somewhere that the output is like this to preserve backward-compatibility with something-or-other, but I'm not worried about that.

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  • ado.net slow updating large tables

    - by brett
    The problem: 100,000+ name & address records in an access table (2003). Need to iterate through the table & update detail with the output from a 3rd party dll. I currently use ado, and it works at an acceptable speed (less than 5 minutes on a network share). We will soon need to update to access 2007 and its 'non jet' accdb format to maintain compatability with clients. I've tried using ado.net datsets, but updating the records takes hours! We process 5-10 of these tables per day - so this cannot be a solution. Any ideas on the fastest way to update individual records using ado.net? Surely we didn't take such a hugh backward step with ado.net? Any help would be appreciated.

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  • Is there a way to split a widescreen monitor in to two or more virtual monitors?

    - by Mike Thompson
    Like most developers I have grown to love dual monitors. I won't go into all the reasons for their goodness; just take it as a given. However, they are not perfect. You can never seem to line them up "just right". You always end up with the monitors at slight funny angles. And of course the bezel always gets in the way. And this is with identical monitors. The problem is much worse with different monitors -- VMWare's multi monitor feature won't even work with monitors of differnt resolutions. When you use multiple monnitors, one of them becomes your primary monitor of focus. Your focus may flip from one monitor to the other, but at any point in time you are usually focusing on only one monitor. There are exceptions to this (WinDiff, Excel), but this is generally the case. I suggest that having a single large monitor with all the benefits of multiple smaller monitors would be a better solution. Wide screen monitors are fantastic, but it is hard to use all the space efficiently. If you are writing code you are generally working on the left-hand side of the window. If you maximize an editor on a wide-screen monitor the right-hand side of the window will be a sea of white. Programs like WinSplit Revolution will help to organise your windows, but this is really just addressing the symptom, not the problem. Even with WinSplit Revolution, when you maximise a window it will take up the whole screen. You can't lock a window into a specific section of the screen. This is where virtual monitors comes in. What would be really nice is a video driver that sits on top of the existing driver, but allows a single monitor to be virtualised into multiple monitors. Control Panel would see your single physical monitor as two or more virtual monitors. The software could even support a virtual bezel to emphasise what is happening, or you could opt for seamless mode. Programs like WinSplit Revolution and UltraMon would still work. This virtual video driver would allow you to slice & dice your physical monitor into as many virtual monitors as you want. Does anybody know if such software exists? If not, are there any budding Windows display driver guru's out there willing to take up the challenge? I am not after the myriad of virtual desktop/window manager programs that are available. I get frustrated with these programs. They seem good at first but they usually have some strange behaviour and don't work well with other programs (such as WinSplit Revolution). I want the real thing!

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  • How to read from a method that returns a filehandle in perl?

    - by Ryan Thompson
    I have an object with a method that returns a filehandle, and I want to read from that handle. The following doesn't work, because the right angle bracket of the method call is interpreted as the closing angle bracket of the input reader: my $input = <$object->get_handle()>; That gets parsed as: my $input = ( < $object- > ) get_handle() >; which is obviously a syntax error. Is there any way I can perform a method call within an angle operator, or do I need to break it into two steps like this? my $handle = $object->get_handle(); my $input = <$handle>;

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  • Routing zend request through a default controller when controller not found.

    - by Brett Pontarelli
    Below is a function defined in my Bootstrap class. I must be missing something fundamental in the way Zend does routing and dispatching. What I am trying to accomplish is simple: For any request /foo/bar/* that is not dispatchable for any reason try /index/foo/bar/. The problem I'm having is when the FooController exists I get Action "foo" does not exist. Basically, the isDispatchable is always false. public function run() { $front = Zend_Controller_Front::getInstance(); $request = $front->getRequest(); $dispatcher = $front->getDispatcher(); //$controller = $dispatcher->getControllerClass($request); if (!$dispatcher->isDispatchable($request)) { $route = new Zend_Controller_Router_Route( ':action/*', array('controller' => 'index') ); $router = $front->getRouter(); $router->addRoute('FallBack', $route); } $front->dispatch(); }

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  • Integration (math) in C++

    - by Chris Thompson
    Hi all, I'm looking for a library to find the integral of a given set of random data (rather than a function) in C++ (or C, but preferably C++). There is another question asking about integration in C but the answers discuss more how to integrate a function (I think...). I understand that this can be done simply by calculating the area under the line segment between each pair of points from start to finish, but I'd rather not reinvent the wheel if this has already been done. I apologize in advance if this is a duplicate; I searched pretty extensively to no avail. My math isn't as strong as I'd like it so it's entirely possible I'm using the wrong terminology. Thanks in advance for any help! Chris

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  • Help with Assembly/SSE Multiplication

    - by Brett
    I've been trying to figure out how to gain some improvement in my code at a very crucial couple lines: float x = a*b; float y = c*d; float z = e*f; float w = g*h; all a, b, c... are floats. I decided to look into using SSE, but can't seem to find any improvement, in fact it turns out to be twice as slow. My SSE code is: Vector4 abcd, efgh, result; abcd = [float a, float b, float c, float d]; efgh = [float e, float f, float g, float h]; _asm { movups xmm1, abcd movups xmm2, efgh mulps xmm1, xmm2 movups result, xmm1 } I also attempted using standard inline assembly, but it doesn't appear that I can pack the register with the four floating points like I can with SSE. Any comments, or help would be greatly appreciated, I mainly need to understand why my calculations using SSE are slower than the serial C++ code? I'm compiling in Visual Studio 2005, on a Windows XP, using a Pentium 4 with HT if that provides any additional information to assit. Thanks in advance!

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  • WPF Issues with Control Layout

    - by Brett Powell
    I am making an application that connects to our billing software using its API, and I am running into a few issues getting the layout working properly. I want to make it so that when one of the expanders is minimized, the other window fills the gap, and when it is expanded again the other expander goes back to where it was. Right now when the arrow is clicked on one, there is just an empty gap. I used a DockPanel as the parent which I assumed would automatically do this, but it isn't working. Second question, is there a way to make these areas resizable? I don't want to try and get too frisky with allowing the user to undock the menus (don't even know if that is possible with just straight WPF) but it would be nice if they could change the width/height of them. Also, just a newbie question to C#, but what is the equivalent of a C++ header file? It looks like you just use .cs files, but I am not sure. I want to extract all of my functions that pull the data from the billing software and put them into a different file to clean up the code. Here is my XAML... <Window x:Class="WpfApplication3.MainWindow" xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" Title="Billing Management" Height="550" Width="754" xmlns:shared="http://schemas.actiprosoftware.com/winfx/xaml/shared" WindowStartupLocation="CenterScreen" WindowStyle="ThreeDBorderWindow"> <Grid> <Grid.RowDefinitions> <RowDefinition Height="22" /> <RowDefinition /> </Grid.RowDefinitions> <Menu Height="22" Name="menu1" Margin="0" HorizontalAlignment="Stretch" VerticalAlignment="Top" HorizontalContentAlignment="Left" IsEnabled="True" IsMainMenu="True"> <MenuItem Header="_File"> <MenuItem Header="_Open" /> <MenuItem Header="_Close" /> <Separator/> <MenuItem Header="_Exit" /> </MenuItem> </Menu> <TabControl Name="tabControl1" HorizontalContentAlignment="Stretch" VerticalContentAlignment="Stretch" BorderThickness="1" Padding="0" TabStripPlacement="Bottom" UseLayoutRounding="False" FlowDirection="LeftToRight" Grid.Row="1"> <TabItem Header="Main" Name="tabItem1" Margin="0"> <DockPanel Name="dockPanel1" LastChildFill="True"> <ListBox Height="100" Name="listBox3" DockPanel.Dock="Top" /> <ListBox Name="listBox4" Width="200" DockPanel.Dock="Right" /> <DockPanel Height="Auto" Name="dockPanel2" Width="Auto" VerticalAlignment="Stretch" LastChildFill="True"> <shared:AnimatedExpander Header="Staff Online" Width="200" Name="expanderStaffOnline" IsExpanded="True" Height="194" BorderThickness="0" DockPanel.Dock="Top" VerticalContentAlignment="Stretch"> <ListBox Name="listboxStaffOnline" Width="Auto" Height="Auto" Margin="0" VerticalAlignment="Stretch" Loaded="listboxStaffOnline_Loaded" /> </shared:AnimatedExpander> <shared:AnimatedExpander Header="Test Menu 2" Height="Auto" Name="animatedExpander1" BorderThickness="1" Margin="0,0,0,0" IsExpanded="True" VerticalContentAlignment="Stretch"> <ListBox Height="Auto" HorizontalAlignment="Stretch" Name="listBox6" VerticalAlignment="Stretch" Margin="0" BorderThickness="1" /> </shared:AnimatedExpander> </DockPanel> <ListBox Height="100" Name="listboxAdminLogs" DockPanel.Dock="Bottom" Loaded="listboxAdminLogs_Loaded" /> <ListBox Name="listBox5" /> </DockPanel> </TabItem> <TabItem Header="Support" Name="tabItem2" Margin="0"> </TabItem> <TabItem Header="Clients" /> <TabItem Header="Billing" /> <TabItem Header="Orders" /> </TabControl> </Grid> </Window>

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  • When opening a file in perl, how can I automatically use STDIN/OUT if the file name is "-"?

    - by Ryan Thompson
    I have a perl program that takes input and output file arguments, and I'd like to support the convention of using "-" to specify standard input/output. The problem is that I can't just open the file name, because open(my $input, '<', '-') opens a file called -, not standard input. So I have to do something like this: my $input_fh; if ($input_filename eq '-') { # Special case: get the stdin handle $input_fh = *STDIN{IO}; } else { # Standard case: open the file open($input_fh, '<', $input_filename); } And similarly for the output file. Is there any way to do this without testing for the special case myself? I know I could hack the ARGV filehandle to do this for input, but that won't work for output.

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  • How do I process Proxy Digg JSON for use with jQuery?

    - by Brett
    I'm trying to deal with: "Requests made from Javascript running on your web pages must be proxied to avoid same-origin policy conflicts." I know how to work with the JSON once I've got it. But aside from copy-pasting the JSON results via my browser, I don't know how to localize it for use.

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  • SWI-Prolog Semantic Web Library and Python Interface

    - by John Peter Thompson Garcés
    I want to write a Python web application that queries RDF triples using Prolog. I found pyswip for interfacing Python with SWI-Prolog, and I am currently looking into SWI-Prolog's RDF capabilities. I am wondering if anyone has tried this before--and if anyone has: what did your setup look like? How do you get pyswip to work with the SWI-Prolog semantic web library? Or is there another Python-Prolog interface that makes this easier?

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  • Error loading SQL_VARIANT data type using Python

    - by Brett D
    I am using Python and SQLAlchemy to query a database that I did not create. I have run into a problem querying a table that contains the SQL_VARIANT data type. I get the error: sqlalchemy.exc.DBAPIError: (Error) ('ODBC data type -150 is not supported. Cannot read column Value.', 'HY000') I confirmed with the database creator that the "Value" column is of type SQL_VARIANT. Does anyone know a way to load this data type using Python? I am currently using mssql with pyodbc. Thank you for any help you can offer! Versions: Python 2.7, SQLAlchemy 0.7.8

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  • Massive speed diff in upgrade to Java 7

    - by Brett Rigby
    We use Java within our build process, as it is used to resolve/publish our dependencies via Ivy. No problem, nor have we had with it for 2 years, until we've tried to upgrade Java 6 Update 26 to Version 7 Update 7, whereas a build on a local developer PC (WinXP) now takes 2 hours to complete, instead of 10 minutes!! Nothing else has changed on the PC, making it the absolute target for our concerns. Does anyone know of any reason as to why version 7 of Java would make such a speed difference like this?

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  • Failure remediation strategy for File I/O

    - by Brett
    I'm doing buffered IO into a file, both read and write. I'm using fopen(), fseeko(), standard ANSI C file I/O functions. In all cases, I'm writing to a standard local file on a disk. How often do these file I/O operations fail, and what should the strategy be for failures? I'm not exactly looking for stats, but I'm looking for a general purpose statement on how far I should go to handle error conditions. For instance, I think everyone recognizes that malloc() could and probably will fail someday on some user's machine and the developer should check for a NULL being returned, but there is no great remediation strategy since it probably means the system is out of memory. At least, this seems to be the approach taken with malloc() on desktop systems, embedded systems are different. Likewise, is it worth reattempting a file I/O operation, or should I just consider a failure to be basically unrecoverable, etc. I would appreciate some code samples demonstrating proper usage, or a library guide reference that indicates how this is to be handled. Any other data is, of course, welcome.

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  • Can An Assembly Be Installed In The GAC but not Show Up In Gacutil.exe?

    - by Brett Bim
    I've got an application where some assemblies are copied to C:\Windows\assembly upon deployment under the assumption that this installs them in the GAC. The application seems to work but when I run gacutil.exe on the copied assemblies, it says the Global Assembly Cache contains 0 assemblies. Should all assemblies in c:\Windows\assembly show up in gacutil? If not, why not? How can I verify that the assembly is in fact installed in the GAC? I have always used gacutil.exe in the past to register assemblies so doing a file copy is new to me and I'm trying to understand the ramifications.

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  • WCF competitive consumer pattern

    - by Simon Thompson
    Is it possible to create a WCF service (web service) that only accepts a single connection at any one time with all other calls either queued or rejected. Need to implement the competitive consumer pattern where there are a number of clients which could deal with task at hand but when a client askes for more work a task must go to only one of them. Usual done as part of an enterprise service bus but can not find one that I'm happy to start using so looking to get this behaviour through a WCF service. Any ideas people ?

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  • Group / User based security. Table / SQL question

    - by Brett
    Hi, I'm setting up a group / user based security system. I have 4 tables as follows: user groups group_user_mappings acl where acl is the mapping between an item_id and either a group or a user. The way I've done the acl table, I have 3 columns of note (actually 4th one as an auto-id, but that is irrelevant) col 1 item_id (item to access) col 3 user_id (user that is allowed to access) col 3 group_id (group that is allowed to access) So for example item1, peter, , item2, , group1 item3, jane, , so either the acl will give access to a user or a group. Any one line in the ACL table with either have an item - user mapping, or an item group. If I want to have a query that returns all objects a user has access to, I think I need to have a SQL query with a UNION, because I need 2 separate queries that join like.. item - acl - group - user AND item - acl - user This I guess will work OK. Is this how its normally done? Am I doing this the right way? Seems a little messy. I was thinking I could get around it by creating a single user group for each person, so I only ever deal with groups in my SQL, but this seems a little messy as well..

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