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• Needs free/ opensource network monitoring tool for office LAN

  - by Amit Ranjan

  I know there must be a lot similar questions on SU. Let me explain my setup first. I have 4-5 PC, Laptops and Few Android Phones in my office. To get them on a network , I have a UTStarCom, WA3002G1 ADSL2+ router with a landline broadband connection which has nothing to do with any PC except the configuration settings. Broadband channel is always on, we need to switch on the router and the internet is ready for us. No Internet Connection sharing is done via any PC. I have a limited 20GB monthly plan, which is consumed in 10-20 days, depending upon the download requirements. So in the above case, i need some suggestions from you: How do I monitor my Internet Bandwidth along-with the connected systems, realtime? Any free opensource tool available? Tweaks / Changes in PC to save bandwidth as my ISP do not have any Unlimited plan. PC and Laptops are Windows XP and/Or windows 7. Either of the platform tools are welcome.

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• No headphone or speakers plugged in - Windows 7 issue

  - by Amit Ranjan

  I am facing a wierd issue between my sound card driver and Windows7(any edition). I have a sony vaio notebook (VPCEB24EN). Two days ago, on start I got diabled wifi, charging and speakers. Then I restart the PC and everthing worked fine. Later on I again restarted my machine, and then I found the my speakers were not working. I thought, restart will work. I restarted many more times but it did'nt work. I searched google and found that , it might be due to : 1. Hardware is not switched on from bios. 2. No hardware. 3. overriding 64-bit drivers with 32-bit drivers. To make it working, I restored my laptop from scratched, but while restoring pc, the realtek HD drivers, it gave me an error 505. I then formatted the drive and installed Win7 Ultimate 32bit (With PC was, Win7 64-bit Home Basic). I got lots of yellow exclamation in device manager, thinking now this will resolve my issue. But Even after the installing all drivers on a fresh installation, I was still with the same position. A red cross on speaker- No Speakers or Headphone plugged in. Please Note: My Laptop is Vaio , E Series, VPCEB24EN. Audio : Intel® High Definition Audio compatible but accepts Realted Audio. While using BIOS Agent, I got Intel Chipset 5 Series Audio Adapter and ATI RV370 Audio adapter found on my board. Installed is Win7 32bit Ultimate. factory default was Win7 64-bit Home Basic Memory: RAM 3GB/ 320GB HDD Display : ATI Mobility Radeon™ HD 5145 Graphics

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• macbook video chat not working

  - by amit

  I am on a macbook. on ichat, i am unable to initialise video chat. I can see the other person's camera, but the other person is uanble to see mine. What could be the problem? Also, in iChat, if i right click on the other person's name, the option to "Invite to Video Chat" is greyed out. I am using Snow Leopard.

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• How to configure to URLs for One Server using wildcard supported certificates?

  - by Amit

  Hi, We have wildcard supported certificate installed in our production environment. One of our client wants his name to appear in the URL (e.g. companyname.sitename.net). How we should facilitate this? Do we need to make any entries for this in DNS? If yes can you please let me know about it? I need to set this up before Fridat PST, any help in this is highly appriciated. Thanks.

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• Suspicious process running under user named

  - by Amit

  I get a lot of emails reporting this and I want this issue to auto correct itself. These process are run by my server and are a result of updates, session deletion and other legitimate session handling reported as false positives. Here's a sample report: Time: Sat Oct 20 00:00:03 2012 -0400 PID: 20077 Account: named Uptime: 326117 seconds Executable: /usr/sbin/nsd\00507d27e9\0053\00\00\00\00\00 (deleted) The file system shows this process is running an executable file that has been deleted. This typically happens when the original file has been replaced by a new file when the application is updated. To prevent this being reported again, restart the process that runs this excecutable file. See csf.conf and the PT_DELETED text for more information about the security implications of processes running deleted executable files. Command Line (often faked in exploits): /usr/sbin/nsd -c /etc/nsd/nsd.conf Network connections by the process (if any): udp: xx.xx.xxx.xx:53 -> 0.0.0.0:0 udp: 127.0.0.1:53 -> 0.0.0.0:0 udp: xx.xx.xxx.xx:53 -> 0.0.0.0:0 tcp: xx.xx.xxx.xx:53 -> 0.0.0.0:0 tcp: 127.0.0.1:53 -> 0.0.0.0:0 tcp: xx.xx.xxx.xx:53 -> 0.0.0.0:0 Files open by the process (if any): /dev/null /dev/null /dev/null Memory maps by the process (if any): 0045e000-00479000 r-xp 00000000 fd:00 2582025 /lib/ld-2.5.so 00479000-0047a000 r--p 0001a000 fd:00 2582025 /lib/ld-2.5.so 0047a000-0047b000 rw-p 0001b000 fd:00 2582025 /lib/ld-2.5.so 0047d000-005d5000 r-xp 00000000 fd:00 2582073 /lib/i686/nosegneg/libc-2.5.so 005d5000-005d7000 r--p 00157000 fd:00 2582073 /lib/i686/nosegneg/libc-2.5.so 005d7000-005d8000 rw-p 00159000 fd:00 2582073 /lib/i686/nosegneg/libc-2.5.so 005d8000-005db000 rw-p 005d8000 00:00 0 005dd000-005e0000 r-xp 00000000 fd:00 2582087 /lib/libdl-2.5.so 005e0000-005e1000 r--p 00002000 fd:00 2582087 /lib/libdl-2.5.so 005e1000-005e2000 rw-p 00003000 fd:00 2582087 /lib/libdl-2.5.so 0062b000-0063d000 r-xp 00000000 fd:00 2582079 /lib/libz.so.1.2.3 0063d000-0063e000 rw-p 00011000 fd:00 2582079 /lib/libz.so.1.2.3 00855000-0085f000 r-xp 00000000 fd:00 2582022 /lib/libnss_files-2.5.so 0085f000-00860000 r--p 00009000 fd:00 2582022 /lib/libnss_files-2.5.so 00860000-00861000 rw-p 0000a000 fd:00 2582022 /lib/libnss_files-2.5.so 00ac0000-00bea000 r-xp 00000000 fd:00 2582166 /lib/libcrypto.so.0.9.8e 00bea000-00bfe000 rw-p 00129000 fd:00 2582166 /lib/libcrypto.so.0.9.8e 00bfe000-00c01000 rw-p 00bfe000 00:00 0 00e68000-00e69000 r-xp 00e68000 00:00 0 [vdso] 08048000-08074000 r-xp 00000000 fd:00 927261 /usr/sbin/nsd 08074000-08079000 rw-p 0002b000 fd:00 927261 /usr/sbin/nsd 08079000-0808c000 rw-p 08079000 00:00 0 08a20000-08a67000 rw-p 08a20000 00:00 0 b7f8d000-b7ff2000 rw-p b7f8d000 00:00 0 b7ffd000-b7ffe000 rw-p b7ffd000 00:00 0 bfa6d000-bfa91000 rw-p bffda000 00:00 0 [stack] Would /etc/nsd/restart or kill -1 20077 solve the problem?

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• RRAS Svr on win 2003 provides same gateway as the ip to vpn clients and subnet as 255.255.255.255

  - by Amit Phatarphekar

  Hello - I've setup a RRAS Svr on win 2003 svr, to provide VPN access to clients. I've followed all directions in microsoft documentation to finish the setup. A VPN client successfully connects when I connect to the VPN svr. But when I look at the ipconfig info, I see that the IP and Gateway are same and subnet is 255.255.255.255. Example IP - 10.0.0.121 Gateway - 10.0.0.121 subnet - 255.255.255.255 DNS - 10.0.0.12 What am I doing wrong?

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• ATI Radeon Drivers works with which linux distribution and version?

  - by amit.codename13

  I have ATI Mobility Radeon HD 5850 graphics card. Almost every new linux distribution seems to have an issue with it, when i install the drivers. Working without utilizing the graphics card leaves me so unproductive. So i made a plan to use older versions of linux, any distribution suitable as a desktop distribution. UPDATE: The kind of problems that i am facing are, 1) After installing drivers the system boots and hangs, 2) There are unusual lines over the screen 3) After upgrade system doesn't start properly(hangs the usual old way) The kind of answers i am looking for is, distribution X(the newer the version the better) doesn't have the above problem after installing drivers for ATI Mobility Radeon HD 5850 graphics card. UPDATE: The new drivers released by AMD seems to fix all the issues, although they are still beta Thanks

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• Internet Explorer - selected language is changing to English when opening a new window

  - by Amit

  When opening a new window in IE8 or IE9 (doesn't matter if using a link or window.open), my selected keyboard language is changing to English (doesn't matter what was the previous selection, tried it with a few different languages). This doesn't happen for me in Chrome or Firefox (all the browsers are installed in their English version), and I tested it in Windows 7 and Windows 2008R2. Is there any way to avoid that? If there isn't - supposing the new window is within my website or application, is there a way to change it back?

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• Vipul Lavanya Sector 81 Gurgaon 09899299961 Resale Urban Expressions Property

  - by amit

  2, 3, 4 BHK Resale Urban Expressions Property Research 09899299961 Vipul Lavanya Gurgaon. {RESIDENTIAL} Vipul 2/3/4 BHK Residential Apartments for Sale in * Vipul LAVANYA * Sector-81 Near Upcoming Metro Station & 500 Mtrs away from Northern Periphery Expressway (Dwarka Expressway)& Gurgaon - Jaipur Expressway (N.H.8) Near IMT Manesar one of the Biggest Industrial HUB in NCR Zone Please Contact for More Details & Informations: Vipul Lavanya Gurgaon Located In Sector 81 on NH 8 Gurgaon

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• How to configure a new subdomain for a wildcard certificate?

  - by Amit

  Hi, We have wildcard certificate installed in our production environment. One of our client wants his name to appear in the URL (e.g. companyname.example.com). How we should facilitate this? Do we need to make any entries for this in DNS? If yes can you please let me know about it? I need to set this up before Fridat PST, any help in this is highly appriciated. Thanks.

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• how to type/send hex on a putty session

  - by Amit Phatarphekar

  I'm using Putty to make a serial connection to a device. I need to send a Hex string on this session. How do I do this? The Hex String is FF7E414244 This is required to break the serial device into command interface mode... From an XP machine, I can use HyperTerminal. And then on the serial connection, do a "send file", where the file has this hexstring entered using hex editing means. So this mechanism works. But now I have a windows 7 with no hyperterminal. so I'm using putty. But now how do I send the hex string? Thanks

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• tell me how to corrupt my hard disk ???? please..

  - by amit

  Hi superuser, Please tell me how to corrupt my hard disk. I have dell inspiron 6400 & it's under complete cover insurance. Operating system is Window Vista Premium. So please tell me the method which actually work & damage/corrupt my hd.

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• Logging upload attempt with proftpd

  - by Amit Sonnenschein

  I have a logging server that i use with external hardware, the idea is that a special hardware is uploading logs about it's operation every few hours and from the server i can do whatever i need to do with the information, the old server was getting a bit too old and i've moved to a new one, i've install lamp,proftpd and ssh (just the same as i had on the old server). now for some reason the logs are not being uploaded and i don't know why. the hardware uses a direct ftp access - i've the proftpd.log and saw that the connection is not being rejected (just to make sure i didn't make a mistake with the user/pass) my problem is that for some reason the upload itself is failing... it might be due to wrong path (as it's hard coded in the hardware) but i can't really know as proftpd wont give me any details.. i've tried to change the loglevel to "debug" thinking it would give me more information but i don't see any change... is there any other way i can make sure proftpd logs EVERTHING ?

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• Secure against c99 and similar shells

  - by Amit Sonnenschein

  I'm trying to secure my server as much as i can without limiting my options, so as a first step i've prevented dangerous functions with php disable_functions = "apache_child_terminate, apache_setenv, define_syslog_variables, escapeshellarg, escapeshellcmd, eval, exec, fp, fput, ftp_connect, ftp_exec, ftp_get, ftp_login, ftp_nb_fput, ftp_put, ftp_raw, ftp_rawlist, highlight_file, ini_alter, ini_get_all, ini_restore, inject_code, mysql_pconnect, openlog, passthru, php_uname, phpAds_remoteInfo, phpAds_XmlRpc, phpAds_xmlrpcDecode, phpAds_xmlrpcEncode, popen, posix_getpwuid, posix_kill, posix_mkfifo, posix_setpgid, posix_setsid, posix_setuid, posix_setuid, posix_uname, proc_close, proc_get_status, proc_nice, proc_open, proc_terminate, shell_exec, syslog, system, xmlrpc_entity_decode" but i'm still fighting directory travel, i can't seems to be able to limit it, by using a shell script like c99 i can travel from my /home/dir to anywhere on the disc. how can i limit it once and for all ?

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• How to corrupt my hard disk ?

  - by amit

  Hi superuser, Please tell me how to corrupt my hard disk. I have Dell Inspiron 6400 & it's under complete cover insurance. Operating system is WindowS Vista Premium. So please tell me the method which actually work & damage/corrupt my hd.

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• people_dl_import shows millions of records

  - by amit lohogaonkar

  We have a situation now on prod in sharepoint 2007 based intranet platform and it shows thousands of records under people_dl_import category with format spsimport://?$$dl$$/domain1/domain2/domain3/ Also import was not stopping and added millions of records in database and was on verge of disk full. On other servers like dev we have very less data in this category and format is also like spsimport://doaminname?$$dl$$?... which is good and has only 6000 rows and in prod its 2 millions Crawled under people_dl_import category. I need to know the cause of this garbage data and how to fix it. I tried resetting content source and I will do full import in this weekend to see if this garbage data gets cleared. Any idea on cause for thiss issue?

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• No sigal showing on LCD TV when Conects Leptop via VGA Cable [migrated]

  - by Amit Prajapati

  I am trying to connect my laptop to Samsung LCD TV by VGA TO HDMI cable My Laptop find Samsung tv on display setting. But When I press fn+F7 key my TV display No Signal My laptop specifications are: "Lenovo R61 ThinkPad, Model: 8935AE7 Window7 Ultimate 32 bits 2GB RAM VGA Port available No HDMI Port My TV specification are: Samsung LCD 26 HDMI Port available VGA Port Available I want to know what is problem? When I connect Another Dell Laptop (Window7 32 bit) with HDMI to HDMI cable it work properly. Thanks in Advance!

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• C Drive Hard Disk Problem

  - by Amit

  I have Windows XP OS. C: Drive has 7 Gb disk space out of that I can see only 4 GB are occopied. Currently only 265 MB are free space showing. I am not sure how to retrive remaining 3 GB space. Can any one have any idea.

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• ATI Radeon Drivers works with which linux distribution and version? [closed]

  - by amit.codename13

  I have ATI Mobility Radeon HD 5850 graphics card. Almost every new linux distribution seems to have an issue with it, when i install the drivers. Working without utilizing the graphics card leaves me so unproductive. So i made a plan to use older versions of linux, any distribution suitable as a desktop distribution. The problems that i am facing are, 1) After installing drivers the system boots and hangs, 2) There are unusual lines over the screen 3) After upgrade system doesn't start properly(hangs the usual old way) The kind of answers i am looking for is, distribution X(the newer the version the better) doesn't have the above problem after installing drivers for ATI Mobility Radeon HD 5850 graphics card. UPDATE: The new drivers released by AMD seems to fix all the issues, although they are still beta

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• No sigal showing on LCD TV when Conects Leptop via VGA Cable

  - by Amit Prajapati

  I am trying to connect my laptop to Samsung LCD TV by VGA TO HDMI cable My Laptop find Samsung tv on display setting. But When I press fn+F7 key my TV display No Signal My laptop specifications are: "Lenovo R61 ThinkPad, Model: 8935AE7 Window7 Ultimate 32 bits 2GB RAM VGA Port available No HDMI Port My TV specification are: Samsung LCD 26 HDMI Port available VGA Port Available I want to know what is problem? When I connect Another Dell Laptop (Window7 32 bit) with HDMI to HDMI cable it work properly. Thanks in Advance!

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• How Spanning Tree Protocol detects Loops

  - by AMIT

  For last few days I've been reading about Spanning Tree Protocol ,L2 protocol and understood how it prevents loop in network ,various steps in STP but one thing i wanted to know how STP actually detects the loops in network so that it can prevent it.Somewhere I read STP uses BPDU as probe and detects loops I mean how it happen is when switch send a BPDU with Destination Address as multicast and receive same BPDU again mean there is loop in network . But is it how STP detects loops in network?

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• Mix content warning on ASPX page

  - by Amit

  Hi, We have started receiving the mixed content warning on ASPX pages on our secured site. We do not have any mix content, we load all our JS, Images, CSS and ASPX files using HTTPS. I dont know why we have started receiving these warnings now. The latest thing which we have added is the third party control for Dialog boxes from Essential Object. We are previously using their Menu control but added dialog box recently. Also we have made our application browser compatible. I feel the reason is something between these two points. Can anyone suggest any solution or any workaround if they know any or have used Essential Object controls and faced simililar issue? Essential object is saying it is not their problem. The mix content warning appears any time and not specifically when the Essential Control dialog box popsup, thats why I am bit confused. Any help is highly appriciated. Thanks.

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• Object of type 'customObject' cannot be converted to type 'customObject'.

  - by Phani Kumar PV

  i am receiving the follwing error when i am invoking a custom object "Object of type 'customObject' cannot be converted to type 'customObject'." Following is the scenario when i am getting the error i am invoking a method in a dll dynamically. Load an assembly CreateInstance.... calling MethodInfo.Invoke() passing int, string as a parameter for my method is working fine = No exceptions are thrown. But if I try and pass a one of my own custom class objects as a parameter, then I get an ArgumentException exception, and it is not either an ArgumentOutOfRangeException or ArgumentNullException. "Object of type 'customObject' cannot be converted to type 'customObject'." I am doing this in a web application. The class file containing the method is in a different proj . also the custom object is a sepearte class in the same file. there is no such thing called a static aseembly in my code. I am trying to invoke a webmethod dynamically. this webmethod is having the customObject type as an input parameter. So when i invoke the webmethod i am dynamically creating the proxy assembly and all. From the same assembly i am trying to create an instance of the cusotm object assinging the values to its properties and then passing this object as a parameter and invoking the method. everything is dynamic and nothing is created static.. :( add reference is not used. Following is a sample code i tried to create it public static object CallWebService(string webServiceAsmxUrl, string serviceName, string methodName, object[] args) { System.Net.WebClient client = new System.Net.WebClient(); //-Connect To the web service using (System.IO.Stream stream = client.OpenRead(webServiceAsmxUrl + "?wsdl")) { //--Now read the WSDL file describing a service. ServiceDescription description = ServiceDescription.Read(stream); ///// LOAD THE DOM ///////// //--Initialize a service description importer. ServiceDescriptionImporter importer = new ServiceDescriptionImporter(); importer.ProtocolName = "Soap12"; // Use SOAP 1.2. importer.AddServiceDescription(description, null, null); //--Generate a proxy client. importer.Style = ServiceDescriptionImportStyle.Client; //--Generate properties to represent primitive values. importer.CodeGenerationOptions = System.Xml.Serialization.CodeGenerationOptions.GenerateProperties; //--Initialize a Code-DOM tree into which we will import the service. CodeNamespace nmspace = new CodeNamespace(); CodeCompileUnit unit1 = new CodeCompileUnit(); unit1.Namespaces.Add(nmspace); //--Import the service into the Code-DOM tree. This creates proxy code //--that uses the service. ServiceDescriptionImportWarnings warning = importer.Import(nmspace, unit1); if (warning == 0) //--If zero then we are good to go { //--Generate the proxy code CodeDomProvider provider1 = CodeDomProvider.CreateProvider("CSharp"); //--Compile the assembly proxy with the appropriate references string[] assemblyReferences = new string[5] { "System.dll", "System.Web.Services.dll", "System.Web.dll", "System.Xml.dll", "System.Data.dll" }; CompilerParameters parms = new CompilerParameters(assemblyReferences); CompilerResults results = provider1.CompileAssemblyFromDom(parms, unit1); //-Check For Errors if (results.Errors.Count > 0) { StringBuilder sb = new StringBuilder(); foreach (CompilerError oops in results.Errors) { sb.AppendLine("========Compiler error============"); sb.AppendLine(oops.ErrorText); } throw new System.ApplicationException("Compile Error Occured calling webservice. " + sb.ToString()); } //--Finally, Invoke the web service method Type foundType = null; Type[] types = results.CompiledAssembly.GetTypes(); foreach (Type type in types) { if (type.BaseType == typeof(System.Web.Services.Protocols.SoapHttpClientProtocol)) { Console.WriteLine(type.ToString()); foundType = type; } } object wsvcClass = results.CompiledAssembly.CreateInstance(foundType.ToString()); MethodInfo mi = wsvcClass.GetType().GetMethod(methodName); return mi.Invoke(wsvcClass, args); } else { return null; } } } I cant find anything static being done by me. any help is greatly appreciated. Regards, Phani Kumar PV

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• How to set BackGround color to a divider in JSplitPane

  - by Sunil Kumar Sahoo

  I have created a divider in JSplitPane. I am unable to set the color of divider. I want to set the color of divider. please help me how to set color of that divider import javax.swing.; import java.awt.; import java.awt.event.*; public class SplitPaneDemo { JFrame frame; JPanel left, right; JSplitPane pane; int lastDividerLocation = -1; public static void main(String[] args) { SplitPaneDemo demo = new SplitPaneDemo(); demo.makeFrame(); demo.frame.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { System.exit(0); } }); demo.frame.show(); } public JFrame makeFrame() { frame = new JFrame(); // Create a horizontal split pane. pane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT); left = new JPanel(); left.setBackground(Color.red); pane.setLeftComponent(left); right = new JPanel(); right.setBackground(Color.green); pane.setRightComponent(right); JButton showleft = new JButton("Left"); showleft.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { Container c = frame.getContentPane(); if (pane.isShowing()) { lastDividerLocation = pane.getDividerLocation(); } c.remove(pane); c.remove(left); c.remove(right); c.add(left, BorderLayout.CENTER); c.validate(); c.repaint(); } }); JButton showright = new JButton("Right"); showright.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { Container c = frame.getContentPane(); if (pane.isShowing()) { lastDividerLocation = pane.getDividerLocation(); } c.remove(pane); c.remove(left); c.remove(right); c.add(right, BorderLayout.CENTER); c.validate(); c.repaint(); } }); JButton showboth = new JButton("Both"); showboth.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { Container c = frame.getContentPane(); c.remove(pane); c.remove(left); c.remove(right); pane.setLeftComponent(left); pane.setRightComponent(right); c.add(pane, BorderLayout.CENTER); if (lastDividerLocation >= 0) { pane.setDividerLocation(lastDividerLocation); } c.validate(); c.repaint(); } }); JPanel buttons = new JPanel(); buttons.setLayout(new GridBagLayout()); buttons.add(showleft); buttons.add(showright); buttons.add(showboth); frame.getContentPane().add(buttons, BorderLayout.NORTH); pane.setPreferredSize(new Dimension(400, 300)); frame.getContentPane().add(pane, BorderLayout.CENTER); frame.pack(); pane.setDividerLocation(0.5); return frame; } } Thanks Sunil kumar Sahoo

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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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