Example Any words: php_solr

Example All words: Simple PHP Agenda




saxerator

A SAX-based XML parser for parsing large files into manageable chunks,

xqgrammar

XQGrammarANTLR grammar for XQuery with Update, Scripting and Full TextThis is a project to build and maintain ANTLR 3 grammar and generated Java parser for XQuery with Update, Scripting and Full Text extensions. It implements the following W3C recommendations : XQuery 1.0 Recommendation / 23 January 2007 XQuery Update Facility 1.0 Candidate Recommendation / 09 June 2009 XQuery Scripting Extension 1.0 Working Draft / 3 December 2008 with added fix for bug #6852 from W3C public Bugzilla XQuery Full Text 1.0Candidate Recommendation / 28 January 2010 XQuery 1.1Working Draft / 15 December 2009 with added fix for bug #8694 from W3C public Bugzilla. Generated parser passes 100% of published W3C test suites.

grammar antlr parser full text scripting xquery generator update

node-htmlparser

Forgiving HTML/XML/RSS Parser in JS for *both* Node and Browsers,

fabpot's yaml

A PHP YAML parser and dumper library,

mac-optimization

WARNING: THIS IS INTENDED ONLY FOR EDUCATIONAL, SCIENTIFIC AND SOFTWARE RESEARCH PURPOSES. MAKE SURE YOU BACKUP YOUR FILES BEFORE RUNNING THE SCRIPT. WHEN DONE IN THE WHOLE OSX SYSTEM, IT'S LIKELY TO PRODUCE SOFTWARE INCOMPATIBILITIES. SUMMARY: In theory, small is good, everything small performs better. An atomic reaction provides more power than a chemical reaction, a nano material will produce an indestructible fabric. So do in software, small applications runs faster, with less consumed memory, and more instances possible. This method of optimization reduces the file size of metadata files through pre-formatting and trimming. INTRODUCTION: XML Optimization is a set of method that reformat the XML metadata for use with XML stream. The process is used in websites to minimize network bandwidth consumption and increase the memory space for the applications who store them locally. XML metadata is used throughout modern OS & Desktops today. (Mac OS X, GNOME/KDE). By Optimizing the XML metadata that those applications use, the application who parse them will require less memory usage, and less time parsing the document, thus improving speed and responsiveness of the applications that use those documents. By XML Optimization, the metadata will be preformatted, by removing the whitespace between the tags, and compacting the whole XML content into a single line, without making any changes in the data inside the tags. The process will make the file much smaller, giving increased memory space, and increased ease for the xml parser to read it. INSTRUCTIONS: Download xml-optimizer.sh script Edit and change the "$start_path" where it would search the XML files. Run the file by typing "sh ./xml-optimizer.sh"

macbook speedup bleeding-edge imac optimization speed mac responsiveness xml tiger apple osx leopard improve optimize

xmlcpg

XML C Parser Generator (xmlcpg) is a xml processor coupled with a flex/bison C parser generator. A DTD can be processed to build a specialized parser for the grammar.

appleworks-parser

Parser for Appleworks and Clarisworks file formats.,

ChangesetMD

Simple XML parser to shove OpenStreetMap changeset metadata dump files into a postgres database

IronMeta

IronMeta is an implementation of Alessandro Warth's OMeta metaprogramming system in C#. It provides a packrat parser generator that generates parsers for Parsing Expression Grammars that operate on arbitrary streams of objects.

peg parser_generator c# parsing_expression_grammar

ical-parser

I created this project because I couldn't find anywhere that helps with importing of ical calendars to google calendar. This is not a complete parser (not to icalendar http://www.ietf.org/rfc/rfc2445.txt standard). I add features as I need them.

icsfiles converter ical python gdata

zcode_parser

A free parser for the XML-based language called zCode,

xmlknuparser

XML Parser, parse your XML data into objects or arrays for manipulate data easily.

as20 actionscript flash

xmlknuparser

XML Parser, parse your XML data into objects or arrays for manipulate data easily.

as20 actionscript flash

fragmentation-analyzer

Fragmentation AnalyzerNews What is Fragmentation Analyzer? Supported Input Data Downloading and Installing Requirements Downloading Troubleshooting Tutorial Importing Data Supported Text File Format Upgrading Support Source Screenshots NewsFebruary 27. 2010: Fragmentation Analyzer v1.5 is now available: Two new plotting types have been added: Intensity Correlation and Intensity Meta Plots. Both to help analyze the varations in intensity. Fixed the plotting colors so that b ions are always blue and y ions are always red in all plots. See ReleaseNotes for complete list of changes. January 11. 2010: Fragmentation Analyzer v1.4.3 is now available: Fixed a bug in the accuracy drop down menu for the 'Individual Spectra' table. Renamed and reordered the scoring types in the preference dialog. See ReleaseNotes for complete list of changes. December 04. 2009: Fragmentation Analyzer v1.4.2 is now available: It's now possible to duplicate some of the plot internal frames without having to recreate the plot. Moved the text for the fragment ion markers so that singly charged b and y ions no longer overlap. See ReleaseNotes for complete list of changes. Go to top of page What is Fragmentation Analyzer?Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data. Currently nine different analysis types are supported: Spectra Visualization - visualize the MS/MS spectra with fragment ion annotation, zooming and manual de-novo-sequencing. Intensity Box Plots - analyze intensity variation for a set of identification of the same peptide. Mass Error Scatter Plots - visualize the mass error spread in a set of selected identifications/spectra. Mass Error Bubble Plots - same as Mass Error Scatter Plots but with peak intensities added. Mass Error Box Plot - analyze the variation in mass errors. Fragment Ion Probability Plot - analyze the probability of observing specific fragment ions. Fragment Ion Heat Map - compare fragmentations using heat maps of correlation data. Intensity Correlation - detect how the intensity correlates with the spread in intensity. Intensity Meta Plots - further analyze the variations in intensity. See the screenshots for examples of the tool in action. Fragmentation Analyzer has been developed by Harald Barsnes (University of Bergen, Norway under the guidance of Prof. Dr. Lennart Martens. Go to top of page Supported Input DataFragmentation Analyzer currently supports three input formats: ms_lims 7 Mascot Dat Files OMSSA OMX Files In addition any files that can be converted to the supported text file format supported text file format can be used. (See the importing data section for details on how to import data.) Go to top of page Downloading and InstallingRequirementsFragmentation Analyzer requires Java 1.5 (or newer), which you can download for free here. Most modern computers will have Java installed already, so first try to follow the instructions below to download and run Fragmentation Analyzer before downloading Java. You only need the JRE version (and not the JDK version) to run Fragmentation Analyzer. Unless your data is stored in, or can be converted to, one of the supported data formats, the software will unfortunately not be of much help. The current version has been tested on Windows XP, Windows Vista, Mac and Linux, but should also work on other platforms, as long as Java 1.5 (or newer) is installed. If you come across problems on your platform please let us know. Go to top of page DownloadingFollow the download link, and download the latest version of FragmentationAnalyzer_X.Y.zip (where X and Y represent the version of the software). Unzipping the file, creates the following directory structure: FragmentationAnalyzer_X.Y FragmentationAnalyzer-X.Y.jar README.txt Properties (folder) DataSets (folder) lib (folder)To start the software, simply double-click the file named FragmentationAnalyzer-X.Y.jar. If this fails, try to download and install Java 1.5 or above, as explained in the previous section. (The program can also be started from the command line using the following command: java -jar FragmentationAnalyzer-X.Y.jar.) A Fragmentation Analyzer icon that can be used for shortcuts etc linking to the program is included in the zip file. An example data set is included in the DataSet folder. Go to top of page TroubleshootingDoes Not Start - If nothing happens when double clicking the Fragmentation Analyzer jar file, the most likely cause is that you don't have Java installed. Download the latest version of Java here and try again. (You only need the JRE version (and not the JDK version) to run Fragmentation Analyzer.) Does Not Start II - If Fragmentation Analyzer fails during start-up and you get the "Fragmentation Analyzer - Startup Failed" message, a file called fragmentation_analyzer.log will be created in your home directory. In this file you will find detailed information about why the program was not able to start. Does Not Start III - The most likely reason for the "Fragmentation Analyzer - Startup Failed" message is that you have installed Fragmentation Analyzer in a path containing special characters, i.e. [, %, æ, ø, å, etc. Move the converter to a different folder or rename the folder(s) causing the problem and try again. (On Linux Fragmentation Analyzer also has to be run from a path not containing spaces). Does Not Start IV - Another reason for the "Fragmentation Analyzer - Startup Failed" message could be that you have set the upper memory limit higher than your computer can handle (see points below). General Error Diagnosis - In the Properties folder (see section above for the folder structure), there is a file called ErrorLog.txt. This file contains transcripts of any errors that the application has encountered, and can be very useful in diagnosing your problem. Memory Issues - Big datasets can require a lot of memory. If the software unexpectedly fails on a big data set, and the software mentions that it ran out of memory, you should try to give the program more memory. This can be done by editing the JavaOptions.txt file in the Properties folder (see section above for the folder structure). In this file, change the -Xmx768M option to a higher number (e.g., -Xmx1500M for a maximum of appr. 1.5GB of memory). Please note that on a 32-bit operating system you can not increase this value beyond 2000M. Problem Not Solved? Or Problem Not In List Above? - See Support. Go to top of page TutorialSee Tutorial. Go to top of page Importing DataData can be imported from three different sources: ms_lims Mascot Dat Files OMSSA OMX Files ms_limsFor ms_lims one logs on to the ms_lims database via a dialog in the tool using ones normal login details. When connected all the required details about the identifications will be downloaded, while some details, e.g., the fragment ion information, is not downloaded but extracted when needed. The database connection will therefore be required during the use of the tool. Please note that depending on the size of the database the process of importing data from ms_lims might take a while. However, the progress of the import will be monitored closely and presented to the user. Mascot Dat FilesWhen importing Mascot dat files one simply selects the set of dat files to import and select the Mascot confidence level to use for the identifications. Only identifications above the selected confidence will be imported. OMSSA OMX FilesImporting OMSSA omx files is done in the same way as for Mascot dat files (except for the setting of the Mascot confidence level of course). However, the instrument name is not included in the omx file and has to be provided manually by the user for each imported file. Also note that the omx file includes very little details about the amino acid modifications, only a number , etc. The OMMSA installation folder (containing the mods.xml and usermods.xml files) therefore also has to be provided. Go to top of page Supported Text File FormatWhen a data set is imported into Fragmentation Analyzer it is divided into three parts: identifications.tx - details about the peptide identifications fragmentIons.txt - details about the fragment ions a folder of pkl files - details about the spectra identifications.txtFor ms_lims data only the identifications.txt file is created. The remaining information is extracted from the database when needed. However, a file called 'ms_lims.prop' is also created containing information about the database used. identifications.txt is a tab separated text file where the first line includes the number of lines in the file, i.e., the number of identifications. The rest of the file consists of one row per identification with the following elements: a unique identification index - Integer the identified peptide sequence (without terminals and modifications) - String the modified peptide sequence (with terminals and modifications) - String peptide precursor charge - Integer name of instrument used - String name of corresponding pkl spectrum file (see below) - String spectrum file id (if in ms_lims database) - Integer the total intensity of all the peaks in the spectrum - Double original file name (a reference to the original spectrum file) - String Either spectrum file name or spectrum id has to be provided, but the other can be set to "null". fragmentIons.txtfragmentIons.txt is also a tab separated consisting of one row per fragment ion with the following elements: a unique fragment ion index - Integer identification index (a reference to the identification the fragment comes from - Integer fragment ion type, e.g., y2, b3-H20 etc. - String fragment ion m/z value - Double fragment ion intensity - Double fragment ion number, e.g., y2 has the fragment ion number 2 - Double fragment ion mass error (the (absolute) distance between the theoretical and the experimental mass of the fragment ion (experimental mass - theoretical mass)) - Double The following fragment ion type names are recommended and will result in the best integration with the tool: Standard fragment ions, singly charged: b1, b2, y1, y2, etc. Neutral loss ions: y5-H2O, y4-NH3, etc. Doubly charged fragment ions: b2++, b4++-NH3, etc. Precursor ions: Prec, Prec-H2O 2+, etc. Immonium ions: iA, iC, etc. Spectra FolderFor non-ms_lims data sets the spectra are stored as pkl files in a folder called 'spectra'. One file per spectrum. The first line in each file contains the precursor m/z, intensity and charge. Next follows one line per peak in the spectrum with the m/z and intensity values. For more details see the example data set or the source code. Go to top of page UpgradingWhen a new version of Fragmentation Analyzer becomes available, existing users will be notified of this the next time they start the program. Upgrading is done by downloading the latest version from the download section, unzipping the file in a (preferably) empty folder, and then double clicking on the FragmentationAnalyzer_X.Y.jar file. Upgrading does not delete the older version of Fragmentation Analyzer. But after making sure that the new version is working, you can safely delete the folder containing the old version. Installing the new version in the same folder as the previously installed version can result in problems and is not recommended. DataSets created using the previous version are not automatically imported, but this can easily be achieved by copying the contents of the old DataSet folder into the DataSet folder of the newly installed version of Fragmentation Analyzer (see section above for the folder structure). A detailed overview of the changes between each Fragmentation Analyzer version can be found in the Release Notes. Go to top of page SupportFor questions or additional help, feel free to contact the authors. If appropriate please include a (preferably zipped) copy of the ErrorLog.txt file from the Properties folder. Go to top of page SourceThe source code can be viewed and downloaded by clicking the Source tab. It has mainly been developed using Netbeans, and is built and deployed using Maven. Fragmentation Analyzer also uses code from a couple of other projects: ms_lims - mass spectrometry laboratory information management system MascotDatfile Library OMSSA Parser JGoodies - Looks SwingLabs SwingX JFreeChart Spectrum Panel etc Commons-Math: The Apache Commons Mathematics Library Batik SVG Toolkit Go to top of page Screenshots(Click on the screenshot to see the full size version) Screenshot 1: Main interface of Fragmentation Analyzer. Go to top of page (Click on the screenshot to see the full size version) Screenshot 2: Boxplot of fragment ions for modified vs unmodified peptides. Go to top of page (Click on the screenshot to see the full size version) Screenshot 3: MS/MS spectra with fragment ion annotation. Go to top of page (Click on the screenshot to see the full size version) Screenshot 4: Mass Error Bubble Plot. Size of bubble relative to intensity. Color coding: instrument type. Go to top of page (Click on the screenshot to see the full size version) Screenshot 5: Mass Error Bubble Plot. Size of bubble relative to intensity. Color coding fragment ion type. Go to top of page (Click on the screenshot to see the full size version) Screenshot 6: Fragment Ion Probability Plot. Go to top of page (Click on the screenshot to see the full size version) Screenshot 7: Fragment Ion Heat Map - analyze the correlation of different fragmentation patterns. Go to top of page

mascot fragmentions proteomics massspectrometry ms_lims omssa

JWebToolkit

JWebToolkit is a Java web-application framework that provides a database pool (schema configured by XML), data interfaces, command pattern implementation, JSP tag libraries, JDK1.1 compatible XML parser, and XML tools.

tallerprogvisual

Proyecto de Taller de Programación Visual Tusso-Diab,

net parser taller logs reader

com.nklein.parser-generator

Lisp program for creating SAX-based XML parsers for Lisp or Objective-C,

httpxmldemo

Sourcecode gives an example of implementing HTTP and XML classes in Android. It's a kind of best practice for the communication with webservices. HTTP classes which are implemented: org.apache.http.client.HttpClient java.net.HttpURLConnection XML parser which are implemented: javax.xml.parsers.SAXParser (SAX) javax.xml.parsers.DocumentBuilder (DOM) The application also compares the working speed of the classes.

android httpurlconnection xml httpclient webservice http sax communication dom

MultipartRequest File Upload parser

HttpServletMultipartRequest parses multipart form data. From version 2.0 of the API only Servlets using Java 2 or later are supported.

jsdatatypelibrary

That API validates a string against a datatype specified in an object datatype(Uri, LocalName). It mainly implements two methods : this.datatypeAllows = function(datatype, paramList, string, context) { and this.datatypeEqual = function(datatype, patternString, patternContext, string, context) { which returns a pattern Empty() if string is valid or a pattern NotAllowed(message, datatype, string) if string is invalid.

validation library datatype javascript xmlschemadefinition xml data xsd parser