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  • Oracle @ AIIM Conference

    - by [email protected]
    Oracle will be at the AIIM Conference and Exposition next week in Philadelphia. On the opening morning, Robert Shimp, Group Vice President, Global Technology Business Unit, of Oracle Corporation, will moderate an executive keynote panel. Mr. Shimp will lead four Oracle customer executives through a lively discussion of how innovative organizations are driving the integration of content management with their core business processes on Tuesday April 20th at 8:45 AM. Our panelists are: CINDY BIXLER, CIO, Embry Riddle Aeronautical University TOM SHOWALTER, Managing Director, JP Morgan Chase IRFAN MOTIWALA, Vice President, Moody's Investors Service MIT MONICA CROCKER, CRM, PMP, Corporate Records Manager, Land O'Lakes For more information on our panelists, click here. Oracle will be in booth #2113 at the AIIM Expo. Come by and enter the daily raffle to win a Netbook! Oracle and Oracle partners will demonstrate solutions that increase productivity, reduce costs and ensure compliance for business processes such as accounts payable, human resource onboarding, marketing campaigns, sales management, large scale diagrams for facilities and manufacturing, case management, and others Oracle products including Oracle Universal Content Management, Oracle Imaging and Process Management, Oracle Universal Records Management, Oracle WebCenter, Oracle AutoVue, and Oracle Secure Enterprise Search will be demonstrated in the booth. Oracle will host a private event at The Field House Sports Bar - see your Oracle representative for more details Oracle customers can meet in private meeting rooms with their Oracle representatives Key Sessions Besides the opening morning keynote panel, Oracle will have a number of other sessions at the conference. Oracle Content Management will be featured in the session G08 - A Passage to Improving Healthcare: Enhancing EMR with Electronic Records Wednesday April 21st 2:25PM-3:10PM Kristina Parma of Oracle partner ImageSource will deliver this session, along with Pam Doyle of Fujitsu and Nancy Gladish of Swedish Medical Center. Kristina will also be in the Oracle booth to talk about this solution. On Tuesday April 20th at 4:05 PM Ajay Gandhi of Oracle will deliver a session entitled Harnessing SharePoint Content for Enterprise Processes in PeopleSoft, Siebel, E-Business Suite and JD Edwards Tuesday April 20th 1:15PM-1:45PM - Bringing Content Management to Your AP, HR, Sales and Marketing Processes - Application Showcase Theater (on the AIIM Expo Floor - Booth 1549 Wednesday April 21st 12:30PM-1:00PM - Embed and Edit Content Anywhere - Application Showcase Theater (on the AIIM Expo Floor - Booth 1549 For more information, see the AIIM Expo page on the Oracle website.

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  • ArchBeat Link-o-Rama for 2012-06-15

    - by Bob Rhubart
    URGENT BULLETIN: Disable JRE Auto-Update for All E-Business Suite End-Users All desktop administrators must IMMEDIATELY disable the Java Runtime Environment (JRE) Auto-Update option for all Windows end-user desktops connecting to Oracle E-Business Suite Release 11i, 12.0, and 12.1. WebLogic JMS / AQ bridge with JBoss AS 7 | Edwin Biemond Oracle ACE Edwin Biemond explains "how you can retrieve JMS messages from JBoss with the help of a WebLogic Foreign Server and how to push messages to JBoss AS with the help of a WebLogic JMS Bridge." The Healthy Tension That Mobility Creates | Hernan Capdevila "Mobile device management in the cloud makes good sense," says Hernan Capdevila. "I don't think IT departments should be hosting device management and managing that complexity. It should be a cloud service." OPN: Fusion Middleware Summer Camps in July in Lisbon and Munich For specialized Oracle Partners. Participation is limited to two people per company at each bootcamp. Registration is first come first serve. Take note of the skill requirements and, prerequisites. Podcast: Cows in the Cloud and the importance of standards In part two of a four-part program Cloud experts Jim Baty, Mark Nelson, William Vambenepe, and Ajay Srivastava explain cows in the cloud and talk about the importance of standards. Community members talk about the challenges and opportunities mobile computing presents for IT architects. Apple has sold 55 million iPads since 2010. Gartner expects a 98% increase in tablet sales in 2012, to 118 million. Nielsen reports that smartphones now account for nearly half of all mobile phones in the U.S., a 38% increase over 2011. And the mobile juggernaut is just getting started. Thought for the Day "Why are video games so much better designed than office software? Because people who design video games love to play video games. People who design office software look forward to doing something else on the weekend." — Ted Nelson Source: SoftwareQuotes.com

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  • Podcast Show Notes: Public, Private, and Hybrid Clouds

    - by Bob Rhubart
    This week the OTN ArchBeat Podcast begins a four-part series featuring a panel of some of Oracle's top cloud experts in a conversation about the similarities and differences between, public, private, and hybrid clouds. The Panelists Dr. James Baty Vice President of Oracle’s Global Enterprise Architecture Program, and a frequent speaker at OTN Architect Days and other events. Mark T. Nelson Lead architect for Oracle Cloud and is responsible for designing the infrastructure for Oracle's public Software as a Service, and Platform as a Service offerings. Ajay Srivastava Vice President of Oracle’s On Demand Platform. William Vambenepe Architect for Oracle’s Middleware/Applications Management and Cloud Computing. The Conversation Listen to Part 1: The panel offers an overview of the various flavors of cloud computing. Listen to Part 2 (June 13): Cows in the cloud and the importance of standards. Listen to Part 3 (June 20): Why cloud computing is a paradigm shift -- and why it isn’t. Listen to Part 4 (June 27): Advice on what architects need to know to take advantage of the cloud. Coming Soon Highlights from the Roundtable Discussion at OTN Architect Day in Reston, VA. An expert panel discusses the role of the Cloud Architect. Stay tuned: RSS

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  • Oracle BPM Marketing Update

    - by JuergenKress
    Thanks to Ajay Khanna from the global marketing team for the comprehensive BPM marketing overview: Content and Collateral Whitepaper: What's New in Oracle BPM Suite 11g: Review By Bruce Silver Business Driven Process Management Analyst Report: [Ovum] SWOT Assessment: Oracle BPM Suite 11g Solution Brief: Managing Unpredictability with BPM for Adaptive Case Management Solution brief: BPM in the Public Sector: Increasing Efficiency and Responsiveness Datasheet: Automating Financial Reports Approval with Oracle Process Accelerators Financial Services Loan Origination Business Account Opening Electronic Forms Management Public Sector Incident Reporting Oracle Process Accelerators for Horizontal Solutions Employee Onboarding References: BPM Suite Customers in Action Video: Avea Legal Department runs Better with BPM University of Melbourne Improves Efficiency with Oracle BPM Press: San Joaquin County Leverages Oracle to Deliver Better Services to its 650,000 Residents On-Demand Assets Webcast: New Directions with Business-Driven BPM - New Oracle BPM Suite Extend Your Applications with Oracle Business Process Management Screen Cast: Customer Experience on Your Mind? Think BPM + Social + Mobile Video: Introducing Oracle BPM Suite Assessment Tool : BPM Maturity Self Assessment Blog Series Transforming Public Sector With Process Excellence New Oracle Process Accelerators in Financial Services & Telco Blog: Detect, Analyze, Act Fast with BPM Part I - Manage Processes, the way Octopus does Part II - Perry Mason and the Case of the Unstructured Process Part III - Managing the Unstructured, the Flexible and the Adaptive Resource Kits BPM Resource Kit Financial Services: BPM in Financial Services Public Sector: Transforming Public Sector with Process Excellence SOA & BPM Partner Community For regular information on Oracle SOA Suite become a member in the SOA & BPM Partner Community for registration please visit www.oracle.com/goto/emea/soa (OPN account required) If you need support with your account please contact the Oracle Partner Business Center. Blog Twitter LinkedIn Facebook Wiki Mix Forum Technorati Tags: BPM,bpm marketing,SOA Community,Oracle SOA,Oracle BPM,Community,OPN,Jürgen Kress

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  • TechCast Live: "Java and Oracle, One Year Later" Replay Now Available

    - by Justin Kestelyn
    Earlier this week I had the opportunity to chat with Ajay Patel, Oracle's VP leading the Java Evangelist team, about "the state of the union" wrt Oracle and Java. Take a look: And here are some choice quotes, some paraphrased, as helpfully transcribed by Java evangelist Terrence Barr: "One key thing we have learned ... Java is not just a platform, it is also an ecosystem, and you can't have an ecosystem without a community." "The objectives, strategically [for Java at Oracle] have been pretty clear: How do we drive adoption, how do we build a larger, stronger developer community, how do we really make the platform much more competitive." "It's about transparency, involvement. IBM, RedHat, Apple have all agreed to working with us to make OpenJDK the best platform for open source development ... it is a sign that the community has been waiting to move the Java platform forward." "It's not just about Oracle anymore, it's about Java, the technology, the community, the developer base, and how we work with them to move the innovation forward." "Java is strategic to Oracle, and the community is strategic for Java to be successful ... it is critical to our business." On JavaFX 2.0: "... is coming to beta soon, with a release planned in second half [of 2011] ... will give you a new, high-performance graphics engine, the new API for JavaFX ... you will see a very strong, relevant platform for levering rich media platforms." On the JDK and SE: "... aggressively moving forward, JDK 7 is now code complete ... looking good for getting JDK 7 out by summer as we promised. Started work on JDK 8, Jigsaw and Lambda are moving along nicely, on track for JDK 8 release next year ... good progress." On Java EE and Glassfish: "... Very excited to have Glassfish 3.1 released, with clustering and management capabilities ... working with the JCP to shortly submit a number of JSRs for Java EE 7 ... You'll see Java EE 7 becoming the platform for cloud-based development." "You will see Oracle continue to step up to this role of Java steward, making sure that the language, the technology, the platform ... is competitive, relevant, and widely adopted." Making progress!

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  • SOA Community Newsletter October 2013

    - by JuergenKress
    Dear SOA & BPM Partner Community member, Our October newsletter edition focuses on Oracle OpenWorld 2013, highlights, keynotes and all presentations. Thanks to all partners who made the conference a huge success. If you could not come to San Francisco you will find all the details within this newsletter. As the newsletter edition contains a lot of content thus we have three sections - SOA, BPM & ACM, and AppAdvantage & UX. Make sure you share your content with the community, best via twitter @soacommunity #soacommunity! What is new in SOA Suite 12c? At OOW the product management team demonstrated some of the key features of the upcoming version. The important SOA topics are mobile integration and cloud integration - make sure you re-use your existing SOA platform! Bruce Tierney showcased the Agilent mobile integration and you try the new Mobile Order Management for EBS GSE Demo using middleware technology. On cloud integration the product management team presented several OOW sessions and published two whitepapers. As SOA becomes mature the awareness for SOA Governance continues to raise, Introducing Oracle Enterprise Repository Express Workflows and watch Luis Weir: Challenges to Implementing SOA Governance. Thanks to Ronald for the SOA Made Simple | Introduction to SOA series, the next article in the Industrial SOA series is SOA and User Interfaces (UI). Have you achieved successful BPM implementation? Nominate your customer references for the Gartner Business Process Management Excellence Awards 2014. Do you want to showcase the latest BPM Suite? Make sure you use the hosted BPM PS6 (11.1.1.7) demo. Do you want to become an expert in BPM Suite? Attend one of our BPM Bootcamps in Germany, Netherland, Spain or UK! If you can not make it – we offer plenty of on-demand content Advanced BPM Scenarios & BPM Architecture Topics & Process Modeling and Life Cycle & Adaptive Case Management & Smart Application Extensibility with Oracle Process Accelerators. I would also recommend to watch great introduction to Adaptive Case Management the on-demand webcast with Bruce Silver & Ajay Khanna. Thanks to Mark Foster from the A-team for the ACM article series & Leon Smiers for their blog posts. If you accomplished a SOA Suite or BPM Suite project and want to become a certified SOA or BPM expert, we are offering again free vouchers to become a certified SOA & BPM expert (limited to partners in Europe Middle East and Africa). Don't miss this opportunity and become Specialized! Best regards, Jürgen Kress To read the newsletter please visit http://tinyurl.com/soaNewsOctober2013 (OPN Account required) To become a member of the SOA Partner Community please register at http://www.oracle.com/goto/emea/soa (OPN account required) If you need support with your account please contact the Oracle Partner Business Center. Blog Twitter LinkedIn Facebook Wiki Mix Forum Technorati Tags: newsletter,SOA Community newsletter,SOA Community,Oracle,OPN,Jürgen Kress

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  • ArchBeat Link-o-Rama for 2012-06-29

    - by Bob Rhubart
    Backward-compatible vs. forward-compatible: a tale of two clouds | William Vambenepe "There is the Cloud that provides value by requiring as few changes as possible. And there is the Cloud that provides value by raising the abstraction and operation level," says William Vambenepe. "The backward-compatible Cloud versus the forward-compatible Cloud." Vambenepe was a panelist on the recent ArchBeat podcast Public, Private, and Hybrid Clouds. Andrejus Baranovskis's Blog: ADF 11g PS5 Application with Customized BPM Worklist Task Flow (MDS Seeded Customization) Oracle ACE Director Andrejus Baranovskis investigates "how you can customize a standard BPM Task Flow through MDS Seeded customization." Oracle OpenWorld 2012 Music Festival If, after a day spent in sessions at Oracle Openworld, you want nothing more than to head back to your hotel for a quiet evening spent responding to email, please ignore the rest of this message. Because every night from Sept 30 to Oct 4 the streets of San Francisco will pulsate with music from a vast array of bands representing more musical styles than a single human brain an comprehend. It's the first ever Oracle Music Festival, baby, 7:00pm to 1:00am every night. Are those emails that important...? Resource Kit: Oracle Exadata - includes demos, videos, product datasheets, and technical white papers. This free resource kit includes several customer case study videos, two 3D product demos, several product datasheets, and three technical architecture white papers. Registration is required for the who don't already have a free Oracle.com membership account. Some execs contemplate making 'Bring Your Own Device' mandatory | ZDNet "Companies and agencies are recognizing that individual employees are doing a better job of handling and managing their devices than their harried and overworked IT departments – who need to focus on bigger priorities, such as analytics and cloud," says ZDNet SOA blogger Joe McKendrick. Podcast Show Notes: Public, Private, and Hybrid Clouds All three parts of this discussion are now available. Featuring a panel of leading Oracle cloud computing experts, including Dr. James Baty, Mark T. Nelson, Ajay Srivastava, and William Vambenepe, the discussion covers an overview of the various flavors of cloud computing, the importance of standards, Why cloud computing is a paradigm shift—and why it isn't, and advice on what architects need to know to take advantage of the cloud. And for those who prefer reading to listening, a complete transcript is also available. Amazon AMIs and Oracle VM templates (Cloud Migrations) Cloud migration expert Tom Laszewski shares an objective comparison of these two resources. IOUC : Blogs : Read the latest news on the global user group community - June 2012! The June 2012 edition of "Are You a Member Yet?"—the quarterly newsletter about Oracle user group communities around the world. Webcast: Introducing Identity Management 11g R2 - July 19 Date: Thursday, July 19, 2012 Time: 10am PT / 1pm ET Please join Oracle and customer executives for the launch of Oracle Identity Management 11g R2, the breakthrough technology that dramatically expands the reach of identity management to cloud and mobile environments. Thought for the Day "The most important single aspect of software development is to be clear about what you are trying to build." — Bjarne Stroustrup Source: SoftwareQuotes.com

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  • Java Server Client Program I/O Exception

    - by AjayP
    I made this program: http://java.sun.com/docs/books/tutorial/networking/sockets/clientServer.html And it works perfectly if I put the server's hostname as 127.0.0.1 or my computers name (Ajay-PC). However these 2 methods are LAN or local only not internet. So I changed it to my internet ip. 70.128.xxx.xxx etc. But it didn't work. I checked: canyouseeme.org and it said 4444 was CLOSED. So I did a quick port forward. Portforward: Name: My Java Program Start Port: 4444 End Port: 4444 Server IP: 10.0.0.12 <-- (Yeah this is my Local IP I checked) then I tried canyouseeme.org AGAIN: and it said 4444 was OPEN I ran my server client program and it yet to work. So my problem is the client server program is not working on the internet just locally. So something is blocking it and I don't know what. Computer: Windows Vista x64 Norton AntiVirus 2010 Thanks! I'll give best answer or whatever to who ever answers the best ;) :)

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  • Problem with jQuery selector and MasterPage

    - by Daemon
    Hi, I have a problem with a master page containing a asp:textbox that I'm trying to access using jQuery. I have read lot sof thread regarding this and tried all the different approaches I have seen, but regardless, the end result end up as Undefined. This is the relevant part of the MasterPage code: <p><asp:Label ID="Label1" AssociatedControlID="osxinputfrom" runat="server">Navn</asp:Label><asp:TextBox CssClass="osxinputform" ID="osxinputfrom" runat="server"></asp:TextBox></p> When I click the button, the following code from a jQuery .js file is run: show: function(d) { $('#osx-modal-content .osxsubmitbutton').click(function (e) { e.preventDefault(); if (OSX.validate()){ $('#osx-modal-data').fadeOut(200); d.container.animate( {height:80}, 500, function () { $('#osx-modal-data').html("<h2>Sender...</h2>").fadeIn(250, function () { $.ajax({ type: "POST", url: "Default.aspx/GetDate", data: "{'from':'" + $("#osxinputfrom").val() + "','mailaddress':'" + $("#osxinputmail").val() + "','header':'Test3','message':'Test4'}", contentType: "application/json; charset=utf-8", dataType: "json", success: function(msg) { $('#osx-modal-data').fadeOut(200, function () { $('#osx-modal-data').html('<h2>Meldingen er sendt!</h2>'); $('#osx-modal-data').fadeIn(200); }); }, error: function(msg){ $('#osx-modal-data').fadeOut(200, function () { $('#osx-modal-data').html('<h2>Feil oppstod ved sending av melding!</h2>'); $('#osx-modal-data').fadeIn(200); }); } }); }); } ); } else{ $('#osxinputstatus').fadeOut(250, function () { $('#osxinputstatus').html('<p id="osxinputstatus">' + OSX.message + '</a>'); $('#osxinputstatus').fadeIn(250); }); } }); }, So the problem here is that $("#osxinputfrom").val() evaluated to Undefined. I understand that the masterpage will add some prefix to the ID, so I tried using the ID from the page when it's run that ends up as ct100_osxinputfrom, and I also tried some other hinds that I found while searching like $("#<%=osxinputfrom.ClientID%"), but it ends up as Undefined in the method that is called from the jQuery ajax method anyway. The third and fourth parameters to the ajay function that is hardcoded as Test3 and Test4 comes fine in the C# backend method. So my question is simply: How can I rewrite the jQuery selector to fetch the correct value from the textbox? (before I used master pages it worked fine by the way) Best regards Daemon

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  • Feedback on meeting of the Linux User Group of Mauritius

    Once upon a time in a country far far away... Okay, actually it's not that bad but it has been a while since the last meeting of the Linux User Group of Mauritius (LUGM). There have been plans in the past but it never really happened. Finally, Selven took the opportunity and organised a new meetup with low administrative overhead, proper scheduling on alternative dates and a small attendee's survey on the preferred option. All the pre-work was nicely executed. First, I wasn't sure whether it would be possible to attend. Luckily I got some additional information, like children should come, too, and I was sold to this community gathering. According to other long-term members of the LUGM it was the first time 'ever' that a gathering was organised outside of Quatre Bornes, and I have to admit it was great! LUGM - user group meeting on the 15.06.2013 in L'Escalier Quick overview of Linux & the LUGM With a little bit of delay the LUGM meeting officially started with a quick overview and introduction to Linux presented by Avinash. During the session he told the audience that there had been quite some activity over the island some years ago but unfortunately it had been quiet during recent times. Of course, we also spoke about the acknowledged world dominance of Linux - thanks to Android - and the interesting possibilities for countries like Mauritius. It is known that a couple of public institutions have there back-end infrastructure running on Red Hat Linux systems but the presence on the desktop is still very low. Users are simply hanging on to Windows XP and older versions of Microsoft Office. Following the introduction of the LUGM Ajay joined into the session and it quickly changed into a panel discussion with lots of interesting questions and answers, sharing of first-hand experience either on the job or in private use of Linux, and a couple of ideas about how the LUGM could promote Linux a bit more in Mauritius. It was great to get an insight into other attendee's opinion and activities. Especially taking into consideration that I'm already using Linux since around 1996/97. Frankly speaking, I bought a SuSE 4.x distribution back in those days because I couldn't achieve certain tasks on Windows NT 4.0 without spending a fortune. OpenELEC Mediacenter Next, Selven gave us decent introduction on OpenELEC: Open Embedded Linux Entertainment Center (OpenELEC) is a small Linux distribution built from scratch as a platform to turn your computer into an XBMC media center. OpenELEC is designed to make your system boot fast, and the install is so easy that anyone can turn a blank PC into a media machine in less than 15 minutes. I didn't know about it until this presentation. In the past, I was mainly attached to Video Disk Recorder (VDR) as it allows the use of satellite receiver cards very easily. Hm, somehow I'm still missing my precious HTPC that I had to leave back in Germany years ago. It was great piece of hardware and software; self-built PC in a standard HiFi-sized (43cm) black desktop casing with 2 full-featured Hauppauge DVB-s cards, an old-fashioned Voodoo graphics card, WiFi card, Pioneer slot-in DVD drive, and fully remote controlled via infra-red thanks to Debian, VDR and LIRC. With EP Guide, scheduled recordings and general multimedia centre it offered all the necessary comfort in the living room, besides a Nintendo game console; actually a GameCube at that time... But I have to admit that putting OpenELEC on a Raspberry Pi would be a cool DIY project in the near future. LUGM - our next generation of linux users (15.06.2013) Project Evil Genius (PEG) Don't be scared of the paragraph header. Ish gave us a cool explanation why he named it PEG - Project Evil Genius; it's because of the time of the day when he was scripting down his ideas to be able to build, package and provide software applications to various Linux distributions. The main influence came from openSuSE but the platform didn't cater for his needs and ideas, so he started to work out something on his own. During his passionate session he also talked about the amazing experience he had due to other Linux users from all over the world. During the next couple of days Ish promised to put his script to GitHub... Looking forward to that. Check out Ish's personal blog over at hacklog.in. Highly recommended to read. Why India? Simply because the registration fees per year for an Indian domain are approximately 20 times less than for a Mauritian domain (.mu). Exploring the beach of L'Escalier af the meeting 'After-party' at the beach of L'Escalier Puh, after such interesting sessions, ideas around Linux and good conversation during the breaks and over lunch it was time for a little break-out. Selven suggested that we all should head down to the beach of L'Escalier and get some impressions of nature down here in the south of the island. Talking about 'beach' ;-) - absolutely not comparable to the white-sanded ones here in Flic en Flac... There are no lagoons down at the south coast of Mauriitus, and watching the breaking waves is a different experience and joy after all. Unfortunately, I was a little bit worried about the thoughtless littering at such a remote location. You have to drive on natural paths through the sugar cane fields and I was really shocked by the amount of rubbish lying around almost everywhere. Sad, really sad and it concurs with Yasir's recent article on the same topic. Resumé & outlook It was a great event. I met with new people, had some good conversations, and even my children enjoyed themselves the whole day. The location was well-chosen, enough space for each and everyone, parking spaces and even a playground for the children. Also, a big "Thank You" to Selven and his helpers for the organisation and preparation of lunch. I'm kind of sure that this was an exceptional meeting of LUGM and I'm really looking forward to the next gathering of Linux geeks. Hopefully, soon. All images are courtesy of Avinash Meetoo. More pictures are available on Flickr.

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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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