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  • Hang while starting several daemons

    - by Adrian Lang
    I’m running a Debian Squeeze AMD64 server. Target runlevel after boot is runlevel 2, which includes rsyslogd, cron, sshd and some other stuff, but not dovecot, postfix, apache2, etc. The system fails to reach runlevel 2 with several symptoms: The system hangs at trying to start rsyslogd Booting into runlevel 1 works, then login from the console works Starting rsyslogd from runlevel 1 via /etc/init.d/rsyslog hangs Starting runlevel 2 with rsyslogd disabled works But then, logging in via console fails: I get the motd, and then nothing Starting sshd from runlevel 1 succeeds But then, I cannot login via ssh. Sometimes password ssh login gives me the motd and then nothing, sometimes not even this. Trying to offer a public key seems to annoy the sshd enough to not talk to me any further. When rebooting from runlevel 1, the server hangs at trying to stop apache2 (which is not running, so this really should be trivial). Trying to stop apache2 when logged in in runleve 1 does hang as well. And that’s just the stuff which fails all the time. RAM has been tested, dmesg shows no problems. I have no clue. Update: (shortened) output from rsyslogd -c4 -d called in runlevel 1 rsyslogd 4.6.4 startup, compatibility mode 4, module path '' caller requested object 'net', not found (iRet -3003) Requested to load module 'lmnet' loading module '/user/lib/rsyslog/lmnet.so' module of type 2 being loaded conf.c requested ref for 'lmnet', refcount 1 rsylog runtime initialized, version 4.6.4, current users 1 syslogd.c requested ref for 'lmnet', refcount now 2 I can kill rsyslogd with Strg+C, then. /var/log shows none of the configured log files, though. Update2: Thanks to @DerfK I still have no clue, but at least I narrowed down the problem. I’m now testing with /etc/init.d/apache2 stop (without an apache2 running, of course) which hangs as well and looks like an even more obvious failure. After some testing I found out that a file with one single line: /usr/sbin/apache2ctl configtest /dev/null 2&1 hangs, while the same line executed in an interactive shell works. I was not able to further reduce this line while, i. e. every single part, the stream redirections and the commando itself is necessary to reproduce the hang. @DerfK also pointed me to strace which gave a shallow hint about what kind of hang we have here: wait4(-1for the init scripts futex(0xsomepointer, FUTEX_WAIT_PRIVATE, 2, NULL for rsyslogd / apache2 binaries called by the init scripts The system was installed as a Debian Lenny by my hoster in autumn 2011, I upgraded it to Squeeze immediately and kept it up to date with Squeeze, which then used to be testing. There were no big changes, though. I guess I never tried to reboot the system before.

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  • Can a 32-bit RHEL4 userland work with a 64-bit kernel?

    - by James
    Is there a way to change an i386 RHEL4 machine to run an amd64 kernel, but ensure that it still builds software into same i386 binaries? On Debian this seems quite straightforward: just install an amd64 kernel (worst case, build one like this guy: http://www.debian-administration.org/users/jonesy/weblog/1) and prefix everything with "linux32". Then everything that considers uname -m will be unchanged, I just need to handle the few cases that consider uname -r. What is the Red Hat equivalent? Is the only way a full 64-bit installation on another disk and then chrooting back to the 32-bit system before anyone builds anything? (Even the best examples of that seem to be Debian-based.) Background: We make a large system that runs on (a variant of) i386 RHEL4. However, some of the larger RHEL build machines now have enough RAM that they might benefit from going 64-bit (for the kernel and maybe some of the bigger build steps). Our build system doesn't support cross-compilation.

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  • Send file by webservice

    - by phenevo
    Hi, I have webservice, wwith method: [WebMethod] public byte[] GetFile(string FName) { System.IO.FileStream fs1 = null; fs1 = System.IO.File.Open(FName, FileMode.Open, FileAccess.Read); byte[] b1 = new byte[fs1.Length]; fs1.Read(b1, 0, (int)fs1.Length); fs1.Close(); return b1; } and it works with small file like 1mb, but when it comes to photoshop's file (about 1,5gb) I get: System.OutOfMemoryException The idea is I have winforms application which get this file and saving it on local disc.

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  • extend web server to serve static files

    - by Turtle
    Hello, I want to extend a web server which is only able to handle RPC handling now. The web server is written in C#. It provides a abstract handler function like following: public string owsHandler(string request, string path, string param, OSHttpRequest httpRequest, OSHttpResponse httpResponse) And I wrote following code to handle image files: Bitmap queryImg = new Bitmap(path); System.IO.MemoryStream stream = new System.IO.MemoryStream(); queryImg.Save(stream, System.Drawing.Imaging.ImageFormat.Bmp); queryImg.Dispose(); byte[] byteImage = stream.ToArray(); stream.Dispose(); return Convert.ToBase64String(byteImage); And I test it in the browser, the image is returned but the image dimension info is missed. Shall I add something more to the code? Or is any general way to server static files? I do not want to serve it in a ASP.net server. Thanks

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  • ASP.NET: Turning on errors

    - by JamesBrownIsDead
    This is what I see when I visit my web site. How do I instead get the Yellow Screen of Death so I know what the error is? I have GoDaddy shared hosting and I think the problem is that I don't have the correct MVC binaries in the /bin folder. My web.config shows this: <add assembly="System.Web.Mvc, Version=2.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/> <add assembly="System.Web.Abstractions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/> <add assembly="System.Web.Routing, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/> But I'm not positive I copied the right .DLL files into /bin. I've got like 8 of each file--which version is which?!

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  • Can't Use Path in ASP MVC Action

    - by user1477388
    I am trying to use Path() but it has a blue line under it and says, "local variable (path) cannot be referred to until it is declared." How can I use Path()? Imports System.Globalization Imports System.IO Public Class MessageController Inherits System.Web.Mvc.Controller <EmployeeAuthorize()> <HttpPost()> Function SendReply(ByVal id As Integer, ByVal message As String, ByVal files As IEnumerable(Of HttpPostedFileBase)) As JsonResult ' upload files For Each i In files If (i.ContentLength > 0) Then Dim fileName = path.GetFileName(i.FileName) Dim path = path.Combine(Server.MapPath("~/App_Data/uploads"), fileName) i.SaveAs(path) End If Next End Function End Class

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  • Function call within XAML code?

    - by Matt H.
    I'd like to set a style on all my TextBox controls that does the following when it receives keyboard focus: 1) Change the background color 2) Call .SelectAll() to highlight all text I have this so far: <Style TargetType="TextBox"> <Style.Triggers> <Trigger Property="IsKeyboardFocusWithin" Value="True"> <Setter Property="Background"> <Setter.Value> <SolidColorBrush Color="#FFFFD1D9"/> </Setter.Value> </Setter> </Trigger> </Style.Triggers> </Style> Is there a way to also call .SelectAll() ? Thanks.

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  • Problem with jQuery's fade in/out in Firefox

    - by GaVrA
    I already asked here with no luck, but feel free to read it: http://groups.google.com/group/jquery-en/browse%5Fthread/thread/fdf7a584b30d4bb9 Hmm check out my site: http://www.crtaci.info/ on top-right position i have search field. When you move your mouse over there small text shows up that says: Napredna pretraga Now, for some reason those letters change color to like yellow for very short period of time in ff 3.5 and to some strange color in safari 4.0.2 for win. In ie8, opera and chrome it works just the way it should, white letters stay white during the animation. Any sugestions? here is function that do this job ;) $('#header_search').hover(function() { $('#naprednaPretraga').stop({clearQueue:true}).show().animate({"opacity" : 1},500); }, function(){ $('#naprednaPretraga').stop({clearQueue:true}).animate({"opacity" : 0},500,function() { $('#naprednaPretraga').hide(); }); });

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  • Automate refactor import/using directives, using ReSharper and Visual Studio 2010

    - by Mendy
    I want to automate the Visual Studio 2010 / Resharper 5 auto inserting import directives to put my internal namespaces into the namespace sphere. Like this: using System; using System.Collections.Generic; using System.Linq; using StructureMap; using MyProject.Core; // <--- Move inside. using MyProject.Core.Common; // <--- Move inside. namespace MyProject.DependencyResolution { using Core; using Core.Common; // <--- My internal namespaces to be here! public class DependencyRegistrar { ........... } }

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  • SecurityException from Activator.CreateInstance(), How to grant permissons to Assembly?

    - by user365164
    I have been loading an assembly via Assembly.LoadFrom(@"path"); and then doing Type t = asm.GetType("Test.Test"); test = Activator.CreateInstance(t, new Object[] { ... }); and it was working fine, but now I moved the dll I am getting the following System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. --- System.Security.SecurityException: Request for the permission of type 'System.Security.Permissons.SecurityPermission, etc .. For the sake of brevity it seems the demand was for an PermissionSet that allowed ControlAppDomain and it's not getting it. My question is how can I create this permissionset and pass it to the instance or assembly? I've been googling for hours to no avail.

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  • Need advice on which PCI SATA Controller Card to Purchase

    - by Matt1776
    I have a major issue with the build of a machine I am trying to get up and running. My goal is to create a file server that will service the needs of my software development, personal media storage and streaming/media server needs, as well as provide a strong platform for backing up all this data in a routine, cron-job oriented German efficiency sort of way. The issue is a simple one - all my drives are SATA drives and my motherboard controller only contains 4 ports. Solving the issue has proven to be an unmitigated nightmare. I would like advice on the purchase of the following: 4 Port internal SATA / 2 Port external eSATA PCI SATA Controller Card that has the following features and/or advantages: It must function. If I plug it in and attach drives, I expect my system to still make it to the Operating System login screen. It must function on CentOS, and I mean it must function WELL and with MINIMAL hassle. If hassle is unavoidable, there shall be CLEAR CUT and EASY TO FOLLOW instructions on how to install drivers and other supporting software. I do not need nor want fakeRAID - I will be setting up any RAID configurations from within the operating system. Now, if I am able to find such a mythical device, I would be eternally grateful to whomever would be able to point me in the right direction, a direction which I assume will be paved with yellow bricks. I am prepared to pay a considerable sum of money (as SATA controller cards go) and so paying anywhere between 60 to 120 dollars will not be an issue whatsoever. Does such a magical device exist? The following link shows an "example" of the type of thing I am looking for, however, I have no way of verifying that once I plug this baby in that my system will still continue to function once I've attached the drives, or that once I've made it to the OS, I will be able to install whatever drivers or software programs I need to make it work with relative ease. It doesn't have to be dog-shit simple, but it cannot involve kernels or brain surgery. http://www.amazon.com/gp/product/B00552PLN4/ref=pd_lpo_k2_dp_sr_1?pf_rd_p=486539851&pf_rd_s=lpo-top-stripe-1&pf_rd_t=201&pf_rd_i=B003GSGMPU&pf_rd_m=ATVPDKIKX0DER&pf_rd_r=1HJG60XTZFJ48Z173HKY So does anyone have a suggestion regarding the subject I am asking about? PCI SATA Controller Cards? It would help if you've had experience with the component before - that is after all why I am asking here - for those who have had experience that I do not have. Bear in mind that this is for a home setup and that I do not have a company credit card. I have a budget with a 'relative' upper limit of about $150.00.

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  • Using Delphi's ShellExecute() with the process inheriting the original console?

    - by Phil
    In C I've used the system() function before in a console application and if I start another process using system() it inherits the console window of the process that called it. In Delphi system() doesn't exist so I'm using ShellExecute() to create a new process, but the new process comes up in a new console window. Is there some way that I can make it inherit the handle of the window that's calling it? I've used function GetConsoleWindow(): HWND; stdcall; external 'kernel32.dll'; to get the console window and passed it in the HWND part of ShellExecute(), but that didn't work.

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  • EBS with RAID0 (striping) and restoring snapshots

    - by grourk
    We have a MySQL database on EC2 and are looking at the disk IO performance there. Currently we have a single EBS volume with XFS and take snapshots for backup. It seems that a lot of people have seen significant performance gains by striping across multiple EBS volumes with software RAID. If this is done, how does one take snapshots and ensure the consistency of the file system? It seems to me that restoring the file system from multiple snapshots could be tricky.

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  • Text Getting weird when jquery animate fade on chrome

    - by Robson Silveira
    JavaScript $(function() { $('#lol').hover(function() { $(this).stop().animate({opacity:0.5}); },function() { $(this).stop().animate({opacity:1}); }); }); CSS #lol { padding:20px; background-color:#FF0000; color:#FFF; font-size:15px; font-family:arial; width:300px; opacity:1; filter:alpha(opacity=100); position:relative; } HTML <div id="lol">text</div> In Firefox and Internet Explorer it works fine but in Chrome, the text get weird on fade -- it look like that text is losing cleartype. How can I fix it? How it looks on fade: Click to see

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  • Changing a limited user account in XP fails

    - by javamonkey79
    I have the following: using System; using System.DirectoryServices.AccountManagement; public class ChangePassword { public static void Main() { PrincipalContext context = new PrincipalContext(ContextType.Machine); UserPrincipal user = UserPrincipal.FindByIdentity(context, "someLimitedAccount"); user.ChangePassword( "xxx", "zzz" ); } } This works just fine with administrator accounts, but seems to crash like so when I try to change limited accounts in XP: Unhandled Exception: System.NullReferenceException: Object reference not set to an instance of an object. at ChangePassword.Main() Is what I am trying to do possible? If so, how? EDIT #1: I added the following: Console.WriteLine( "user: " + user ); Below this line: UserPrincipal user = UserPrincipal.FindByIdentity(context, "someLimitedAccount"); And I get this: user: It doesn't look like user is null when I print it, but then again I'm not really a .Net guy - I seem to remember this being expected behavior.

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  • How to make a shape with left-top round rounded corner and left-bottom rounded corner?

    - by kknight
    I want to make a shape with with left-top rounded corner and left-bottom rounded corner: <?xml version="1.0" encoding="UTF-8"?> <shape xmlns:android="http://schemas.android.com/apk/res/android"> <solid android:color="#555555"/> <stroke android:width="3dp" android:color="#555555" /> <padding android:left="1dp" android:top="1dp" android:right="1dp" android:bottom="1dp" /> <corners android:bottomRightRadius="0dp" android:bottomLeftRadius="2dp" android:topLeftRadius="2dp" android:topRightRadius="0dp"/> </shape> But the shape above didn't give me what I want. It gives me a rectangle without any rounded corners. Can anyone help? Thanks.

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  • Programmatically assigning an existing ssl cert to a website in iis6 via powershell or vbscript

    - by dagda1
    Hi, I have the following powershell script that creates a new website in IIS6: https://github.com/dagda1/iis6/blob/master/create-site.ps1 Does anyone know how I can assign an existing ssl cert to the website? I know I can set the port number using adsutil.vbs like this: cscript adsutil.vbs set w3svc/xxx/securebindings ":443:somewhere.com" But I am drawing a big blank when it comes to assigning an existing ssl certificate. Thanks Paul

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  • http://localhost/ always gives 502 unknown host

    - by Nitesh Panchal
    My service for World Wide Web Publishing Service started successfully but whenever I browse to http://localhost/ I always get 502 Unknown host. Also, wampapache is installed side by side but when I stop IIS service and start wampapache from services.msc I get error and when I view it in System event log I get this error: - <Event xmlns="http://schemas.microsoft.com/win/2004/08/events/event"> - <System> <Provider Name="Service Control Manager" Guid="{555908d1-a6d7-4695-8e1e-26931d2012f4}" EventSourceName="Service Control Manager" /> <EventID Qualifiers="49152">7024</EventID> <Version>0</Version> <Level>2</Level> <Task>0</Task> <Opcode>0</Opcode> <Keywords>0x8080000000000000</Keywords> <TimeCreated SystemTime="2011-06-12T17:43:28.223498400Z" /> <EventRecordID>346799</EventRecordID> <Correlation /> <Execution ProcessID="456" ThreadID="3936" /> <Channel>System</Channel> <Computer>MACHINENAME</Computer> <Security /> </System> - <EventData> <Data Name="param1">wampapache</Data> <Data Name="param2">%%1</Data> </EventData> </Event> I am fed up of this error and it is driving me nuts. I feel like banging my head against the laptop. I am really serious. Without concentrating on my real application I am trying to solve this issue since 3 hours. I google various threads and few of them said that there could be issue of Reporting Services or Skype. But I have uninstalled Skype and Reporting Services are disabled. What more should I do? I have hosts file present in etc directory and it does have mapping for localhost to 127.0.0.1. What more could I do?

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  • SWT Filedialog Open into home folder

    - by Ivan
    I want to open a FileDialog window into the user home folder (i.e. /home/user or /Users/unsername) I read the user home folder, using System.getProperty: String homefolder = System.getProperty(user.home); And the variable containts the correct home folder. But when i set the filterpath in FileDialog, it opens (in linux) only the /home level not entering into the user home dir. This is the source code: FileDialog dialog = new FileDialog(shell); dialog.setText("Choose a certificate"); String platform = SWT.getPlatform(); String homefolder = System.getProperty("user.home"); dialog.setFilterPath(homefolder); Any idea? Here a screenshot:

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  • Agile Approach for WCM

    - by cameron.f.logan
    Can anyone provide me with advice, opinions, or experience with using an agile methodology to delivery an enterprise-scale Web Content Management system (e.g., Interwoven TeamSite, Tridion)? My current opinion is that to implement a CM system there is a certain--relatively high--amount of upfront work that needs to happen to make sure the system is going to be scalable and efficient for future projects for the multi-year lifespan an WCM is expected to have. This suggests a hybrid approach at best, if not a more waterfall-like approach. I'm really interested to learn what approaches others have taken. Thanks.

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  • Using java.util.logging, is it possible to restart logs after a certain period of time?

    - by Fry
    I have some java code that will be running as an importer for data for a much larger project. The initial logging code was done with the java.util.logging classes, so I'd like to keep it if possible, but it seems to be a little inadequate now given he amount of data passing through the importer. Often times in the system, the importer will get data that the main system doesn't have information for or doesn't match the system's data so it is ignored but a message is written to the log about what information was dropped and why it wasn't imported. The problem is that this tends to grow in size very quickly, so we'd like to be able to start a fresh log daily or weekly. Does anybody have an idea if this can be done in the logging classes or would I have to switch to log4j or custom? Thanks for any help!

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  • Sending the files (At least 11 files) from folder through web service to android app.

    - by Shashank_Itmaster
    Hello All, I stuck in middle of this situation,Please help me out. My question is that I want to send files (Total 11 PDF Files) to android app using web service. I tried it with below code.Main Class from which web service is created public class MultipleFilesImpl implements MultipleFiles { public FileData[] sendPDFs() { FileData fileData = null; // List<FileData> filesDetails = new ArrayList<FileData>(); File fileFolder = new File( "C:/eclipse/workspace/AIPWebService/src/pdfs/"); // File fileTwo = new File( // "C:/eclipse/workspace/AIPWebService/src/simple.pdf"); File sendFiles[] = fileFolder.listFiles(); // sendFiles[0] = fileOne; // sendFiles[1] = fileTwo; DataHandler handler = null; char[] readLine = null; byte[] data = null; int offset = 0; int numRead = 0; InputStream stream = null; FileOutputStream outputStream = null; FileData[] filesData = null; try { System.out.println("Web Service Called Successfully"); for (int i = 0; i < sendFiles.length; i++) { handler = new DataHandler(new FileDataSource(sendFiles[i])); fileData = new FileData(); data = new byte[(int) sendFiles[i].length()]; stream = handler.getInputStream(); while (offset < data.length && (numRead = stream.read(data, offset, data.length - offset)) >= 0) { offset += numRead; } readLine = Base64Coder.encode(data); offset = 0; numRead = 0; System.out.println("'Reading File............................"); System.out.println("\n"); System.out.println(readLine); System.out.println("Data Reading Successful"); fileData.setFileName(sendFiles[i].getName()); fileData.setFileData(String.valueOf(readLine)); readLine = null; System.out.println("Data from bean " + fileData.getFileData()); outputStream = new FileOutputStream("D:/" + sendFiles[i].getName()); outputStream.write(Base64Coder.decode(fileData.getFileData())); outputStream.flush(); outputStream.close(); stream.close(); // FileData fileDetails = new FileData(); // fileDetails = fileData; // filesDetails.add(fileData); filesData = new FileData[(int) sendFiles[i].length()]; } // return fileData; } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } return filesData; } } Also The Interface MultipleFiles:- public interface MultipleFiles extends Remote { public FileData[] sendPDFs() throws FileNotFoundException, IOException, Exception; } Here I am sending an array of bean "File Data",having properties viz. FileData & FileName. FileData- contains file data in encoded. FileName- encoded file name. The Bean:- (FileData) public class FileData { private String fileName; private String fileData; public String getFileName() { return fileName; } public void setFileName(String fileName) { this.fileName = fileName; } public String getFileData() { return fileData; } public void setFileData(String string) { this.fileData = string; } } The android DDMS gives out of memory exception when tried below code & when i tried to send two files then only first file is created. public class PDFActivity extends Activity { private final String METHOD_NAME = "sendPDFs"; private final String NAMESPACE = "http://webservice.uks.com/"; private final String SOAP_ACTION = NAMESPACE + METHOD_NAME; private final String URL = "http://192.168.1.123:8080/AIPWebService/services/MultipleFilesImpl"; /** Called when the activity is first created. */ @Override public void onCreate(Bundle savedInstanceState) { super.onCreate(savedInstanceState); setContentView(R.layout.main); TextView textViewOne = (TextView) findViewById(R.id.textViewOne); try { SoapObject soapObject = new SoapObject(NAMESPACE, METHOD_NAME); SoapSerializationEnvelope envelope = new SoapSerializationEnvelope( SoapEnvelope.VER11); envelope.setOutputSoapObject(soapObject); textViewOne.setText("Web Service Started"); AndroidHttpTransport httpTransport = new AndroidHttpTransport(URL); httpTransport.call(SOAP_ACTION, envelope); // SoapObject result = (SoapObject) envelope.getResponse(); Object result = envelope.getResponse(); Log.i("Result", result.toString()); // String fileName = result.getProperty("fileName").toString(); // String fileData = result.getProperty("fileData").toString(); // Log.i("File Name", fileName); // Log.i("File Data", fileData); // File pdfFile = new File(fileName); // FileOutputStream outputStream = // openFileOutput(pdfFile.toString(), // MODE_PRIVATE); // outputStream.write(Base64Coder.decode(fileData)); Log.i("File", "File Created"); // textViewTwo.setText(result); // Object result = envelope.getResponse(); // FileOutputStream outputStream = openFileOutput(name, mode) } catch (Exception e) { e.printStackTrace(); } } } Please help with some explanation or changes in my code. Thanks in Advance.

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  • Parse a text file into multiple text file

    - by Vijay Kumar Singh
    I want to get multiple file by parsing a input file Through Java. The Input file contains many fasta format of thousands of protein sequence and I want to generate raw format(i.e., without any comma semicolon and without any extra symbol like "", "[", "]" etc) of each protein sequence. A fasta sequence starts form "" symbol followed by description of protein and then sequence of protein. For example ? lcl|NC_000001.10_cdsid_XP_003403591.1 [gene=LOC100652771] [protein=hypothetical protein LOC100652771] [protein_id=XP_003403591.1] [location=join(12190..12227,12595..12721,13403..13639)] MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCL PSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH Like above formate the input file contains 1000s of protein sequence. I have to generate thousands of raw file containing only individual protein sequence without any special symbol or gaps. I have developed the code for it in Java but out put is : Cannot open a file followed by cannot find file. Please help me to solve my problem. Regards Vijay Kumar Garg Varanasi Bharat (India) The code is /*Java code to convert FASTA format to a raw format*/ import java.io.*; import java.util.*; import java.util.regex.*; import java.io.FileInputStream; // java package for using regular expression public class Arrayren { public static void main(String args[]) throws IOException { String a[]=new String[1000]; String b[][] =new String[1000][1000]; /*open the id file*/ try { File f = new File ("input.txt"); //opening the text document containing genbank ids FileInputStream fis = new FileInputStream("input.txt"); //Reading the file contents through inputstream BufferedInputStream bis = new BufferedInputStream(fis); // Writing the contents to a buffered stream DataInputStream dis = new DataInputStream(bis); //Method for reading Java Standard data types String inputline; String line; String separator = System.getProperty("line.separator"); // reads a line till next line operator is found int i=0; while ((inputline=dis.readLine()) != null) { i++; a[i]=inputline; a[i]=a[i].replaceAll(separator,""); //replaces unwanted patterns like /n with space a[i]=a[i].trim(); // trims out if any space is available a[i]=a[i]+".txt"; //takes the file name into an array try // to handle run time error /*take the sequence in to an array*/ { BufferedReader in = new BufferedReader (new FileReader(a[i])); String inline = null; int j=0; while((inline=in.readLine()) != null) { j++; b[i][j]=inline; Pattern q=Pattern.compile(">"); //Compiling the regular expression Matcher n=q.matcher(inline); //creates the matcher for the above pattern if(n.find()) { /*appending the comment line*/ b[i][j]=b[i][j].replaceAll(">gi",""); //identify the pattern and replace it with a space b[i][j]=b[i][j].replaceAll("[a-zA-Z]",""); b[i][j]=b[i][j].replaceAll("|",""); b[i][j]=b[i][j].replaceAll("\\d{1,15}",""); b[i][j]=b[i][j].replaceAll(".",""); b[i][j]=b[i][j].replaceAll("_",""); b[i][j]=b[i][j].replaceAll("\\(",""); b[i][j]=b[i][j].replaceAll("\\)",""); } /*printing the sequence in to a text file*/ b[i][j]=b[i][j].replaceAll(separator,""); b[i][j]=b[i][j].trim(); // trims out if any space is available File create = new File(inputline+"R.txt"); try { if(!create.exists()) { create.createNewFile(); // creates a new file } else { System.out.println("file already exists"); } } catch(IOException e) // to catch the exception and print the error if cannot open a file { System.err.println("cannot create a file"); } BufferedWriter outt = new BufferedWriter(new FileWriter(inputline+"R.txt", true)); outt.write(b[i][j]); // printing the contents to a text file outt.close(); // closing the text file System.out.println(b[i][j]); } } catch(Exception e) { System.out.println("cannot open a file"); } } } catch(Exception ex) // catch the exception and prints the error if cannot find file { System.out.println("cannot find file "); } } } If you provide me correct it will be much easier to understand.

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