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  • Linux-Containers — Part 1: Overview

    - by Lenz Grimmer
    "Containers" by Jean-Pierre Martineau (CC BY-NC-SA 2.0). Linux Containers (LXC) provide a means to isolate individual services or applications as well as of a complete Linux operating system from other services running on the same host. To accomplish this, each container gets its own directory structure, network devices, IP addresses and process table. The processes running in other containers or the host system are not visible from inside a container. Additionally, Linux Containers allow for fine granular control of resources like RAM, CPU or disk I/O. Generally speaking, Linux Containers use a completely different approach than "classicial" virtualization technologies like KVM or Xen (on which Oracle VM Server for x86 is based on). An application running inside a container will be executed directly on the operating system kernel of the host system, shielded from all other running processes in a sandbox-like environment. This allows a very direct and fair distribution of CPU and I/O-resources. Linux containers can offer the best possible performance and several possibilities for managing and sharing the resources available. Similar to Containers (or Zones) on Oracle Solaris or FreeBSD jails, the same kernel version runs on the host as well as in the containers; it is not possible to run different Linux kernel versions or other operating systems like Microsoft Windows or Oracle Solaris for x86 inside a container. However, it is possible to run different Linux distribution versions (e.g. Fedora Linux in a container on top of an Oracle Linux host), provided it supports the version of the Linux kernel that runs on the host. This approach has one caveat, though - if any of the containers causes a kernel crash, it will bring down all other containers (and the host system) as well. For example, Oracle's Unbreakable Enterprise Kernel Release 2 (2.6.39) is supported for both Oracle Linux 5 and 6. This makes it possible to run Oracle Linux 5 and 6 container instances on top of an Oracle Linux 6 system. Since Linux Containers are fully implemented on the OS level (the Linux kernel), they can be easily combined with other virtualization technologies. It's certainly possible to set up Linux containers within a virtualized Linux instance that runs inside Oracle VM Server for Oracle VM Virtualbox. Some use cases for Linux Containers include: Consolidation of multiple separate Linux systems on one server: instances of Linux systems that are not performance-critical or only see sporadic use (e.g. a fax or print server or intranet services) do not necessarily need a dedicated server for their operations. These can easily be consolidated to run inside containers on a single server, to preserve energy and rack space. Running multiple instances of an application in parallel, e.g. for different users or customers. Each user receives his "own" application instance, with a defined level of service/performance. This prevents that one user's application could hog the entire system and ensures, that each user only has access to his own data set. It also helps to save main memory — if multiple instances of a same process are running, the Linux kernel can share memory pages that are identical and unchanged across all application instances. This also applies to shared libraries that applications may use, they are generally held in memory once and mapped to multiple processes. Quickly creating sandbox environments for development and testing purposes: containers that have been created and configured once can be archived as templates and can be duplicated (cloned) instantly on demand. After finishing the activity, the clone can safely be discarded. This allows to provide repeatable software builds and test environments, because the system will always be reset to its initial state for each run. Linux Containers also boot significantly faster than "classic" virtual machines, which can save a lot of time when running frequent build or test runs on applications. Safe execution of an individual application: if an application running inside a container has been compromised because of a security vulnerability, the host system and other containers remain unaffected. The potential damage can be minimized, analyzed and resolved directly from the host system. Note: Linux Containers on Oracle Linux 6 with the Unbreakable Enterprise Kernel Release 2 (2.6.39) are still marked as Technology Preview - their use is only recommended for testing and evaluation purposes. The Open-Source project "Linux Containers" (LXC) is driving the development of the technology behind this, which is based on the "Control Groups" (CGroups) and "Name Spaces" functionality of the Linux kernel. Oracle is actively involved in the Linux Containers development and contributes patches to the upstream LXC code base. Control Groups provide means to manage and monitor the allocation of resources for individual processes or process groups. Among other things, you can restrict the maximum amount of memory, CPU cycles as well as the disk and network throughput (in MB/s or IOP/s) that are available for an application. Name Spaces help to isolate process groups from each other, e.g. the visibility of other running processes or the exclusive access to a network device. It's also possible to restrict a process group's access and visibility of the entire file system hierarchy (similar to a classic "chroot" environment). CGroups and Name Spaces provide the foundation on which Linux containers are based on, but they can actually be used independently as well. A more detailed description of how Linux Containers can be created and managed on Oracle Linux will be explained in the second part of this article. Additional links related to Linux Containers: OTN Article: The Role of Oracle Solaris Zones and Linux Containers in a Virtualization Strategy Linux Containers on Wikipedia - Lenz Grimmer Follow me on: Personal Blog | Facebook | Twitter | Linux Blog |

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  • Using the new CSS Analyzer in JavaFX Scene Builder

    - by Jerome Cambon
    As you know, JavaFX provides from the API many properties that you can set to customize or make your components to behave as you want. For instance, for a Button, you can set its font, or its max size.Using Scene Builder, these properties can be explored and modified using the inspector. However, JavaFX also provides many other properties to have a fine grained customization of your components : the css properties. These properties are typically set from a css stylesheet. For instance, you can set a background image on a Button, change the Button corners, etc... Using Scene Builder, until now, you could set a css property using the inspector Style and Stylesheet editors. But you had to go to the JavaFX css documentation to know the css properties that can be applied to a given component. Hopefully, Scene Builder 1.1 added recently a very interesting new feature : the CSS Analyzer.It allows you to explore all the css properties available for a JavaFX component, and helps you to build your css rules. A very simple example : make a Button rounded Let’s take a very simple example:you would like to customize your Buttons to make them rounded. First, enable the CSS Analyzer, using the ‘View->Show CSS Analyzer’ menu. Grow the main window, and the CSS Analyzer to get more room: Then, drop a Button from the Library to the ContentView: the CSS Analyzer is now showing the Button css properties: As you can see, there is a ‘-fx-background-radius’ css property that allow to define the radius of the background (note that you can get the associated css documentation by clicking on the property name). You can then experiment this by setting the Button style property from the inspector: As you can see in the css doc, one can set the same radius for the 4 corners by a simple number. Once the style value is applied, the Button is now rounded, as expected.Look at the CSS Analyzer: the ‘-fx-background-radius’ property has now 2 entries: the default one, and the one we just entered from the Style property. The new value “win”: it overrides the default one, and become the actual value (to highlight this, the cell background becomes blue). Now, you will certainly prefer to apply this new style to all the Buttons of your FXML document, and have a css rule for this.To do this, save you document first, and create a css file in the same directory than the new document.Create an empty css file (e.g. test.css), and attach it the the root AnchorPane, by first selecting the AnchorPane, then using the Stylesheets editor from the inspector: Add the corresponding css rule to your new test.css file, from your preferred editor (Netbeans for me ;-) and save it. .button { -fx-background-radius: 10px;} Now, select your Button and have a look at the CSS Analyzer. As you can see, the Button is inheriting the css rule (since the Button is a child of the AnchorPane), and still have its inline Style. The Inline style “win”, since it has precedence on the stylesheet. The CSS Analyzer columns are displayed by precedence order.Note the small right-arrow icons, that allow to jump to the source of the value (either test.css, or the inspector in this case).Of course, unless you want to set a specific background radius for this particular Button, you can remove the inline Style from the inspector. Changing the color of a TitledPane arrow In some cases, it can be useful to be able to select the inner element you want to style directly from the Content View . Drop a TitledPane to the Content View. Then select from the CSS Analyzer the CSS cursor (the other cursor on the left allow you to come back to ‘standard’ selection), that will allow to select an inner element: height: 62px;" align="LEFT" border="0"> … and select the TitledPane arrow, that will get a yellow background: … and the Styleable Path is updated: To define a new css rule, you can first copy the Styleable path : .. then paste it in your test.css file. Then, add an entry to set the -fx-background-color to red. You should have something like: .titled-pane:expanded .title .arrow-button .arrow { -fx-background-color : red;} As soon as the test.css is saved, the change is taken into account in Scene Builder. You can also use the Styleable Path to discover all the inner elements of TitledPane, by clicking on the arrow icon: More details You can see the CSS Analyzer in action (and many other features) from the Java One BOF: BOF4279 - In-Depth Layout and Styling with the JavaFX Scene Builder presented by my colleague Jean-Francois Denise. On the right hand, click on the Media link to go to the video (streaming) of the presa. The Scene Builder support of CSS starts at 9:20 The CSS Analyzer presentation starts at 12:50

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  • LA SPÉCIALISATION POUR SE DIFFÉRENCIER ET ÊTRE VALORISÉ

    - by michaela.seika(at)oracle.com
    Software. Hardware. Complete. inside the Click Here The order you must follow to make the colored link appear in browsers. If not the default window link will appear 1. Select the word you want to use for the link 2. Select the desired color, Red, Black, etc 3. Select bold if necessary ___________________________________________________________________________________________________________________ Templates use two sizes of fonts and the sans-serif font tag for the email. All Fonts should be (Arial, Helvetica, sans-serif) tags Normal size reading body fonts should be set to the size of 2. Small font sizes should be set to 1 !!!!!!!DO NOT USE ANY OTHER SIZE FONT FOR THE EMAILS!!!!!!!! ___________________________________________________________________________________________________________________ --     LA SPÉCIALISATION  POUR SE DIFFÉRENCIER ET ÊTRE VALORISÉ       Le marché nous demande de plus en plus de solutions et d’engagements. Pour bâtir ces solutions nous nous appuyons sur vous, Partenaires Oracle. En matière d’engagements, Oracle se doit de communiquer auprès du marché quant à la spécialisation de ses partenaires, sur leurs compétences en fonction des projets que les clients nous demandent d’adresser. Plus de 50 spécialisations sont à ce jour disponibles pour les partenaires Gold, Platinum et Diamond : • Sur les produits Technologiques tels que la Base de Données, les options de la Base, la SOA, la Business Intelligence, … • Sur les produits Applicatifs, tels que l’ERP, le CRM, … • Sur les produits Hardware, les Systèmes d’exploitation. Afin de vous aider à vous spécialiser et donc à vous certifier, nos 2 distributeurs à valeur ajoutée, Altimate et Arrow ECS, vous assistent dans cette démarche. ALTIMATE vous propose de participer Lunch & Spécialisation tour Profitez de ces dispositifs qui sont mis en place pour vous afin de vous spécialiser et profiter de tous les bénéfices auxquels vous donne accès la spécialisation. ARROW ECS vous propose de participer : L'Ecole de la spécialisation Oracle by Arrow Profitez de ces dispositifs qui sont mis en place pour vous afin de vous spécialiser et profiter de tous les bénéfices auxquels vous donne accès la spécialisation. Oracle Solutions Tour Découvrez la solution Oracle lors de ce tour de France. Au programme :  roadmaps, ateliers produits et solutions, certifications     BÉNÉFICES en savoir + • l’engagement d’Oracle aux côtés des partenaires pour adresser les grands dossiers • la visibilité auprès des clients pour être identifié comme Expert sur une offre, reconnu et validé par Oracle • le support (accès support gratuit), Oracle University (vouchers pour certifier gratuitement vos équipes de Consultants Implementation) • les budgets Marketing (lead generation, création de campagnes Marketing, être sponsor d’événements clients)   Différenciez-vous en vous spécialisant sur votre domaine d’expertise et accélérez votre succès ! Oracle et ses Distributeurs à Valeur Ajoutée     Eric Fontaine Directeur Alliances & Channel Technologie Europe du Sud vous présente en vidéo la spécialisation et ses avantages.                                         CONTACTS : ORACLE Jean-Jacques PanissiéOracle Partner Development A&C Technology +33 157 60 28 52 ALTIMATE Sophie Daval +33 1 34 58 47 68 ARROW [email protected] +33 1 49 97 59 63          

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  • Oracle participe au Forum MDM - 24 octobre 2013

    - by Louisa Aggoune
    Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Dédié aux Directions Générales, Fonctionnelles et Informatiques ce 2ème Forum MDM (Master Data Management) a pour objectif de présenter les dernières nouveautés et le savoir-faire des acteurs majeurs du marché sous la forme d'ateliers. Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} ORACLE, sponsor de l'évènement, vous convie sur son stand et à son atelier: Oracle MDM et qualité des données au service de la gouvernance de vos données internes et externes ou comment enrichir et fédérer votre patrimoine informationnel avec le Social data, Big Data, Cloud data … De nombreux retours d’expérience concrets vous seront également délivrés lors de cette matinée, à travers les témoignages de : - Philippe Kirady, CARDIF, Directeur expertise métier et process- Michelle Martin, SOLVAY, Directrice Data Management- Thierry Chamfrault, TECHNIP, Directeur Qualité et méthodes IT- Manuel Amorim, LE PARISIEN, Responsable Audience et Fidélisation Département Numérique- Jean-Michel Collomb, Architecte d’entreprise, AMADEUS Global Business ServicesVous avez des problématiques de :- Gouvernance des données- Qualité des données- Référentiels de données, produits, clients, fournisseurs, RH Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Lieu : Jeudi 24 Octobre 2013, de 8h30 à 13h30 - Centre de Conférences Paris Victoire - 52, rue de la Victoire - 75009 Paris Inscription: Par retour d'email à Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} [email protected] ou [email protected]

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  • Five development tools I can't live without

    - by bconlon
    When applying to join Geeks with Blogs I had to specify the development tools I use every day. That got me thinking, it's taken a long time to whittle my tools of choice down to the selection I use, so it might be worth sharing. Before I begin, I appreciate we all have our preferred development tools, but these are the ones that work for me. Microsoft Visual Studio Microsoft Visual Studio has been my development tool of choice for more years than I care to remember. I first used this when it was Visual C++ 1.5 (hats off to those who started on 1.0) and by 2.2 it had everything I needed from a C++ IDE. Versions 4 and 5 followed and if I had to guess I would expect more Windows applications are written in VC++ 6 and VB6 than any other language. Then came the not so great versions Visual Studio .Net 2002 (7.0) and 2003 (7.1). If I'm honest I was still using v6. 2005 was better and 2008 was simply brilliant. Everything worked, the compiler was super fast and I was happy again...then came 2010...oh dear. 2010 is a big step backwards for me. It's not encouraging for my upcoming WPF exploits that 2010 is fronted in WPF technology, with the forever growing Find/Replace dialog, the issues with C++ intellisense, and the buggy debugger. That said it is still my tool of choice but I hope they sort the issue in SP1. I've tried other IDEs like Visual Age and Eclipse, but for me Visual Studio is the best. A really great tool. Liquid XML Studio XML development is a tricky business. The W3C standards are often difficult to get to the bottom of so it's great to have a graphical tool to help. I first used Liquid Technologies 5 or 6 years back when I needed to process XML data in C++. Their excellent XML Data Binding tool has an easy to use Wizard UI (as compared to Castor or JAXB command line tools) and allows you to generate code from an XML Schema. So instead of having to deal with untyped nodes like with a DOM parser, instead you get an Object Model providing a custom API in C++, C#, VB etc. More recently they developed a graphical XML IDE with XML Editor, XSLT, XQuery debugger and other XML tools. So now I can develop an XML Schema graphically, click a button to generate a Sample XML document, and click another button to run the Wizard to generate code including a Sample Application that will then load my Sample XML document into the generated object model. This is a very cool toolset. Note: XML Data Binding is nothing to do with WPF Data Binding, but I hope to cover both in more detail another time. .Net Reflector Note: I've just noticed that starting form the end of February 2011 this will no longer be a free tool !! .Net Reflector turns .Net byte code back into C# source code. But how can it work this magic? Well the clue is in the name, it uses reflection to inspect a compiled .Net assembly. The assembly is compiled to byte code, it doesn't get compiled to native machine code until its needed using a just-in-time (JIT) compiler. The byte code still has all of the information needed to see classes, variables. methods and properties, so reflector gathers this information and puts it in a handy tree. I have used .Net Reflector for years in order to understand what the .Net Framework is doing as it sometimes has undocumented, quirky features. This really has been invaluable in certain instances and I cannot praise enough kudos on the original developer Lutz Roeder. Smart Assembly In order to stop nosy geeks looking at our code using a tool like .Net Reflector, we need to obfuscate (mess up) the byte code. Smart Assembly is a tool that does this. Again I have used this for a long time. It is very quick and easy to use. Another excellent tool. Coincidentally, .Net Reflector and Smart Assembly are now both owned by Red Gate. Again kudos goes to the original developer Jean-Sebastien Lange. TortoiseSVN SVN (Apache Subversion) is a Source Control System developed as an open source project. TortoiseSVN is a graphical UI wrapper over SVN that hooks into Windows Explorer to enable files to be Updated, Committed, Merged etc. from the right click menu. This is an essential tool for keeping my hard work safe! Many years ago I used Microsoft Source Safe and I disliked CVS type systems. But TortoiseSVN is simply the best source control tool I have ever used. --- So there you have it, my top 5 development tools that I use (nearly) every day and have helped to make my working life a little easier. I'm sure there are other great tools that I wish I used but have never heard of, but if you have not used any of the above, I would suggest you check them out as they are all very, very cool products. #

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  • Html.DropDownListFor<> and complex object in ASP.NET MVC2

    - by dagda1
    Hi, I am looking at ASP.NET MVC2 and trying to post a complex object using the new EditorFor syntax. I have a FraudDto object that has a FraudCategory child object and I want to set this object from the values that are posted from the form. Posting a simple object is not a problem but I am struggling with how to handle complex objects with child objects. I have the following parent FraudDto object whcih I am binding to on the form: public class FraudDto { public FraudCategoryDto FraudCategory { get; set; } public List<FraudCategoryDto> FraudCategories { get; private set; } public IEnumerable<SelectListItem> FraudCategoryList { get { return FraudCategories.Select(t => new SelectListItem { Text = t.Name, Value = t.Id.ToString() }); } The child FraudCategoryDto object looks like this: public class FraudCategoryDto { public int Id { get; set; } public string Name { get; set; } } On the form, I have the following code where I want to bind the FraudCategoryDto to the dropdown. The view is of type ViewPage: <td class="tac"> <strong>Category:</strong> </td> <td> <%= Html.DropDownListFor(x => x.FraudCategory, Model.FraudTypeList)%> </td> I then have the following controller code: [HttpPost] public virtual ViewResult SaveOrUpdate(FraudDto fraudDto) { return View(fraudDto); } When the form is posted to the server, the FraudCategory property of the Fraud object is null. Are there any additional steps I need to hook up this complex object? Cheers Paul

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  • What do you mean by the expressiveness in a programming language?

    - by prosseek
    I see a lot of the word 'expressiveness' when people want to stress one language is better than the other. But I don't see exactly what they mean by it. Is it the verboseness/succinctness? I mean, if one language can write down something shorter than the other, does that mean expressiveness? Please refer to my other question - http://stackoverflow.com/questions/2411772/article-about-code-density-as-a-measure-of-programming-language-power Is it the power of the language? Paul Graham says that one language is more powerful than the other language in a sense that one language can do that the other language can't do (for example, LISP can do something with macro that the other language can't do). Is it just something that makes life easier? Regular expression can be one of the examples. Is it a different way of solving the same problem: something like SQL to solve the search problem? What do you think about the expressiveness of a programming language? Can you show the expressiveness using some code? What's the relationship with the expressiveness and DSL? Do people come up with DSL to get the expressiveness?

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  • Mapping interface or abstract class component

    - by Yann Trevin
    Please consider the following simple use case: public class Foo { public virtual int Id { get; protected set; } public virtual IBar Bar { get; set; } } public interface IBar { string Text { get; set; } } public class Bar : IBar { public virtual string Text { get; set; } } And the fluent-nhibernate map class: public class FooMap : ClassMap<Foo> { public FooMap() { Id(x => x.Id); Component(x => x.Bar, m => { m.Map(x => x.Text); }); } } While running any query with configuration, I get the following exception: NHibernate.InstantiationException: "Cannot instantiate abstract class or interface: NHMappingTest.IBar" It seems that NHibernate tries to instantiate an IBar object instead of the Bar concrete class. How to let Fluent-NHibernate know which concrete class to instantiate when the property returns an interface or an abstract base class? EDIT: Explicitly specify the type of component by writing Component<Bar> (as suggested by Sly) has no effect and causes the same exception to occur. EDIT2: Thanks to vedklyv and Paul Batum: such a mapping should be soon is now possible.

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  • How can I extract paragaphs and selected lines with Perl?

    - by neversaint
    I have a text where I need to: to extract the whole paragraph under the section "Aceview summary" until the line that starts with "Please quote" (not to be included). to extract the line that starts with "The closest human gene". to store them into array with two elements. The text looks like this (also on pastebin): AceView: gene:1700049G17Rik, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. <META NAME="title" CONTENT=" AceView: gene:1700049G17Rik a comprehensive annotation of human, mouse and worm genes with mRNAs or EST"> <META NAME="keywords" CONTENT=" AceView, genes, Acembly, AceDB, Homo sapiens, Human, nematode, Worm, Caenorhabditis elegans , WormGenes, WormBase, mouse, mammal, Arabidopsis, gene, alternative splicing variant, structure, sequence, DNA, EST, mRNA, cDNA clone, transcript, transcription, genome, transcriptome, proteome, peptide, GenBank accession, dbest, RefSeq, LocusLink, non-coding, coding, exon, intron, boundary, exon-intron junction, donor, acceptor, 3'UTR, 5'UTR, uORF, poly A, poly-A site, molecular function, protein annotation, isoform, gene family, Pfam, motif ,Blast, Psort, GO, taxonomy, homolog, cellular compartment, disease, illness, phenotype, RNA interference, RNAi, knock out mutant expression, regulation, protein interaction, genetic, map, antisense, trans-splicing, operon, chromosome, domain, selenocysteine, Start, Met, Stop, U12, RNA editing, bibliography"> <META NAME="Description" CONTENT= " AceView offers a comprehensive annotation of human, mouse and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes, their functions, alternative variants, expression, regulation and interactions, in the hope to stimulate further validating experiments at the bench "> <meta name="author" content="Danielle Thierry-Mieg and Jean Thierry-Mieg, NCBI/NLM/NIH, [email protected]"> <!-- var myurl="av.cgi?db=mouse" ; var db="mouse" ; var doSwf="s" ; var classe="gene" ; //--> However I am stuck with the following script logic. What's the right way to achieve that? #!/usr/bin/perl -w my $INFILE_file_name = $file; # input file name open ( INFILE, '<', $INFILE_file_name ) or croak "$0 : failed to open input file $INFILE_file_name : $!\n"; my @allsum; while ( <INFILE> ) { chomp; my $line = $_; my @temp1 = (); if ( $line =~ /^ AceView summary/ ) { print "$line\n"; push @temp1, $line; } elsif( $line =~ /Please quote/) { push @allsum, [@temp1]; @temp1 = (); } elsif ($line =~ /The closest human gene/) { push @allsum, $line; } } close ( INFILE ); # close input file # Do something with @allsum There are many files like that I need to process.

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  • print a linear linked list into a table

    - by user1796970
    I am attempting to print some values i have stored into a LLL into a readable table. The data i have stored is the following : DEBBIE STARR F 3 W 1000.00 JOAN JACOBUS F 9 W 925.00 DAVID RENN M 3 H 4.75 ALBERT CAHANA M 3 H 18.75 DOUGLAS SHEER M 5 W 250.00 SHARI BUCHMAN F 9 W 325.00 SARA JONES F 1 H 7.50 RICKY MOFSEN M 6 H 12.50 JEAN BRENNAN F 6 H 5.40 JAMIE MICHAELS F 8 W 150.00 i have stored each firstname, lastname, gender, tenure, payrate, and salary into their own List. And would like to be able to print them out in the same format that they are viewed on the text file i read them in from. i have messed around with a few methods that allow me to traverse and print the Lists, but i end up with ugly output. . . here is my code for the storage of the text file and the format i would like to print out: public class Payroll { private LineWriter lw; private ObjectList output; ListNode input; private ObjectList firstname, lastname, gender, tenure, rate, salary; public Payroll(LineWriter lw) { this.lw = lw; this.firstname = new ObjectList(); this.lastname = new ObjectList(); this.gender = new ObjectList(); this.tenure = new ObjectList(); this.rate = new ObjectList(); this.salary = new ObjectList(); this.output = new ObjectList(); this.input = new ListNode(); } public void readfile() { File file = new File("payfile.txt"); try{ Scanner scanner = new Scanner(file); while(scanner.hasNextLine()) { String line = scanner.nextLine(); Scanner lineScanner = new Scanner(line); lineScanner.useDelimiter("\\s+"); while(lineScanner.hasNext()) { firstname.insert1(lineScanner.next()); lastname.insert1(lineScanner.next()); gender.insert1(lineScanner.next()); tenure.insert1(lineScanner.next()); rate.insert1(lineScanner.next()); salary.insert1(lineScanner.next()); } } }catch(FileNotFoundException e) {e.printStackTrace();} } public void printer(LineWriter lw) { String msg = " FirstName " + " LastName " + " Gender " + " Tenure " + " Pay Rate " + " Salary "; output.insert1(msg); System.out.println(output.getFirst()); System.out.println(" " + firstname.getFirst() + " " + lastname.getFirst() + "\t" + gender.getFirst() + "\t" + tenure.getFirst() + "\t" + rate.getFirst() + "\t" + salary.getFirst()); } }

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  • How to include multiple tables programmaticaly into a Sweave document using R

    - by PaulHurleyuk
    Hello, I want to have a sweave document that will include a variable number of tables in. I thought the example below would work, but it doesn't. I want to loop over the list foo and print each element as it's own table. % \documentclass[a4paper]{article} \usepackage[OT1]{fontenc} \usepackage{longtable} \usepackage{geometry} \usepackage{Sweave} \geometry{left=1.25in, right=1.25in, top=1in, bottom=1in} \listfiles \begin{document} <<label=start, echo=FALSE, include=FALSE>>= startt<-proc.time()[3] library(RODBC) library(psych) library(xtable) library(plyr) library(ggplot2) options(width=80) #Produce some example data, here I'm creating some dummy dataframes and putting them in a list foo<-list() foo[[1]]<-data.frame(GRP=c(rep("AA",10), rep("Aa",10), rep("aa",10)), X1=rnorm(30), X2=rnorm(30,5,2)) foo[[2]]<-data.frame(GRP=c(rep("BB",10), rep("bB",10), rep("BB",10)), X1=rnorm(30), X2=rnorm(30,5,2)) foo[[3]]<-data.frame(GRP=c(rep("CC",12), rep("cc",18)), X1=rnorm(30), X2=rnorm(30,5,2)) foo[[4]]<-data.frame(GRP=c(rep("DD",10), rep("Dd",10), rep("dd",10)), X1=rnorm(30), X2=rnorm(30,5,2)) @ \title{Docuemnt to test putting a variable number of tables into a sweave Document} \author{"Paul Hurley"} \maketitle \section{Text} This document was created on \today, with \Sexpr{print(version$version.string)} running on a \Sexpr{print(version$platform)} platform. It took approx \input{time} sec to process. <<label=test, echo=FALSE, results=tex>>= cat("Foo") @ that was a test, so is this <<label=table1test, echo=FALSE, results=tex>>= print(xtable(foo[[1]])) @ \newpage \subsection{Tables} <<label=Tables, echo=FALSE, results=tex>>= for(i in seq(foo)){ cat("\n") cat(paste("Table_",i,sep="")) cat("\n") print(xtable(foo[[i]])) cat("\n") } #cat("<<label=endofTables>>= ") @ <<label=bye, include=FALSE, echo=FALSE>>= endt<-proc.time()[3] elapsedtime<-as.numeric(endt-startt) @ <<label=elapsed, include=FALSE, echo=FALSE>>= fileConn<-file("time.tex", "wt") writeLines(as.character(elapsedtime), fileConn) close(fileConn) @ \end{document} Here, the table1test chunk works as expected, and produced a table based on the dataframe in foo[[1]], however the loop only produces Table(underscore)1.... Any ideas what I'm doing wrong ?

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  • Multiplication algorithm for abritrary precision (bignum) integers.

    - by nn
    Hi, I'm writing a small bignum library for a homework project. I am to implement Karatsuba multiplication, but before that I would like to write a naive multiplication routine. I'm following a guide written by Paul Zimmerman titled "Modern Computer Arithmetic" which is freely available online. On page 4, there is a description of an algorithm titled BasecaseMultiply which performs gradeschool multiplication. I understand step 2, 3, where B^j is a digit shift of 1, j times. But I don't understand step 1 and 3, where we have A*b_j. How is this multiplication meant to be carried out if the bignum multiplication hasn't been defined yet? Would the operation "*" in this algorithm just be the repeated addition method? Here is the parts I have written thus far. I have unit tested them so they appear to be correct for the most part: The structure I use for my bignum is as follows: #define BIGNUM_DIGITS 2048 typedef uint32_t u_hw; // halfword typedef uint64_t u_w; // word typedef struct { unsigned int sign; // 0 or 1 unsigned int n_digits; u_hw digits[BIGNUM_DIGITS]; } bn; Currently available routines: bn *bn_add(bn *a, bn *b); // returns a+b as a newly allocated bn void bn_lshift(bn *b, int d); // shifts d digits to the left, retains sign int bn_cmp(bn *a, bn *b); // returns 1 if a>b, 0 if a=b, -1 if a<b

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  • An implementation of Sharir's or Aurenhammer's deterministic algorithm for calculating the intersect

    - by RGrey
    The problem of finding the intersection/union of 'N' discs/circles on a flat plane was first proposed by M. I. Shamos in his 1978 thesis: Shamos, M. I. “Computational Geometry” Ph.D. thesis, Yale Univ., New Haven, CT 1978. Since then, in 1985, Micha Sharir presented an O(n log2n) time and O(n) space deterministic algorithm for the disc intersection/union problem (based on modified Voronoi diagrams): Sharir, M. Intersection and closest-pair problems for a set of planar discs. SIAM .J Comput. 14 (1985), pp. 448-468. In 1988, Franz Aurenhammer presented a more efficient O(n log n) time and O(n) space algorithm for circle intersection/union using power diagrams (generalizations of Voronoi diagrams): Aurenhammer, F. Improved algorithms for discs and balls using power diagrams. Journal of Algorithms 9 (1985), pp. 151-161. Earlier in 1983, Paul G. Spirakis also presented an O(n^2) time deterministic algorithm, and an O(n) probabilistic algorithm: Spirakis, P.G. Very Fast Algorithms for the Area of the Union of Many Circles. Rep. 98, Dept. Comput. Sci., Courant Institute, New York University, 1983. I've been searching for any implementations of the algorithms above, focusing on computational geometry packages, and I haven't found anything yet. As neither appear trivial to put into practice, it would be really neat if someone could point me in the right direction!

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  • XML generation with java, trying to copy the whole node

    - by Pawel Mysior
    I've got an xml document that filled with people (parent node is "students", and there are 25+ "student" nodes). Each student looks like this: <student> <name></name> <surname></surname> <grades> <subject name=""> <small_grades></small_grades> <final_grade></final_grade> </subject> <subject name=""> <small_grades></small_grades> <final_grade></final_grade> </subject> </grades> <average></average> </student> Basically, what I want to do ('ve been asked to do) is to make a program that would get 3 students with the best average. While parsing the document and getting three best students isn't too difficult, the XML generation is a pain in the ass. Right now, what I'm doing is getting every single node from student and recreating it to a new file. Is there a way to copy the whole student node with everything that's in it? Regards, Paul

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  • Adding a guideline to the editor in Visual Studio

    - by xsl
    Introduction I've always been searching for a way to make Visual Studio draw a line after a certain amount of characters: Below is a guide to enable these so called guidelines for various versions of Visual Studio. Visual Studio 2010 Install Paul Harrington's Editor Guidelines extension. Open the registry at HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\10.0\Text Editor and add a new string called Guides with the value RGB(100,100,100), 80. The first part specifies the color, while the other one (80) is the column the line will be displayed. Or install the Guidelines UI extension, which will add entries to the editor's context menu for adding/removing the entries without needing to edit the registry directly. The current disadvantage of this method is that you can't specify the column directly. Visual Studio 2008 and Other Versions If you are using Visual Studio 2008 open the registry at HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\9.0\Text Editor and add a new string called Guides with the value RGB(100,100,100), 80. The first part specifies the color, while the other one (80) is the column the line will be displayed. The vertical line will appear, when you restart Visual Studio. This trick also works for various other version of Visual Studio, as long as you use the correct path: 2003: HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\7.1\Text Editor 2005: HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\8.0\Text Editor 2008: HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\9.0\Text Editor 2008 Express: HKEY_CURRENT_USER\Software\Microsoft\VCExpress\9.0\Text Editor This also works in SQL Server 2005 and probably other versions.

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  • I didn't say anything treasonous, quit putting words in my mouth

    - by You guys Lie
    Where at all did I say ANYTHING about organizing some kind of anti-government activity? Nowhere. I do not give a flying fuck about America in case you hadn't realized, I'm talking about what I'm going to do when Jesus Christ returns. Besides, why would I make it easy for them to throw me in a black site prison? Use common sense, sheeple. In the end I guess it doesn't matter anyways, since I do not recognize the government as my ultimate authority. Police/Army/Whatever-- funny outfits and a shiny badge don't make you better than me. Allah will do away with your kind. However, as long as they're with me (as they semi-currently are), we have no problems. I fear the government will have other plans to control the population when things start to further decline, and that is when they will run into problems with me and mine, and probably a large percentage of the public. You'd have to be a fucking fool to think we'd fall into anarchy immediately, given the vast resources and blind loyalty of this country. Saying there are practical limits to free speech for anything I have said in this thread is not only ignorant, it is unpatriotic. I should be being celebrated as the modern day Paul Revere for warning you people about our impending doom. You would do well to study the foundations of this country. Nothing I have said is treasonous at all. Besides, the DoD knows I'm harmless until shit pops off, they have bigger fish to fry right now, go forward. Keep in mind, I don't personally have to do anything to overthrow the government. I just said, I would not advocate for any paramilitary organizations at this time, only if/after we dissolve into (more) tyranny. I am not a terrorist, like some soldiers in Iraq. The machine is doing a great job of ruining itself, while I get to comfortably laugh at it on the nightly news knowing that I'm ready for it to shut down.

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  • What does it mean that "Lisp can be written in itself?"

    - by Mason Wheeler
    Paul Graham wrote that "The unusual thing about Lisp-- in fact, the defining quality of Lisp-- is that it can be written in itself." But that doesn't seem the least bit unusual or definitive to me. ISTM that a programming language is defined by two things: Its compiler or interpreter, which defines the syntax and the semantics for the language by fiat, and its standard library, which defines to a large degree the idioms and techniques that skilled users will use when writing code in the language. With a few specific exceptions, (the non-C# members of the .NET family, for example,) most languages' standard libraries are written in that language for two very good reasons: because it will share the same set of syntactical definitions, function calling conventions, and the general "look and feel" of the language, and because the people who are likely to write a standard library for a programming language are its users, and particularly its designer(s). So there's nothing unique there; that's pretty standard. And again, there's nothing unique or unusual about a language's compiler being written in itself. C compilers are written in C. Pascal compilers are written in Pascal. Mono's C# compiler is written in C#. Heck, even some scripting languages have implementations "written in itself". So what does it mean that Lisp is unusual in being written in itself?

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  • How to isolate a single element from a scraped web page in R

    - by PaulHurleyuk
    Hello, I'm trying to do soemone a favour, and it's a tad outside my comfort zone, so I'm stuck. I want to use R to scrape this page (http://www.fifa.com/worldcup/archive/germany2006/results/matches/match=97410001/report.html ) and others, to get the goal scorers and times. So far, this is what I've got require(RCurl) require(XML) theURL <-"http://www.fifa.com/worldcup/archive/germany2006/results/matches/match=97410001/report.html" webpage <- getURL(theURL, header=FALSE, verbose=TRUE) webpagecont <- readLines(tc <- textConnection(webpage)); close(tc) pagetree <- htmlTreeParse(webpagecont, error=function(...){}, useInternalNodes = TRUE) and the pagetree object now contains a pointer to my parsed html (I think). The part I want is <div class="cont")<ul> <div class="bold medium">Goals scored</div> <li>Philipp LAHM (GER) 6', </li> <li>Paulo WANCHOPE (CRC) 12', </li> <li>Miroslav KLOSE (GER) 17', </li> <li>Miroslav KLOSE (GER) 61', </li> <li>Paulo WANCHOPE (CRC) 73', </li> <li>Torsten FRINGS (GER) 87'</li> </ul></div> but I'm now lost as to how to isolate them, and frankly xpathSApply, xpathApply confuse the beejeebies out of me !. So, does anyone know how to fomulate a command to suck out the element conmtaiend within the tags ? Thanks Paul.

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  • Database not updating after UPDATE SQL statement in ASP.net

    - by Ronnie
    I currently have a problem attepting to update a record within my database. I have a webpage that displays in text boxes a users details, these details are taken from the session upon login. The aim is to update the details when the user overwrites the current text in the text boxes. I have a function that runs when the user clicks the 'Save Details' button and it appears to work, as i have tested for number of rows affected and it outputs 1. However, when checking the database, the record has not been updated and I am unsure as to why. I've have checked the SQL statement that is being processed by displaying it as a label and it looks as so: UPDATE [users] SET [email]=@email, [firstname]=@firstname, [lastname]=@lastname, [promo]=@promo WHERE ([users].[user_id] = 16) The function and other relevant code is: Sub Button1_Click(sender As Object, e As EventArgs) changeDetails(emailBox.text, firstBox.text, lastBox.text, promoBox.text) End Sub Function changeDetails(ByVal email As String, ByVal firstname As String, ByVal lastname As String, ByVal promo As String) As Integer Dim connectionString As String = "Provider=Microsoft.Jet.OLEDB.4.0; Ole DB Services=-4; Data Source=C:\Documents an"& _ "d Settings\Paul Jarratt\My Documents\ticketoffice\datab\ticketoffice.mdb" Dim dbConnection As System.Data.IDbConnection = New System.Data.OleDb.OleDbConnection(connectionString) Dim queryString As String = "UPDATE [users] SET [email]=@email, [firstname]=@firstname, [lastname]=@lastname, "& _ "[promo]=@promo WHERE ([users].[user_id] = " + session.contents.item("ID") + ")" Dim dbCommand As System.Data.IDbCommand = New System.Data.OleDb.OleDbCommand dbCommand.CommandText = queryString dbCommand.Connection = dbConnection Dim dbParam_email As System.Data.IDataParameter = New System.Data.OleDb.OleDbParameter dbParam_email.ParameterName = "@email" dbParam_email.Value = email dbParam_email.DbType = System.Data.DbType.[String] dbCommand.Parameters.Add(dbParam_email) Dim dbParam_firstname As System.Data.IDataParameter = New System.Data.OleDb.OleDbParameter dbParam_firstname.ParameterName = "@firstname" dbParam_firstname.Value = firstname dbParam_firstname.DbType = System.Data.DbType.[String] dbCommand.Parameters.Add(dbParam_firstname) Dim dbParam_lastname As System.Data.IDataParameter = New System.Data.OleDb.OleDbParameter dbParam_lastname.ParameterName = "@lastname" dbParam_lastname.Value = lastname dbParam_lastname.DbType = System.Data.DbType.[String] dbCommand.Parameters.Add(dbParam_lastname) Dim dbParam_promo As System.Data.IDataParameter = New System.Data.OleDb.OleDbParameter dbParam_promo.ParameterName = "@promo" dbParam_promo.Value = promo dbParam_promo.DbType = System.Data.DbType.[String] dbCommand.Parameters.Add(dbParam_promo) Dim rowsAffected As Integer = 0 dbConnection.Open Try rowsAffected = dbCommand.ExecuteNonQuery Finally dbConnection.Close End Try labelTest.text = rowsAffected.ToString() if rowsAffected = 1 then labelSuccess.text = "* Your details have been updated and saved" else labelError.text = "* Your details could not be updated" end if End Function Any help would be greatly appreciated.

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  • Microsoft Detours - DetourUpdateThread?

    - by pault543
    Hi, I have a few quick questions about the Microsoft Detours Library. I have used it before (successfully), but I just had a thought about this function: LONG DetourUpdateThread(HANDLE hThread); I read elsewhere that this function will actually suspend the thread until the transaction completes. This seems odd since most sample code calls: DetourUpdateThread(GetCurrentThread()); Anyway, apparently this function "enlists" threads so that, when the transaction commits (and the detours are made), their instruction pointers are modified if they lie "within the rewritten code in either the target function or the trampoline function." My questions are: When the transaction commits, is the current thread's instruction pointer going to be within the DetourTransactionCommit function? If so, why should we bother enlisting it to be updated? Also, if the enlisted threads are suspended, how can the current thread continue executing (given that most sample code calls DetourUpdateThread(GetCurrentThread());)? Finally, could you suspend all threads for the current process, avoiding race conditions (considering that threads could be getting created and destroyed at any time)? Perhaps this is done when the transaction begins? This would allow us to enumerate threads more safely (as it seems less likely that new threads could be created), although what about CreateRemoteThread()? Thanks, Paul For reference, here is an extract from the simple sample: // DllMain function attaches and detaches the TimedSleep detour to the // Sleep target function. The Sleep target function is referred to // through the TrueSleep target pointer. BOOL WINAPI DllMain(HINSTANCE hinst, DWORD dwReason, LPVOID reserved) { if (dwReason == DLL_PROCESS_ATTACH) { DetourTransactionBegin(); DetourUpdateThread(GetCurrentThread()); DetourAttach(&(PVOID&)TrueSleep, TimedSleep); DetourTransactionCommit(); } else if (dwReason == DLL_PROCESS_DETACH) { DetourTransactionBegin(); DetourUpdateThread(GetCurrentThread()); DetourDetach(&(PVOID&)TrueSleep, TimedSleep); DetourTransactionCommit(); } return TRUE; }

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  • return an ArrayList method

    - by Bopeng Liu
    This is a drive method for two other classes. which i posted here http://codereview.stackexchange.com/questions/33148/book-program-with-arraylist I need some help for the private static ArrayList getAuthors(String authors) method. I am kind a beginner. so please help me finish this drive method. or give me some directions. Instruction some of the elements of the allAuthors array contain asterisks “*” between two authors names. The getAuthors method uses this asterisk as a delimiter between names to store them separately in the returned ArrayList of Strings. import java.util.ArrayList; public class LibraryDrive { public static void main(String[] args) { String[] titles = { "The Hobbit", "Acer Dumpling", "A Christmas Carol", "Marley and Me", "Building Java Programs", "Java, How to Program" }; String[] allAuthors = { "Tolkien, J.R.", "Doofus, Robert", "Dickens, Charles", "Remember, SomeoneIdont", "Reges, Stuart*Stepp, Marty", "Deitel, Paul*Deitel, Harvery" }; ArrayList<String> authors = new ArrayList<String>(); ArrayList<Book> books = new ArrayList<Book>(); for (int i = 0; i < titles.length; i++) { authors = getAuthors(allAuthors[i]); Book b = new Book(titles[i], authors); books.add(b); authors.remove(0); } Library lib = new Library(books); System.out.println(lib); lib.sort(); System.out.println(lib); } private static ArrayList<String> getAuthors(String authors) { ArrayList books = new ArrayList<String>(); // need help here. return books; } }

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  • I need to speed up a function. Should I use cython, ctypes, or something else?

    - by Peter Stewart
    I'm having a lot of fun learning Python by writing a genetic programming type of application. I've had some great advice from Torsten Marek, Paul Hankin and Alex Martelli on this site. The program has 4 main functions: generate (randomly) an expression tree. evaluate the fitness of the tree crossbreed mutate As all of generate, crossbreed and mutate call 'evaluate the fitness'. it is the busiest function and is the primary bottleneck speedwise. As is the nature of genetic algorithms, it has to search an immense solution space so the faster the better. I want to speed up each of these functions. I'll start with the fitness evaluator. My question is what is the best way to do this. I've been looking into cython, ctypes and 'linking and embedding'. They are all new to me and quite beyond me at the moment but I look forward to learning one and eventually all of them. The 'fitness function' needs to compare the value of the expression tree to the value of the target expression. So it will consist of a postfix evaluator which will read the tree in a postfix order. I have all the code in python. I need advice on which I should learn and use now: cython, ctypes or linking and embedding. Thank you.

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  • Is it possible to include a Sexpr before the expression has been evaluated in Sweave / R ?

    - by PaulHurleyuk
    Hello, I'm writing a Sweave document, and I want to include a small section that details the R and package versions, platofrms and how long ti took to evalute the doucment, however, I want to put this in the middle of the document ! I was using a \Sexpr{elapsed} to do this (which didn't work), but thought if I put the code printing elapsed in a chunk that evaluates at the end, I could then include the chunk half way through, which also fails. My document looks something like this % \documentclass[a4paper]{article} \usepackage[OT1]{fontenc} \usepackage{longtable} \usepackage{geometry} \usepackage{Sweave} \geometry{left=1.25in, right=1.25in, top=1in, bottom=1in} \begin{document} <<label=start, echo=FALSE, include=FALSE>>= startt<-proc.time()[3] @ Text and Sweave Code in here % This document was created on \today, with \Sexpr{print(version$version.string)} running on a \Sexpr{print(version$platform)} platform. It took approx sec to process. <<>>= <<elapsed>> @ More text and Sweave code in here <<label=bye, include=FALSE, echo=FALSE>>= odbcCloseAll() endt<-proc.time()[3] elapsedtime<-as.numeric(endt-startt) @ <<label=elapsed, include=FALSE, echo=FALSE>>= print(elapsedtime) @ \end{document} But this doesn't seem to work (amazingly !) Does anyone know how I could do this ? Thanks Paul.

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  • Sweave can't see a vector if run from a function ?

    - by PaulHurleyuk
    I have a function that sets a vector to a string, copies a Sweave document with a new name and then runs that Sweave. Inside the Sweave document I want to use the vector I set in the function, but it doesn't seem to see it. (Edit: I changed this function to use tempdir(() as suggested by Dirk) I created a sweave file test_sweave.rnw; % \documentclass[a4paper]{article} \usepackage[OT1]{fontenc} \usepackage{Sweave} \begin{document} \title{Test Sweave Document} \author{gb02413} \maketitle <<>>= ls() Sys.time() print(paste("The chosen study was ",chstud,sep="")) @ \end{document} and I have this function; onOK <- function(){ chstud<-"test" message(paste("Chosen Study is ",chstud,sep="")) newfile<-paste(chstud,"_report",sep="") mypath<-paste(tempdir(),"\\",sep="") setwd(mypath) message(paste("Copying test_sweave.Rnw to ",paste(mypath,newfile,".Rnw",sep=""),sep="")) file.copy("c:\\local\\test_sweave.Rnw", paste(mypath,newfile,".Rnw",sep=""), overwrite=TRUE) Sweave(paste(mypath,newfile,".Rnw",sep="")) require(tools) texi2dvi(file = paste(mypath,newfile,".tex",sep=""), pdf = TRUE) } If I run the code from the function directly, the resulting file has this output for ls(); > ls() [1] "chstud" "mypath" "newfile" "onOK" However If I call onOK() I get this output; > ls() [1] "onOK" and the print(...chstud...)) function generates an error. I suspect this is an environment problem, but I assumed because the call to Sweave occurs within the onOK function, it would be in the same enviroment, and would see all the objects created within the function. How can I get the Sweave process to see the chstud vector ? Thanks Paul.

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  • How can I write a unit test to determine whether an object can be garbage collected?

    - by driis
    In relation to my previous question, I need to check whether a component that will be instantiated by Castle Windsor, can be garbage collected after my code has finished using it. I have tried the suggestion in the answers from the previous question, but it does not seem to work as expected, at least for my code. So I would like to write a unit test that tests whether a specific object instance can be garbage collected after some of my code has run. Is that possible to do in a reliable way ? EDIT I currently have the following test based on Paul Stovell's answer, which succeeds: [TestMethod] public void ReleaseTest() { WindsorContainer container = new WindsorContainer(); container.Kernel.ReleasePolicy = new NoTrackingReleasePolicy(); container.AddComponentWithLifestyle<ReleaseTester>(LifestyleType.Transient); Assert.AreEqual(0, ReleaseTester.refCount); var weakRef = new WeakReference(container.Resolve<ReleaseTester>()); Assert.AreEqual(1, ReleaseTester.refCount); GC.Collect(); GC.WaitForPendingFinalizers(); Assert.AreEqual(0, ReleaseTester.refCount, "Component not released"); } private class ReleaseTester { public static int refCount = 0; public ReleaseTester() { refCount++; } ~ReleaseTester() { refCount--; } } Am I right assuming that, based on the test above, I can conclude that Windsor will not leak memory when using the NoTrackingReleasePolicy ?

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