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  • 50 sequences in one line

    - by user343934
    I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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  • What is a good approach for a Data Access Layer?

    - by Adil Mughal
    Our software is a customized Human Resource Management System (HRMS) using ASP.NET with Oracle as the database and now we are actually moving to make it a product that supports multiple tenants with their own databases. Our options: Use NHibernate to support Multiple databases and use of OO. But we concern related to NHibernate learning curve and any problem we faced. Make a generalized DAL which will continue working with Oracle using stored procedures and use tools to convert it to other databases such as SQL Server or MySql. There is a risk associated with having to support multiple database-dependent versions of a single script. Provide the software as a Service (SaaS) and maintain the way we conduct business. However there can may be clients who do not want or trust the Cloud or other SaaS business models. With this in mind, what's the best Data access layer technique?

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  • Netbean Cannot update Google App Engine server to appengine-java-sdk-1.3.2

    - by sy
    I am using Netbean 6.7.1 I just update my google app engine plugin in netbean with Netbean auto update. I found out there is new app engine SDK. So i want to update my google app engine server to point to appengine-java-sdk-1.3.2 After I download appengine-java-sdk-1.3.2.zip. I unzip it. Then at Netbean: I already have a Google App Engine server under Services - Server. I can't find anyway to point it to the newly installed sdk folder. So I deleted the existing "Google App Engine" server & try to add a new one. Server - Add Server - Google App Engine - at "Installation Location", I point it to google app engine folder, which is "C:\appengine-java-sdk-1.3.2", it show this message at bottom "C:\appengine-java-sdk-1.3.2" & don't allow me to continue. May I know how to solve this? thanks!

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  • Is it OK to pass SQLCommand as a parameter?

    - by TooFat
    I have a Business Layer that passes a Conn string and a SQLCommand to a Data Layer like so public void PopulateLocalData() { System.Data.SqlClient.SqlCommand cmd = new System.Data.SqlClient.SqlCommand(); cmd.CommandType = System.Data.CommandType.StoredProcedure; cmd.CommandText = "usp_PopulateServiceSurveyLocal"; DataLayer.DataProvider.ExecSQL(ConnString, cmd); } The DataLayer then just executes the sql like so public static int ExecSQL(string sqlConnString, System.Data.SqlClient.SqlCommand cmd) { int rowsAffected; using (SqlConnection conn = new SqlConnection(sqlConnString)) { conn.Open(); cmd.Connection = conn; rowsAffected = cmd.ExecuteNonQuery(); cmd.Dispose(); } return rowsAffected; } Is it OK for me to pass the SQLCommand as a parameter like this or is there a better more accepted way of doing it. One of my concerns is if an error occurs when executing the query the cmd.dispose line will never execute. Does that mean it will continue to use up memory that will never be released?

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  • An operator == whose parameters are non-const references

    - by Eduardo León
    I this post, I've seen this: class MonitorObjectString: public MonitorObject { // some other declarations friend inline bool operator==(/*const*/ MonitorObjectString& lhs, /*const*/ MonitorObjectString& rhs) { return lhs.fVal==rhs.fVal; } } Before we can continue, THIS IS VERY IMPORTANT: I am not questioning anyone's ability to code. I am just wondering why someone would need non-const references in a comparison. The poster of that question did not write that code. This was just in case. This is important too: I added both /*const*/s and reformatted the code. Now, we get back to the topic: I can't think of a sane use of the equality operator that lets you modify its by-ref arguments. Do you?

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  • SSIS XML Decryption Message

    - by Vaccano
    My SSIS package says it is successful, but when it runs it ends not doing anything (that I can see). The only thing wrong is this message (that it does not qualify as an error). Description: Failed to decrypt an encrypted XML node because the password was not specified or not correct. Package load will attempt to continue without the encrypted information I do have a password on my packages, but I don't see anywhere to put the password in when I load the Package into SSIS. Am I missing a step?

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  • Best method to cleanly shut down an application launched via another.

    - by JYelton
    I couldn't find any close answers to this, so I'm consulting the experience of SO users: Scenario: I have two small C# winforms applications where one behaves as a server or host, the other as a client. They share data via SQL Server, in terms of configuration settings. I am currently launching the client application (which only needs to run periodically) from the server application via Process.Start() and terminating it via Process.CloseMainWindow() (after finding it in the process list). While it seems clean enough, I wondered if there's a better way. Question: Which way would be best to instruct the client application to shut down: Continue using Process.CloseMainWindow()? Implement WCF between the applications? (I would need help on how to do this.) Set a variable in SQL that the client application checks for? Some other way?

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  • visual studio 2002: c# threading question

    - by dotnet-practitioner
    Hi, I have a piece of code where I send a file content over tcp/ip channel. There are times when this connection hangs causing entire application to freeze. Is there a way for my main thread to spawn a worker thread and monitor that worker thread. If worker thread succeeds, well and good. If it hangs , the main thread could log error message and continue. How can I simulate in my test code that a worker thread is hanging. please let me know what could the code look like. I am using C# Visual studio 2002.

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  • Can't seem to get Prototype AJAX form validation to work in conjunction with Codeigniter

    - by MattB
    Is there some kind of trick involved? Here's how I would envision it working: 1) User tries submitting the form 2) Event.observe captures this and sends an AJAX request to a special validation URL (PHP using Codeigniter) 3) If no errors were returned, continue submitting the original form 4) If errors were found, cancel form submission and display Mostly, I can't seem to get a separate AJAX validation request to work as the form continues submitting. I could use Event.stop(event), but have not found a way to re-start the process if no validation errors exist from the validation call. I'd post code, but I have about 15 examples of things I've tried and it would just clutter this question. Any ideas? :-( I didn't think form validation would be this difficult. Many thanks, - Matt

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  • Transfer of control and data between C and C#

    - by Prithvi
    C# main program needs to call a C program GA.c This C code executes many functions and one function initialize() calls objective() function. But this objective function needs to be written in C#.This call is in a loop in the C code and the C code needs to continue execution after the return from objective() until its main is over and return control to C# main program. C# main() { //code call to GA in C; //remaining code; } GA in C: Ga Main() { //code call to initialize function(); //remaining code } initialize funtion() in GA { for(some condition) { //code call to objective(parameter) function in C#; //code } } How do we do this?

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  • VSTO install package How to check for prerequisites and skip them

    - by ticky
    I created Setup project for my Excel add-in project according to the article: Deploying a Visual Studio Tools for the Office System 3.0 Solution for the 2007 Microsoft Office System Using Windows Installer http://msdn.microsoft.com/en-us/library/cc563937(office.12).aspx I add prerequisites such as 2007 Interop assemblies(Office2007PIA) and when I run my setup file it does install it. But the problem is : That my setup ALWAYS installs it even if my computer already has Office2007PIA. How can I configure my setup project that it will first check if Office2007PIA is installed and continue the installation of my project without installing Office2007PIA? Thanks!

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  • Eclipse debugging "source not found"

    - by James
    I just started using Eclipse so go easy on me ;). But when trying to debug a JUnit test case I get a dialog that states the the source is not found when I get to this line in the code in my test method: Assert.assertEquals(1, contents.size()); I know I should probably go and try and download the source from somewhere, but I really don't want to because I have no interest in stepping into the JUnit code. I have the JUnit runtime jar so Why does Eclipse expect me to have all the referenced tools source code in order to debug my own code (seems somewhat silly)? My main question is though, how can I tell Eclipse to skip this dialog when the source is not available and allow me to continue to debug my own code? [Edit] I've isolated the cause of this. It seems that Eclipse seems to think it needs the source when an exception is thrown by the internal JUnit code. In general is there anyway to tell it that it doesn't and just have it throw up an error dialog of some kind instead?

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  • Is it a good idea to work on header files only, just at the start of the project?

    - by m4design
    To explain my point further, I'm a beginner in programming, and I'm working on a small project. Instead of separating the .cpp file from the header file, I'm implementing the code in the header files, and making one .cpp file for testing. I do this to have less files, hence easier navigation. Then later I'll separate the code as it should be. Will this cause any problems? should I continue doing that? Thanks.

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  • Issue with Java join() method.

    - by gmunk
    First of all here are some code snippets: http://pastebin.com/9ZCwekXs http://pastebin.com/TtLLXPYP I'm trying to animate some images. The thing is that I want the main thread to wait for the animation thread to finish and then to continue. I searched around, read a little bit and decided to use the join() method. It perfectly waits for the thread to finish but I doesn't animate correctly. The repaint() method gets called 2 times instead of nine. I think maybe the problem is because I used singletons. Here is the singleton implementation. http://pastebin.com/bA3qLZJE

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  • Visual Studio add-in for performance benchmarking

    - by chiccodoro
    I'd like to measure the performance of some code blocks in my c# winforms application. In particular I want to measure performance regression/improvement after some restructuring of the code. So long I've seen the System.Diagnostics.Stopwatch. However, I want to avoid writing measuring code into my classes, I would rather prefer to separate measuring from actual code. As for debugging, you can set breakpoints on several code lines and "jump" from one to the next by "Continue Execution", I imagine something similar for measuring: Mark to lines of code and make Visual Studio display the time elapsing from one to the next. Is there any feature/add-in in that direction?

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  • C# SQL Parameter Errors in Loops

    - by jakesankey
    Please help me out with this. I have this small application to load txt files into a sql db and it works fine with sqlite. When I ported to SQL I started getting 'parameter already declared' errors.. If anyone can help me reorganize this code, it would be great! I need to get the parameter definitions outside of the loops or something.. using System; using System.Data; using System.Data.SQLite; using System.IO; using System.Text.RegularExpressions; using System.Threading; using System.Collections.Generic; using System.Linq; using System.Data.SqlClient; namespace JohnDeereCMMDataParser { internal class Program { public static List<string> GetImportedFileList() { List<string> ImportedFiles = new List<string>(); using (SqlConnection connect = new SqlConnection(@"Server=FRXSQLDEV;Database=RX_CMMData;Integrated Security=YES")) { connect.Open(); using (SqlCommand fmd = connect.CreateCommand()) { fmd.CommandText = @"SELECT FileName FROM Import;"; fmd.CommandType = CommandType.Text; SqlDataReader r = fmd.ExecuteReader(); while (r.Read()) { ImportedFiles.Add(Convert.ToString(r["FileName"])); } } } return ImportedFiles; } private static void Main(string[] args) { using (SqlConnection con = new SqlConnection(@"Server=FRXSQLDEV;Database=RX_CMMData;Integrated Security=YES")) { con.Open(); using (SqlCommand insertCommand = con.CreateCommand()) { Console.WriteLine("Connecting to SQL server..."); SqlCommand cmdd = con.CreateCommand(); string[] files = Directory.GetFiles(@"C:\Documents and Settings\js91162\Desktop\", "R.txt*", SearchOption.AllDirectories); insertCommand.Parameters.Add(new SqlParameter("@FeatType", DbType.String)); insertCommand.Parameters.Add(new SqlParameter("@FeatName", DbType.String)); insertCommand.Parameters.Add(new SqlParameter("@Value", DbType.String)); insertCommand.Parameters.Add(new SqlParameter("@Actual", DbType.Decimal)); insertCommand.Parameters.Add(new SqlParameter("@Nominal", DbType.Decimal)); insertCommand.Parameters.Add(new SqlParameter("@Dev", DbType.Decimal)); insertCommand.Parameters.Add(new SqlParameter("@TolMin", DbType.Decimal)); insertCommand.Parameters.Add(new SqlParameter("@TolPlus", DbType.Decimal)); insertCommand.Parameters.Add(new SqlParameter("@OutOfTol", DbType.Decimal)); List<string> ImportedFiles = GetImportedFileList(); foreach (string file in files.Except(ImportedFiles)) { var FileNameExt1 = Path.GetFileName(file); cmdd.Parameters.Add(new SqlParameter("@FileExt", FileNameExt1)); cmdd.CommandText = @" IF (EXISTS (SELECT * FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_SCHEMA = 'RX_CMMData' AND TABLE_NAME = 'Import')) BEGIN SELECT COUNT(*) FROM Import WHERE FileName = @FileExt; END"; int count = Convert.ToInt32(cmdd.ExecuteScalar()); con.Close(); con.Open(); if (count == 0) { Console.WriteLine("Parsing CMM data for SQL database... Please wait."); insertCommand.CommandText = @" INSERT INTO Import (FeatType, FeatName, Value, Actual, Nominal, Dev, TolMin, TolPlus, OutOfTol, PartNumber, CMMNumber, Date, FileName) VALUES (@FeatType, @FeatName, @Value, @Actual, @Nominal, @Dev, @TolMin, @TolPlus, @OutOfTol, @PartNumber, @CMMNumber, @Date, @FileName);"; string FileNameExt = Path.GetFullPath(file); string RNumber = Path.GetFileNameWithoutExtension(file); string RNumberE = RNumber.Split('_')[0]; string RNumberD = RNumber.Split('_')[1]; string RNumberDate = RNumber.Split('_')[2]; DateTime dateTime = DateTime.ParseExact(RNumberDate, "yyyyMMdd", Thread.CurrentThread.CurrentCulture); string cmmDate = dateTime.ToString("dd-MMM-yyyy"); string[] lines = File.ReadAllLines(file); bool parse = false; foreach (string tmpLine in lines) { string line = tmpLine.Trim(); if (!parse && line.StartsWith("Feat. Type,")) { parse = true; continue; } if (!parse || string.IsNullOrEmpty(line)) { continue; } Console.WriteLine(tmpLine); foreach (SqlParameter parameter in insertCommand.Parameters) { parameter.Value = null; } string[] values = line.Split(new[] { ',' }); for (int i = 0; i < values.Length - 1; i++) { SqlParameter param = insertCommand.Parameters[i]; if (param.DbType == DbType.Decimal) { decimal value; param.Value = decimal.TryParse(values[i], out value) ? value : 0; } else { param.Value = values[i]; } } } insertCommand.Parameters.Add(new SqlParameter("@PartNumber", RNumberE)); insertCommand.Parameters.Add(new SqlParameter("@CMMNumber", RNumberD)); insertCommand.Parameters.Add(new SqlParameter("@Date", cmmDate)); insertCommand.Parameters.Add(new SqlParameter("@FileName", FileNameExt)); // insertCommand.ExecuteNonQuery(); } } Console.WriteLine("CMM data successfully imported to SQL database..."); } con.Close(); } } } } FYI - the PartNumber, CMMNumber, Date, etc at the bottom are pulled from the file name and I need it in the table next to each respective record.

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  • how to run progress-bar through insert query ?

    - by Gold
    hi i have this insert query: try { Cmd.CommandText = @"INSERT INTO BarcodTbl SELECT * FROM [Text;DATABASE=" + PathI + @"\].[Tmp.txt];"; Cmd.ExecuteNonQuery(); Cmd.Dispose(); } catch (Exception ex) { MessageBox.Show(ex.Message); } and i have two question: how to run progress-bar from the begging to the end of the insert ? if there any error i got the error exception and the action is stop - the query stop and the BarcodTbl is empty. how i can see the error and that the query will continue to fill the table ? thank's in advance

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  • Storing DateTime (UTC) vs. storing DateTimeOffset

    - by Frederico
    I usually have an "interceptor" that right before reading/writing from/to the database does datetime conversion (from UTC to localtime, and from localtime to utc), so I can use DateTime.Now (derivations and comparisions) throughout the system without worrying about timezones. Regarding serialization and moving data between computers, there is no need to bother, as the datetime is always UTC. Should I continue storing my dates (SQL 2008 - datetime) in UTC format or should I instead store it using DateTimeOffset (SQL 2008 - datetimeoffset)? UTC Dates in the database (datetime type) have been working and known for so long, why change it? What are the advantages? I have already looked into articles like this one, but I'm not 100% convinced though. Any thoughts?

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  • Locking a file to verify a single execution of a service. How reliable?

    - by Camilo Díaz
    Hello, I am deploying a little service to an UNIX(AIX) system. I want to check if there is no active instance of that service running when starting it. How reliable is to implement that check like this? Try to acquire a lock on a file (w/ FileChannel) If succeeds, keep lock and continue execution If fails, exit and refuse to run the main body I am aware of software like the Tanuki wrapper, however, I'm longing for a simpler(maybe not portable) solution. Regarding PIDFILE(s): I want to avoid using them if possible, as I don't have administrative rights on the machine, neither knowledge in AIX's shell programming.

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  • Software Protection: Shuffeling my application?

    - by Martijn Courteaux
    Hi, I want to continue on my previous question: http://stackoverflow.com/questions/3007168/torrents-can-i-protect-my-software-by-sending-wrong-bytes Developer Art suggested to add a unique key to the application, to identifier the cracker. But JAB said that crackers can search where my unique key is located by checking for binary differences, if the cracker has multiple copies of my software. Then crackers change that key to make them self anonymous. That is true. Now comes the question: If I want to add a unique key, are there tools to shuffle (a kind of obfuscation) the program modules? So, that a binary compare would say that the two files are completely different. So they can't locate the identifier key. I'm pretty sure it is possible (maybe by replacing assembler blocks and make some jumps). I think it would be enough to make 30 to 40 shuffles of my software. Thanks

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  • How to skip integers in C++ taken from a fstream txt file?

    - by Elaina
    I need to create a function that uses a loop. This function will open a text file and then must be able to skip a variable number of leading random integers. The program must be able to handle any number of leading random integers. Example if the opened file reads this on its first line: 100 120 92 82 38 49 102 and the SKIP_NUMBER variable is assigned 3 the number the function would grab is 82. The function must continue to grab the integers every SKIP_NUMBER until it reaches the end of the file. These integers taken from the txt file are then placed into another text file. Please help I'm really lost on how to create this loop! :D Here is my function so far... //Function skips variables and returns needed integer int skipVariable (int SKIP_NUMBER) { return 0; //temporary return } These are my program variables: // initialize function/variables ifstream fin; string IN_FILE_NAME, OUT_FILE_NAME; int SKIP_NUMBER;

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  • Generating Mouse-Keyboard combination events in python

    - by freakazo
    I want to be able to do a combination of keypresses and mouseclicks simultaneously, as in for example Control+LeftClick At the moment I am able to do Control and then a left click with the following code: import win32com, win32api, win32con def CopyBox( x, y): time.sleep(.2) wsh = win32com.client.Dispatch("WScript.Shell") wsh.SendKeys("^") win32api.SetCursorPos((x,y)) win32api.mouse_event(win32con.MOUSEEVENTF_LEFTDOWN, x, y, 0, 0) win32api.mouse_event(win32con.MOUSEEVENTF_LEFTUP, x, y, 0, 0) What this does is press control on the keyboard, then it clicks. I need it to keep the controll pressed longer and return while it's still pressed to continue running the code. Is there a maybe lower level way of saying press the key and then later in the code tell it to lift up the key such as like what the mouse is doing?

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  • Using hash to check if page with $_POST values was refreshed

    - by Dieseltime
    When posting a form to the same PHP page, what is the correct method to find if the page was accidentally refreshed instead of submitted again? Here's what I'm using right now: $tmp = implode('',$_POST); $myHash = md5($tmp); if(isset($_SESSION["myHash"]) && $_SESSION["myHash"] == $myHash) { header("Location: index.php"); // page refreshed, send user somewhere else die(); } else { $_SESSION["myHash"] = $myHash; } // continue processing... Is there anything wrong with this solution?

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  • svn working copy spanning 2 physical drives?

    - by ronenosity
    I have a large repository hosted on dreamhost that I backup daily on a remote machine using a windows scheduled task which updates the working copy located on an external USB 300GB drive connected to the remote machine. The 300GB drive is nearly full with only 26GB of free space remaining. Recently I added a second USB external 1TB drive to increase storage capacity. I would like to ask: what is the best way to use the new 1TB drive? Is it possible to span the working copy across both drives (ex: somehow create a 1.3 TB drive)? If I copied the working copy from the 300GB to the 1TB would svn continue form do I need to retarget the update working copy script to the new 1TB drive and start downloading everything again (least desired option) thanks

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  • Drupal. Use AJAX to update view's content

    - by ozke
    Hi, I've created a view in Drupal that retrieves a list of nodes. The display of this view is a page and it works perfectly well. It does even allow me to filter its content by argument. See the current's view configuration (click to enlarge): I want to use AJAX to use the filter (by parameter) functionality without reloading the page. I've enabled the "Use AJAX" option but I am not sure on how to continue. Any ideas on how to do that? By the way, I'm building my own theme (in case that changes anything). Thanks in advance Update: Basically, this view works when I browse through section/parameter1, section/parameter2... but I want to do the same with AJAX, without reloading the page. I hope is clearer now

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