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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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  • Reading data from text file in C

    - by themake
    I have a text file which contains words separated by space. I want to take each word from the file and store it. So i have opened the file but am unsure how to assign the word to a char. FILE *fp; fp = fopen("file.txt", "r"); //then i want char one = the first word in the file char two = the second word in the file

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  • opening and viewing a file in php

    - by Christian Burgos
    how do i open/view for editing an uploaded file in php? i have tried this but it doesn't open the file. $my_file = 'file.txt'; $handle = fopen($my_file, 'r'); $data = fread($handle,filesize($my_file)); i've also tried this but it wont work. $my_file = 'file.txt'; $handle = fopen($my_file, 'w') or die('Cannot open file: '.$my_file); $data = 'This is the data'; fwrite($handle, $data); what i have in mind is like when you want to view an uploaded resume,documents or any other ms office files like .docx,.xls,.pptx and be able to edit them, save and close the said file. edit: latest tried code... <?php // Connects to your Database include "configdb.php"; //Retrieves data from MySQL $data = mysql_query("SELECT * FROM employees") or die(mysql_error()); //Puts it into an array while($info = mysql_fetch_array( $data )) { //Outputs the image and other data //Echo "<img src=localhost/uploadfile/images".$info['photo'] ."> <br>"; Echo "<b>Name:</b> ".$info['name'] . "<br> "; Echo "<b>Email:</b> ".$info['email'] . " <br>"; Echo "<b>Phone:</b> ".$info['phone'] . " <hr>"; //$file=fopen("uploadfile/images/".$info['photo'],"r+"); $file=fopen("Applications/XAMPP/xamppfiles/htdocs/uploadfile/images/file.odt","r") or exit("unable to open file");; } ?> i am getting the error: Warning: fopen(Applications/XAMPP/xamppfiles/htdocs/uploadfile/images/file.odt): failed to open stream: No such file or directory in /Applications/XAMPP/xamppfiles/htdocs/uploadfile/view.php on line 17 unable to open file the file is in that folder, i don't know it wont find it.

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  • Copied a file with winscp; only winscp can see it

    - by nilbus
    I recently copied a 25.5GB file from another machine using WinSCP. I copied it to C:\beth.tar.gz, and WinSCP can still see the file. However no other app (including Explorer) can see the file. What might cause this, and how can I fix it? The details that might or might not matter WinSCP shows the size of the file (C:\beth.tar.gz) correctly as 27,460,124,080 bytes, which matches the filesize on the remote host Neither explorer, cmd (command line prompt w/ dir C:\), the 7Zip archive program, nor any other File Open dialog can see the beth.tar.gz file under C:\ I have configured Explorer to show hidden files I can move the file to other directories using WinSCP If I try to move the file to Users/, UAC prompts me for administrative rights, which I grant, and I get this error: Could not find this item The item is no longer located in C:\ When I try to transfer the file back to the remote host in a new directory, the transfer starts successfully and transfers data The transfer had about 30 minutes remaining when I left it for the night The morning after the file transfer, I was greeted with a message saying that the connection to the server had been lost. I don't think this is relevant, since I did not tell it to disconnect after the file was done transferring, and it likely disconnected after the file transfer finished. I'm using an old version of WinSCP - v4.1.8 from 2008 I can view the file properties in WinSCP: Type of file: 7zip (.gz) Location: C:\ Attributes: none (Ready-only, Hidden, Archive, or Ready for indexing) Security: SYSTEM, my user, and Administrators group have full permissions - everything other than "special permissions" is checked under Allow for all 3 users/groups (my user, Administrators, SYSTEM) What's going on?!

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  • C++, Ifstream opens local file but not file on HTTP Server

    - by fammi
    Hi, I am using ifstream to open a file and then read from it. My program works fine when i give location of the local file on my system. for eg /root/Desktop/abc.xxx works fine But once the location is on the http server the file fails to open. for eg http://192.168.0.10/abc.xxx fails to open. Is there any alternate for ifstream when using a URL address? thanks. part of the code where having problem: bool readTillEof = (endIndex == -1) ? true : false; // Open the file in binary mode and seek to the end to determine file size ifstream file ( fileName.c_str ( ), ios::in|ios::ate|ios::binary ); if ( file.is_open ( ) ) { long size = (long) file.tellg ( ); long numBytesRead; if ( readTillEof ) { numBytesRead = size - startIndex; } else { numBytesRead = endIndex - startIndex + 1; } // Allocate a new buffer ptr to read in the file data BufferSptr buf (new Buffer ( numBytesRead ) ); mpStreamingClientEngine->SetResponseBuffer ( nextRequest, buf ); // Seek to the start index of the byte range // and read the data file.seekg ( startIndex, ios::beg ); file.read ( (char *)buf->GetData(), numBytesRead ); // Pass on the data to the SCE // and signal completion of request mpStreamingClientEngine->HandleDataReceived( nextRequest, numBytesRead); mpStreamingClientEngine->MarkRequestCompleted( nextRequest ); // Close the file file.close ( ); } else { // Report error to the Streaming Client Engine // as unable to open file AHS_ERROR ( ConnectionManager, " Error while opening file \"%s\"\n", fileName.c_str ( ) ); mpStreamingClientEngine->HandleRequestFailed( nextRequest, CONNECTION_FAILED ); } }

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  • How do I open a file in such a way that if the file doesn't exist it will be created and opened automatically?

    - by snakile
    Here's how I open a file for writing+ : if( fopen_s( &f, fileName, "w+" ) !=0 ) { printf("Open file failed\n"); return; } fprintf_s(f, "content"); If the file doesn't exist the open operation fails. What's the right way to fopen if I want to create the file automatically if the file doesn't already exist? EDIT: If the file does exist, I would like fprintf to overwrite the file, not to append to it.

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  • Problem with File uplolad in javascript.

    - by Nikhil
    I have used javascript to upload more than one file. when user clicks on 'add more' javascript appends new object to older div using innerHTML. Now the problem is if I select a file and then click on "add more" then new file button exist but older selected file removes and two blank file buttons display. I want this old file must be selected when user add new file button. If anybody can, Help Plz!!! tnX.

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  • Measuring Usability with Common Industry Format (CIF) Usability Tests

    - by Applications User Experience
    Sean Rice, Manager, Applications User Experience A User-centered Research and Design Process The Oracle Fusion Applications user experience was five years in the making. The development of this suite included an extensive and comprehensive user experience design process: ethnographic research, low-fidelity workflow prototyping, high fidelity user interface (UI) prototyping, iterative formative usability testing, development feedback and iteration, and sales and customer evaluation throughout the design cycle. However, this process does not stop when our products are released. We conduct summative usability testing using the ISO 25062 Common Industry Format (CIF) for usability test reports as an organizational framework. CIF tests allow us to measure the overall usability of our released products.  These studies provide benchmarks that allow for comparisons of a specific product release against previous versions of our product and against other products in the marketplace. What Is a CIF Usability Test? CIF refers to the internationally standardized method for reporting usability test findings used by the software industry. The CIF is based on a formal, lab-based test that is used to benchmark the usability of a product in terms of human performance and subjective data. The CIF was developed and is endorsed by more than 375 software customer and vendor organizations led by the National Institute for Standards and Technology (NIST), a US government entity. NIST sponsored the CIF through the American National Standards Institute (ANSI) and International Organization for Standardization (ISO) standards-making processes. Oracle played a key role in developing the CIF. The CIF report format and metrics are consistent with the ISO 9241-11 definition of usability: “The extent to which a product can be used by specified users to achieve specified goals with effectiveness, efficiency and satisfaction in a specified context of use.” Our goal in conducting CIF tests is to measure performance and satisfaction of a representative sample of users on a set of core tasks and to help predict how usable a product will be with the larger population of customers. Why Do We Perform CIF Testing? The overarching purpose of the CIF for usability test reports is to promote incorporation of usability as part of the procurement decision-making process for interactive products. CIF provides a common format for vendors to report the methods and results of usability tests to customer organizations, and enables customers to compare the usability of our software to that of other suppliers. CIF also enables us to compare our current software with previous versions of our software. CIF Testing for Fusion Applications Oracle Fusion Applications comprises more than 100 modules in seven different product families. These modules encompass more than 400 task flows and 400 user roles. Due to resource constraints, we cannot perform comprehensive CIF testing across the entire product suite. Therefore, we had to develop meaningful inclusion criteria and work with other stakeholders across the applications development organization to prioritize product areas for testing. Ultimately, we want to test the product areas for which customers might be most interested in seeing CIF data. We also want to build credibility with customers; we need to be able to make the case to current and prospective customers that the product areas tested are representative of the product suite as a whole. Our goal is to test the top use cases for each product. The primary activity in the scoping process was to work with the individual product teams to identify the key products and business process task flows in each product to test. We prioritized these products and flows through a series of negotiations among the user experience managers, product strategy, and product management directors for each of the primary product families within the Oracle Fusion Applications suite (Human Capital Management, Supply Chain Management, Customer Relationship Management, Financials, Projects, and Procurement). The end result of the scoping exercise was a list of 47 proposed CIF tests for the Fusion Applications product suite.  Figure 1. A participant completes tasks during a usability test in Oracle’s Usability Labs Fusion Supplier Portal CIF Test The first Fusion CIF test was completed on the Supplier Portal application in July of 2011.  Fusion Supplier Portal is part of an integrated suite of Procurement applications that helps supplier companies manage orders, schedules, shipments, invoices, negotiations and payments. The user roles targeted for the usability study were Supplier Account Receivables Specialists and Supplier Sales Representatives, including both experienced and inexperienced users across a wide demographic range.  The test specifically focused on the following functionality and features: Manage payments – view payments Manage invoices – view invoice status and create invoices Manage account information – create new contact, review bank account information Manage agreements – find and view agreement, upload agreement lines, confirm status of agreement lines upload Manage purchase orders (PO) – view history of PO, request change to PO, find orders Manage negotiations – respond to request for a quote, check the status of a negotiation response These product areas were selected to represent the most important subset of features and functionality of the flow, in terms of frequency and criticality of use by customers. A total of 20 users participated in the usability study. The results of the Supplier Portal evaluation were favorable and exceeded our expectations. Figure 2. Fusion Supplier Portal Next Studies We plan to conduct two Fusion CIF usability studies per product family over the next nine months. The next product to be tested will be Self-service Procurement. End users are currently being recruited to participate in this usability study, and the test sessions are scheduled to begin during the last week of November.

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  • Is it possible to preview arbitrary formats in Nautilus?

    - by alfC
    I recently found out that Nautilus (Ubuntu 12.04 at least) can show thumbnails of files of non-image formats, for example (data grapher) grace files (.agr) shows a small version of the graph contained in its data. Obviously, there some library or script that is processing the file, making the image, and allowing nautilus to show a small version of it. This made me think that in principle any file that potentially can be processed into an image can serve as a Nautilus thumbnail. For example, a .tex file (which can be converted to .pdf) or a gnuplot script can be displayed as a thumbnail when possible. In the case of .tex file, the correspoding .pdf can be created by the command pdflatex file.tex. The question is, how can I tell Nautilus to create a thumbnail for an arbitrary format and how do I specify the commands to do so within Nautilus?

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  • excel cannot open the file xxx.xlsx' because the file format is not valid error

    - by Yavuz
    I have difficulty open opening word and excel files suddenly. Only particular office file give me the problem. These files were previously scanned by combo fix and I believe they were damaged. The error response that I from office is Excel cannot open the file xxx.xlsx because the file format is not valid. Verify that the file has not been corrupted and that the file extension matches the format of the file. This is for excel and a similar kind of error response comes for word. The file looks fine. I mean the size vise... Please help me with this problem. I really appreciate your help and time....

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  • Upon clicking on a file, excel opens but not the file itself

    - by william
    Platform: Windows XP SP2, Excel 2007 Problem description: Upon clicking on a file in Windows Explorer (file is either .xls or .xlsx) Excel 2007 opens, but does not open the file itself. I need either to click on a file again in Windows Explorer or open it manually with File/Open ... from Excel. Does anyone know what could cause this rather strange behaviour ? The old versions of Excel worked "normally" ... i.e. upon clicking on a file, an Excel would open along with the file. Please, help !

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  • How to write files in specific order?

    - by Bernie
    Okay, here's a weird problem -- My wife just bought a 2014 Nissan Altima. So, I took her iTunes library and converted the .m4a files to .mp3, since the car audio system only supports .mp3 and .wma. So far so good. Then I copied the files to a DOS FAT-32 formatted USB thumb drive, and connected the drive to the car's USB port, only to find all of the tracks were out of sequence. All tracks begin with a two digit numeric prefix, i.e., 01, 02, 03, etc. So you would think they would be in order. So I called Nissan Connect support and the rep told me that there is a known problem with reading files in the correct order. He said the files are read in the same order they are written. So, I manually copied a few albums with the tracks in a predetermined order, and sure enough he was correct. So I copied about 6 albums for testing, then changed to the top level directory and did a "find . music.txt". Then I passed this file to rsync like this: rsync -av --files-from=music.txt . ../Marys\ Music\ Sequenced/ The files looked like they were copied in order, but when I listed the files in order of modified time, they were in the same sequence as the original files: ../Marys Music Sequenced/Air Supply/Air Supply Greatest Hits ls -1rt 01 Lost In Love.mp3 04 Every Woman In The World.mp3 03 Chances.mp3 02 All Out Of Love.mp3 06 Here I Am (Just When I Thought I Was Over You).mp3 05 The One That You Love.mp3 08 I Want To Give It All.mp3 07 Sweet Dreams.mp3 11 Young Love.mp3 So the question is, how can I copy files listed in a file named music.txt, and copy them to a destination, and ensure the modification times are in the same sequence as the files are listed?

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  • rename files with the same name

    - by snorpey
    Hi. I use the following function to rename thumbnails. For example, if I upload a file called "image.png" to an upload folder, and this folder already has a file named "image.png" in it, the new file automatically gets renamed to "image-copy-1.png". If there also is a file called "image-copy-1.png" it gets renamed to "image-copy-2.png" and so on. The following function returns the new filename. At least that's what it is supposed to do... The renaming doesn't seeem to work correctly, though. Sometimes it produces strange results, like: 1.png 1-copy-1.png 1-copy-2.png 1-copy-2-copy-1.png 1-copy-2-copy-3.png I hope you understand my problem, despite my description being somewhat complex... Can you tell me what went wrong here? (bonus question: Is regular expressions the right tool for doing this kind of stuff?) <?php function renameDuplicates($path, $file) { $fileName = pathinfo($path . $file, PATHINFO_FILENAME); $fileExtension = "." . pathinfo($path . $file, PATHINFO_EXTENSION); if(file_exists($path . $file)) { $fileCopy = $fileName . "-copy-1"; if(file_exists($path . $fileCopy . $fileExtension)) { if ($contains = preg_match_all ("/.*?(copy)(-)(\\d+)/is", $fileCopy, $matches)) { $copyIndex = $matches[3][0]; $fileName = substr($fileCopy, 0, -(strlen("-copy-" . $copyIndex))) . "-copy-" . ($copyIndex + 1); } } else { $fileName .= "-copy-1"; } } $returnValue = $fileName . $fileExtension; return $returnValue; }?>

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  • SQL Server: What locale should be used to format numeric values into SQL Server format?

    - by Ian Boyd
    It seems that SQL Server does not accept numbers formatted using any particular locale. It also doesn't support locales that have digits other than 0-9. For example, if the current locale is bengali, then the number 123456789 would come out as "?????????". And that's just the digits, nevermind what the digit grouping would be. But the same problem happens for numbers in the Invariant locale, which formats numbers as "123,456,789", which SQL Server won't accept. Is there a culture that matches what SQL Server accepts for numeric values? Or will i have to create some custom "sql server" culture, generating rules for that culture myself from lower level formatting routines? If i was in .NET (which i'm not), i could peruse the Standard Numeric Format strings. Of the format codes available in .NET: c (Currency): $123.46 d (Decimal): 1234 e (Exponentional): 1.052033E+003 f (Fixed Point): 1234.57 g (General): 123.456 n (Number): 1,234.57 p (Percent): 100.00 % r (Round Trip): 123456789.12345678 x (Hexadecimal): FF Only 6 accept all numeric types: c (Currency): $123.46 d (Decimal): 1234 e (Exponentional): 1.052033E+003 f (Fixed Point): 1234.57 g (General): 123.456 n (Number): 1,234.57 p (Percent): 100.00 % r (Round Trip): 123456789.12345678 x (Hexadecimal): FF And of those only 2 generate string representations, in the en-US locale anyway, that would be accepted by SQL Server: c (Currency): $123.46 d (Decimal): 1234 e (Exponentional): 1.052033E+003 f (Fixed Point): 1234.57 g (General): 123.456 n (Number): 1,234.57 p (Percent): 100.00 % r (Round Trip): 123456789.12345678 x (Hexadecimal): FF Of the remaining two, fixed is dependant on the locale's digits, rather than the number being used, leaving General g format: c (Currency): $123.46 d (Decimal): 1234 e (Exponentional): 1.052033E+003 f (Fixed Point): 1234.57 g (General): 123.456 n (Number): 1,234.57 p (Percent): 100.00 % r (Round Trip): 123456789.12345678 x (Hexadecimal): FF And i can't even say for certain that the g format won't add digit groupings (e.g. 1,234). Is there a locale that formats numbers in the way SQL Server expects? Is there a .NET format code? A java format code? A Delphi format code? A VB format code? A stdio format code? latin-numeral-digits

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  • How determine application subsystem from executable file

    - by Luca
    I'm trying to detect console application from the list of the executables files installed on my computer. How to implement it? Every application has a "subsystem" (windows application, console application or library; specified to the linker as option, I think). How to detect it using only the executable file? Are there alternative methods to detect the application characteristic? Additionally, are there any method for detecting the file is a really executable file? Any issue for JAR executables?

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  • Best Solution for Load Balancing NFS File Access?

    - by DairyKnight
    I'm trying to find an optimum solution for accessing the NFS file share in my company. We have a central file server in North America and has 30GB~50GB of updated data everyday. And it's very slow for our Europe and Asia branches to access directly. Therefore, I'm trying to setup two replicate servers in those continents. I'm currently using rsync, but wonder if there exists a better solution acts more like a distributed RAID, which allows the user to transparently access the file whether synced or not. And user request will be dispatched to remote server if the file is not yet synced. I'm now looking into DRBD, but it seems not to have the functionality of auto-dispatching requests. Does anyone know if there's a better solution?

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  • Corrupt file indicative of corrupt hard drive?

    - by Elipsicon
    I have noticed that two files on my (almost full) 2 TB hard drive have been corrupted. One file has 20 kB (!) corrupted, i.e. consecutive 20 kB have changed, even though the modification date of the file hasn't changed and I haven't worked with this file for over a year. This tells me that something "below" the file system level has messed with the data and the only thing I can think of is hardware failure, most likely hard disk failure. I've tested my RAM already and it works flawlessly. I'm using ext4 on Linux, if that is of any help. Is this normal? Is it time to change my hard drive disk before something worse happens? What can I do to prevent that from happening in the future? Is there some built-in feature of, or extension to ext4 that includes additional error correcting code and/or watches files for changes that haven't been caused by the OS?

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