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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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  • CakePHP Bake association problem

    - by Apu
    I have only two tables in my database with a one-to-many relationship between them (user hasMany messages) and am trying to get basic CRUD functionality going. Bake detects the associations correctly and specifies them correctly inside the model classes, but in controllers and views it looks like Cake doesn't know anything about those associations -- I don't even get a select tag for user_id when I go add a new message. Has anyone come across this problem before? What can I be doing wrong? Table structure appears to be fine: CREATE TABLE users ( id int(11) NOT NULL AUTO_INCREMENT, username varchar(255) NOT NULL, `password` varchar(255) NOT NULL, email varchar(255) NOT NULL, created datetime NOT NULL, modified datetime NOT NULL, PRIMARY KEY (id) ) ENGINE=MyISAM DEFAULT CHARSET=utf8; CREATE TABLE IF NOT EXISTS `messages` ( `id` int(11) NOT NULL AUTO_INCREMENT, `user_id` int(11) NOT NULL, `content` varchar(255) NOT NULL, `created` datetime NOT NULL, `modified` datetime NOT NULL, PRIMARY KEY (`id`) ) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=1 ;

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  • How to parse a text file and write the result to an xls file?

    - by Bk
    Hi all i am a junior level SQL developer. I have a situation where I have a text file with 1100 lines of a search result with each line containing a file path and a stored procedure associated with that file. Each line has a structure like the one below: abc\def\ghi\***.cs(40): jkl=******.*****.******, "proc_pqrst", parms); Where abc\def\ghi\***.cs is file path of the file ***.cs. The stored procedure names begin with proc_. I have to extract the ***.cs and the corresponding stored procedure name begining with proc_ and write them to a .xls file. Can some body help me in writing the parsing program to do this? Also can I get a detailed outline on where should I write the code for c# and where should I compile it? This could be a great help as I don't have any knowledge of C#. Thank you, BK.

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  • In search of opinions on web based version control systems

    - by tom smith
    Hi. Researching various open source, web-based document management/version control systems. I've checked google/questions here, etc... I'm looking for a lightweight web-based (apache) document mgmt/version control app that runs on top of SVN. I need to have the ability to: have multiple users checkin/checkout have a workflow (when userA checks the file in, and finishes the app passes it to the next person, etc... the app needs to allow me to have a structure where the files can be moved as a group. the files will be changed on a monthly basis app needs to have a access/premission control system. some people can see certain files, and perform certain actions on the files I imagine that I'm going to have 40-50 people dealing with the different files. I imagine that I'm going to have 2000-3000 files that have to be massaged. I'd prefer that the app be php based if possible, as opposed to a straight java app. Thanks

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  • Passing List (Of ChildClass) as parameter to method expecting List (Of ParentClass)?

    - by Nicholas
    Hi, I have implemented inheritance for two parent classes called Table and Field. Each parent class has several child classes. In the Table parent class, I created a method that expects parameter List(Of Field). I get an error when trying to pass in parameter List(Of ChildField) to the method that expects a parameter of List(Of Field). The error message is as below: Value of type 'System.Collections.Generic.List(Of com.hlb.icisbatch.data.ChildField)' cannot be converted to 'System.Collections.Generic.List(Of com.hlb.icisbatch.data.Field)' My question, is it possible to pass in list of child class as parameter? If it is not a list then it works fine. But somehow it is not possible with lists? Below is sample class structure: Table Field | | ChildTable ChildField I have a method in the parent class: Public Class Table Public Sub New() End Sub Public Overridable Sub setFields(ByVal list As List(Of Field) 'Do work here' End Sub End Class and method in child class: Public Class ChildTable Public Sub New(ByVal list As List(Of ChildField) setFields(ChildField) End Sub End Class

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  • how to send JSON data with server error response code 500

    - by kapil.israni
    I wanted to know if theres a way to send a JSON data along with HTTP response code 500. Basically I want my rest client to know that there is some error on the backend and along with it send a JSON error data structure like this. {"error" : [ {"code": "1001", "desc": "Some error description"}, {"code": "1002", "desc": "Some other error description"} ] } This is using the following java stack = Java 6/JAX-RS/Jersey/Tomcat If not, then is there a way to send a custom response code along with JSON data. Basically looking from JAX-RS API it looks that you can only send JSON data along with 200 OK?? Any thoughts?? I am guessing RESTEasy would be the same, right??

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  • doctrine behaviors , if i did it like this , would be correct ??

    - by tawfekov
    Hi , I am doing a web application in ZF + Doctrine 1.2.3 but i had an old database , it had pretty good structure so i think i can reverse engineer it with doctrine commad ./dcotrine generate-models-db , its amazing but i stopped when i wanted to use some doctrine behaviors like : searchable as an example , my question : if i went to my model and added these two lines : $this->actAs('Searchable', array( 'fields' => array('title', 'content') ) ); i am not sure if that enough and would work as expected , if you had any more tips about creating other behaviors like (versionable , i18n , sluggable or soft delete ) manually or reverse engineer it with doctrine behaviors , could you please list them

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  • Adding value to an Input field on click

    - by Wazdesign
    I have this structure on form, <input type="test" value="" id="username" /> <span class="input-value">John Smith</span> <a href="#" class="fill-input">Fill Input</a> when user click on the Fill Input , the data from span which has class input-value will be added to value, after clicking a tag the code should be look like this, <input type="test" value="john Smith" id="username" /> <span class="input-value">John Smith</span> <a href="#" class="fill-input">Fill Input</a> there are many forms element/input on the single page.

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  • algorithm to find overlaps

    - by Gary
    Hey, Basically I've got some structs of type Ship which are going to go on a board which can have a variable width and height. The information about the ships is read in from a file, and I just need to know the best way to make sure that none of the ships overlap. Here is the structure of Ship: int x // x position of first part of ship int y // y position of first part of ship char dir // direction of the ship, either 'N','S','E' or 'W' int length // length of the ship Also, what would be a good way to handle the directions. Something cleaner than using a switch statement and using a different condition for each direction. Any help would be greatly appreciated!

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  • Subversion for version control

    - by Gabriel Parenza
    Hi, I am working on an application whose primary purpose would be to provide source control management. My idea is to use to SVNKit for file check-out and check-in. However, while working with SVNKit, I realised it does not have the speed I was looking for. For instance, whenever developers create a ChangeRequest, which can encompass change in 3-40 files, I have to create a directory structure distributed across 32 folders. Doing so takes around 50 seconds, Another instance is that after creating change request developers can add files to the request. Copying even a single file from Trunk to branch takes around 6-7 secs. My question is has anyone had experience like this and what did you do to improve the performance? Moreover, is my approach correct? NOTE: I am using "http" protocol and can't use "svn" protocol.

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  • Problem measuring N times the execution time of a code block

    - by Nazgulled
    EDIT: I just found my problem after writing this long post explaining every little detail... If someone can give me a good answer on what I'm doing wrong and how can I get the execution time in seconds (using a float with 5 decimal places or so), I'll mark that as accepted. Hint: The problem was on how I interpreted the clock_getttime() man page. Hi, Let's say I have a function named myOperation that I need to measure the execution time of. To measure it, I'm using clock_gettime() as it was recommend here in one of the comments. My teacher recommends us to measure it N times so we can get an average, standard deviation and median for the final report. He also recommends us to execute myOperation M times instead of just one. If myOperation is a very fast operation, measuring it M times allow us to get a sense of the "real time" it takes; cause the clock being used might not have the required precision to measure such operation. So, execution myOperation only one time or M times really depends if the operation itself takes long enough for the clock precision we are using. I'm having trouble dealing with that M times execution. Increasing M decreases (a lot) the final average value. Which doesn't make sense to me. It's like this, on average you take 3 to 5 seconds to travel from point A to B. But then you go from A to B and back to A 5 times (which makes it 10 times, cause A to B is the same as B to A) and you measure that. Than you divide by 10, the average you get is supposed to be the same average you take traveling from point A to B, which is 3 to 5 seconds. This is what I want my code to do, but it's not working. If I keep increasing the number of times I go from A to B and back A, the average will be lower and lower each time, it makes no sense to me. Enough theory, here's my code: #include <stdio.h> #include <time.h> #define MEASUREMENTS 1 #define OPERATIONS 1 typedef struct timespec TimeClock; TimeClock diffTimeClock(TimeClock start, TimeClock end) { TimeClock aux; if((end.tv_nsec - start.tv_nsec) < 0) { aux.tv_sec = end.tv_sec - start.tv_sec - 1; aux.tv_nsec = 1E9 + end.tv_nsec - start.tv_nsec; } else { aux.tv_sec = end.tv_sec - start.tv_sec; aux.tv_nsec = end.tv_nsec - start.tv_nsec; } return aux; } int main(void) { TimeClock sTime, eTime, dTime; int i, j; for(i = 0; i < MEASUREMENTS; i++) { printf(" » MEASURE %02d\n", i+1); clock_gettime(CLOCK_REALTIME, &sTime); for(j = 0; j < OPERATIONS; j++) { myOperation(); } clock_gettime(CLOCK_REALTIME, &eTime); dTime = diffTimeClock(sTime, eTime); printf(" - NSEC (TOTAL): %ld\n", dTime.tv_nsec); printf(" - NSEC (OP): %ld\n\n", dTime.tv_nsec / OPERATIONS); } return 0; } Notes: The above diffTimeClock function is from this blog post. I replaced my real operation with myOperation() because it doesn't make any sense to post my real functions as I would have to post long blocks of code, you can easily code a myOperation() with whatever you like to compile the code if you wish. As you can see, OPERATIONS = 1 and the results are: » MEASURE 01 - NSEC (TOTAL): 27456580 - NSEC (OP): 27456580 For OPERATIONS = 100 the results are: » MEASURE 01 - NSEC (TOTAL): 218929736 - NSEC (OP): 2189297 For OPERATIONS = 1000 the results are: » MEASURE 01 - NSEC (TOTAL): 862834890 - NSEC (OP): 862834 For OPERATIONS = 10000 the results are: » MEASURE 01 - NSEC (TOTAL): 574133641 - NSEC (OP): 57413 Now, I'm not a math wiz, far from it actually, but this doesn't make any sense to me whatsoever. I've already talked about this with a friend that's on this project with me and he also can't understand the differences. I don't understand why the value is getting lower and lower when I increase OPERATIONS. The operation itself should take the same time (on average of course, not the exact same time), no matter how many times I execute it. You could tell me that that actually depends on the operation itself, the data being read and that some data could already be in the cache and bla bla, but I don't think that's the problem. In my case, myOperation is reading 5000 lines of text from an CSV file, separating the values by ; and inserting those values into a data structure. For each iteration, I'm destroying the data structure and initializing it again. Now that I think of it, I also that think that there's a problem measuring time with clock_gettime(), maybe I'm not using it right. I mean, look at the last example, where OPERATIONS = 10000. The total time it took was 574133641ns, which would be roughly 0,5s; that's impossible, it took a couple of minutes as I couldn't stand looking at the screen waiting and went to eat something.

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  • Weird behaviour of a deserialized class

    - by orloffm
    I've got a huge XML file that's being deserialized by XmlSerializer in an XSD-generated class structure. Everything used to work just fine, but now a weird thing started happening. Sometimes (50% of runs) a field of a certain object of a class that's deep in the class tree just changes to a certain value of the same field of a different object of the same class. It happens when entering some function, when debugger steps from opening "{" to the first line of code. I understand that it's stupid question, but maybe someone have any thoughts?

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  • How to insert all records into a table only one time

    - by Lu Lu
    Hello, I want to get all records from a table1 & insert them into table2. Table1 & table2 are in different databases, table1 and table2 are same structure. Normally, I will get all records from table1, and for each record (foreach), I will insert it into table2 by using "INSERT ...". I want to know a effect way to insert all records into table only one time without foreach. I use C#, .NET 2.0 & WinForm. Thanks.

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  • How do I delete a file from depot, but leave local copy in tact?

    - by Gary
    I'm trying to learn Perforce and want to delete a file from the depot(easy to do with p4 delete, p4 submit), but that deletes it from the client machine dir structure as well. I want to keep my local file in my directory intact. The only way I can see to do this would be to move it out of the hierarchy that is under Perforce control before deleting. I was able to get my file back by syncing an earlier version. Maybe I set up my client workspace wrong? Or am I misunderstanding a fundamental concept of source control? The client workspace is /home/user and I did it this way so I could add any file under my home directory without getting an error about the file not being under client's root. FYI - Linux client and server running P4D/LINUX26X86/2009.1/222893 (2009/11/12) Any advice appreciated. Thanks.

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  • How to select all parents of a node in a hierarchical mysql table?

    - by Ehsan Khodarahmi
    I have a MySQL table that represents data for a tree GUI component, here's the structure of my table: treeTable ( id INT NOT NULL PRIMARY KEY, parentId INT, name VARCHAR(255) ); parentId is a self-referencing foreign key. Now I want to write a stored procedure which gets a node id and returns a result set that contains that node and all of its parents. For example, suppose that my table has filled with this data: 1, null, 'root' 2, 1 , 'level_1' 3, 2 , 'level_2' Now I want to get all parent nodes of node 3 (nodes 1 and 2) and return a result set that contains all tree records. Can anybody help me please?

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  • What do the square brackets in LaTeX logs mean?

    - by stefan-majewsky
    I'm currently working on a parser that reads complete LaTeX logs. Most of the log format is, though weird, easy to figure out, but these square brackets are puzzling me. Here's an example from near the end of one of my logs: Overfull \hbox (10.88788pt too wide) in paragraph at lines 40--40 []$[]$ [] [102]) [103] Kapitel 14. (./Thermo-141-GrenzenFundamentalpostulat.tex [104 ]) (./Thermo-142-Mastergleichung.tex [105]) (./Thermo-143-HTheorem.tex [106pdfTeX warning (ext4): destination with the same identifier (name{equation.14.3.3}) ha s been already used, duplicate ignored Can anybody give me a hint what these square brackets mean? I can't see any structure in them. I have the suspicion that lines 2/3 above are some kind of ASCII art representing the box layout, though I know too less about badboxes to justify this or identify the meaning of the single characters. Then, the "[104" etc. seem to correspond to the page numbers, but I am still not seeing the reason why there is sometimes something inbetween the square brackets (like the pdfTeX warning above), and sometimes not.

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  • Extending configuration for .Net 3.5 Applications

    - by Maximiliano Rios
    Due to a requirement in my current project, I have to build a configuration manager to handle configurations that merge local config info with database one. Custom configuration doesn't fit my needs, problem is that I don't know what's the type before loading certain information, for example: Loading database information I will able to know what's myhandler's type. Not previously. So I thought to write my own handler but I can't let set blank as type for sections, in fact .net requires to know what's the type to match myhandler nodes. I'm thinking on building a different parser to read XML nodes but I would prefer to match this structure. I've not found any information to do that yet, is there any way? Can I extend or hook up something into the framework to be capable of loading on-the-fly types and validate nodes? Thanks in advance.

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  • Software Requirement Specifications for Web Applications

    - by illuminatedtiger
    Hi guys, I'm looking for some guidance/books to read when it comes to creating a software requirement specification for a web application. For inspiration I have read some spec documents for desktop based applications. The documents I have read capture a systems functional requirements in use cases which tend to be rather data oriented with use cases centered around the various CRUD operations the application is intended to perform. I like this structure however I'm finding it rather difficult to marry it to what my web application needs to do, mostly reading data as opposed to manipulating it. I've had a go at writing some use cases however they all tend to boil down to "Search for item", "Change view of search results" or "User selects facet to refine search results". This doesn't sound quite right to me and makes me wonder if I'm going about this the right way. Are there planning differences between web based and desktop based applications?

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  • Generating unobtrusive JS

    - by nico
    I have read quite a bit about unobtrusive JS and how to generate it and all that jazz... My problem is this: I have a website that heavily relies on mod_rewrite, so essentially all the pages requests are sent to index.php that generates the main structure of the page and then includes the appropriate page. Now, there are different sections in the site and each section uses different Javascript functions (e.g. for different AJAX requests). Now, if I just were to attach a function to the onload of the page obviously the thing would not work, as I do not have to initialise the same things for each page... so what is the best way to handle this situation? I hope the situation is clear, I'll be happy to clarify if needed

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  • Error when trying to use PDO object

    - by Nate
    EDIT: I'm going to put my code in here due to comments below. So sit tight for a few minutes ;-) Thanks! I'm an inexperienced php programmer and only found out about PDO a few days ago. I'm now trying to port my website code over to using PDO, but I am getting an error when I try to use the PDO object that I create. I'm using a CMS on my website, and it makes building page output kind of complicated, but I've tried to draw the structure of what is being called below: index.php -class myClass defined --method myFunction defined (it gets called on pageload & returns the page output) ---include file1.php ----require_once('mysql_connect.php') (creates pdo object) ----*I can use the pdo object here successfully* ----require_once('file2.php') -----require_once('mysql_connect.php') -----function myFunction2 defined ------*trying to use the pdo object here results in the error* The error I'm getting is: Fatal error: Call to a member function prepare() on a non-object in /home/rgcpanel/public_html/account/account_functions.php on line 147 Any idea what's going on?

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  • getting detailed information about structured exceptions

    - by Martin
    My Visual C++ application is compiled with /EHA option, letting me catch structured exceptions (division by zero, access violation, etc). I then translate those exceptions to my own exception class using _set_se_translator(). My goal is to improve our logging of those types of exceptions. I can get the type of exception from the EXCEPTION_RECORD structure, and the exception address. I would like to be able to gather more information, like the source file/location where the exception is thrown, the call stack, etc. Is that possible? I do create an exception minidump on structured exceptions - is there a tool to automatically get the call stack from that?

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  • PHP cannot verify if directory exists

    - by ali
    I am going crazy with this one I have this folders and files structure / /projects /mytest /install /index.php /product /resources So, inside my install/index.php file I am trying to verify if /product folder does exist. I know that the folder exists, but looks like PHP doesn't. My code: if(file_exists('../../mytest/product') && is_dir('../../mytest/product')) { echo 'Folder exists!'; } else { echo 'PHP is blind or something!'; } Maybe I am very tired, but I just cannot figure out what is wrong. Some rested minds here maybe will see the problem. Thanks!

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  • Adding valut to Input field on click

    - by Wazdesign
    I have this structure on form, <input type="test" value="" id="username" /> <span class="input-value">John Smith</span> <a href="#" class="fill-input">Fill Input</a> when user click on the Fill Input , the data from span which has class input-value will be added to value, after clicking a tag the code should be look like this, <input type="test" value="john Smith" id="username" /> <span class="input-value">John Smith</span> <a href="#" class="fill-input">Fill Input</a> there are many forms element/input on the single page. thanks!

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  • Licensing your code in Mono

    - by Jerry
    I'm working with some code in Visual Studio. My parter-in-crime fellow developer has suggested that the code also be available to work under Mono. I'm impresed witht he work that is already done in Mono, but I'm very new to Mono, so I don't know what it can/cannot do. I've already written a class in C# using the .NET LicenseManager object. It writes to the windows registry, so I know I'll have to modify it so that it will use some compiler flags like #if Win32 or #if MONO. My question is two-fold: 1) Does Mono implement the same LicenseManager class structure? 2) If so, how do you guys lock down your code using LicenseManager in Linux? (i.e. Write to files, use a hardware dongle, compare to hardware serials, etc??)

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  • Resources for how to design graph/charts well

    - by wesgarrison
    One of my projects needs to show users where they rank in certain calculations. I inherited the graph structure from the previous programmer and had to leave it alone while I worked on other parts of the site. It's time to make the graphs more meaningful, so I'm looking for books/websites/etc about graphs. (Not graph theory!) Charts that convey comparisons at a glance. Everyone suggests The Visual Display of Quantitative Information by Edward Tufte and that's spot on for what I'm looking for, so anything related to that would be great. Naturally, personal experience about what to do or not would be helpful as well.

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