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  • Reliable file copy (move) process - mostly Unix/Linux

    - by mfinni
    Short story : We have a need for a rock-solid reliable file mover process. We have source directories that are often being written to that we need to move files from. The files come in pairs - a big binary, and a small XML index. We get a CTL file that defines these file bundles. There is a process that operates on the files once they are in the destination directory; that gets rid of them when it's done. Would rsync do the best job, or do we need to get more complex? Long story as follows : We have multiple sources to pull from : one set of directories are on a Windows machine (that does have Cygwin and an SSH daemon), and a whole pile of directories are on a set of SFTP servers (Most of these are also Windows.) Our destinations are a list of directories on AIX servers. We used to use a very reliable Perl script on the Windows/Cygwin machine when it was our only source. However, we're working on getting rid of that machine, and there are other sources now, the SFTP servers, that we cannot presently run our own scripts on. For security reasons, we can't run the copy jobs on our AIX servers - they have no access to the source servers. We currently have a homegrown Java program on a Linux machine that uses SFTP to pull from the various new SFTP source directories, copies to a local tmp directory, verifies that everything is present, then copies that to the AIX machines, and then deletes the files from the source. However, we're finding any number of bugs or poorly-handled error checking. None of us are Java experts, so fixing/improving this may be difficult. Concerns for us are: With a remote source (SFTP), will rsync leave alone any file still being written? Some of these files are large. From reading the docs, it seems like rysnc will be very good about not removing the source until the destination is reliably written. Does anyone have experience confirming or disproving this? Additional info We will be concerned about the ingestion process that operates on the files once they are in the destination directory. We don't want it operating on files while we are in the process of copying them; it waits until the small XML index file is present. Our current copy job are supposed to copy the XML file last. Sometimes the network has problems, sometimes the SFTP source servers crap out on us. Sometimes we typo the config files and a destination directory doesn't exist. We never want to lose a file due to this sort of error. We need good logs If you were presented with this, would you just script up some rsync? Or would you build or buy a tool, and if so, what would it be (or what technologies would it use?) I (and others on my team) are decent with Perl.

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  • null pointers vs. Null Object Pattern

    - by GlenH7
    Attribution: This grew out of a related P.SE question My background is in C / C++, but I have worked a fair amount in Java and am currently coding C#. Because of my C background, checking passed and returned pointers is second-hand, but I acknowledge it biases my point of view. I recently saw mention of the Null Object Pattern where the idea is than an object is always returned. Normal case returns the expected, populated object and the error case returns empty object instead of a null pointer. The premise being that the calling function will always have some sort of object to access and therefore avoid null access memory violations. So what are the pros / cons of a null check versus using the Null Object Pattern? I can see cleaner calling code with the NOP, but I can also see where it would create hidden failures that don't otherwise get raised. I would rather have my application fail hard (aka an exception) while I'm developing it than have a silent mistake escape into the wild. Can't the Null Object Pattern have similar problems as not performing a null check? Many of the objects I have worked with hold objects or containers of their own. It seems like I would have to have a special case to guarantee all of the main object's containers had empty objects of their own. Seems like this could get ugly with multiple layers of nesting.

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  • What is the use of Association, Aggregation and Composition (Encapsulation) in Classes

    - by SahilMahajanMj
    I have gone through lots of theories about what is encapsulation and the three techniques of implementing it, which are Association, Aggregation and Composition. What i found is, Encapsulation Encapsulation is the technique of making the fields in a class private and providing access to the fields via public methods. If a field is declared private, it cannot be accessed by anyone outside the class, thereby hiding the fields within the class. For this reason, encapsulation is also referred to as data hiding. Encapsulation can be described as a protective barrier that prevents the code and data being randomly accessed by other code defined outside the class. Access to the data and code is tightly controlled by an interface. The main benefit of encapsulation is the ability to modify our implemented code without breaking the code of others who use our code. With this feature Encapsulation gives maintainability, flexibility and extensibility to our code. Association Association is a relationship where all object have their own lifecycle and there is no owner. Let’s take an example of Teacher and Student. Multiple students can associate with single teacher and single student can associate with multiple teachers but there is no ownership between the objects and both have their own lifecycle. Both can create and delete independently. Aggregation Aggregation is a specialize form of Association where all object have their own lifecycle but there is ownership and child object can not belongs to another parent object. Let’s take an example of Department and teacher. A single teacher can not belongs to multiple departments, but if we delete the department teacher object will not destroy. We can think about “has-a” relationship. Composition Composition is again specialize form of Aggregation and we can call this as a “death” relationship. It is a strong type of Aggregation. Child object dose not have their lifecycle and if parent object deletes all child object will also be deleted. Let’s take again an example of relationship between House and rooms. House can contain multiple rooms there is no independent life of room and any room can not belongs to two different house if we delete the house room will automatically delete. The question is: Now these all are real world examples. I am looking for some description about how to use these techniques in actual class code. I mean what is the point for using three different techniques for encapsulation, How these techniques could be implemented and How to choose which technique is applicable at time.

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  • Validation and Error Generation when using the Data Mapper Pattern

    - by AndyPerlitch
    I am working on saving state of an object to a database using the data mapper pattern, but I am looking for suggestions/guidance on the validation and error message generation step (step 4 below). Here are the general steps as I see them for doing this: (1) The data mapper is used to get current info (assoc array) about the object in db: +=====================================================+ | person_id | name | favorite_color | age | +=====================================================+ | 1 | Andy | Green | 24 | +-----------------------------------------------------+ mapper returns associative array, eg. Person_Mapper::getPersonById($id) : $person_row = array( 'person_id' => 1, 'name' => 'Andy', 'favorite_color' => 'Green', 'age' => '24', ); (2) the Person object constructor takes this array as an argument, populating its fields. class Person { protected $person_id; protected $name; protected $favorite_color; protected $age; function __construct(array $person_row) { $this->person_id = $person_row['person_id']; $this->name = $person_row['name']; $this->favorite_color = $person_row['favorite_color']; $this->age = $person_row['age']; } // getters and setters... public function toArray() { return array( 'person_id' => $this->person_id, 'name' => $this->name, 'favorite_color' => $this->favorite_color, 'age' => $this->age, ); } } (3a) (GET request) Inputs of an HTML form that is used to change info about the person is populated using Person::getters <form> <input type="text" name="name" value="<?=$person->getName()?>" /> <input type="text" name="favorite_color" value="<?=$person->getFavColor()?>" /> <input type="text" name="age" value="<?=$person->getAge()?>" /> </form> (3b) (POST request) Person object is altered with the POST data using Person::setters $person->setName($_POST['name']); $person->setFavColor($_POST['favorite_color']); $person->setAge($_POST['age']); *(4) Validation and error message generation on a per-field basis - Should this take place in the person object or the person mapper object? - Should data be validated BEFORE being placed into fields of the person object? (5) Data mapper saves the person object (updates row in the database): $person_mapper->savePerson($person); // the savePerson method uses $person->toArray() // to get data in a more digestible format for the // db gateway used by person_mapper Any guidance, suggestions, criticism, or name-calling would be greatly appreciated.

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  • Object Oriented Design Questions

    - by Robert
    Hello there. I am going to develop a Tic-Tac-Toe game using Java(or maybe other OO Languages).Now I have a picture in my mind about the general design. Interface: Player ,then I will be able to implement a couple of Player classes,based on how I want the opponent to be,for example,random player,intelligent player. Classes: Board class,with a two-dimensional array of integers,0 indicates open,1 indicates me,-1 indicates opponent.The evaluation function will be in here as well,to return the next best move based on the current board arrangement and whose turn it is. Refree class,which will create instance of the Board and two player instances,then get the game begin. This is a rough idea of my OO design,could anybody give me any critiques please,I find this is really beneficial,thank you very much.

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  • Object.Watch with disabled attribute

    - by Benjamin Fleming
    <html> <head> <script type="text/javascript"> window.onload = function() { var btn = document.getElementById("button"); var tog = document.getElementById("toggle"); tog.onclick = function() { if(btn.disabled) { btn.disabled = false; } else { btn.disabled = true; } }; //btn.watch("disabled", function(prop, val, newval) { }); }; </script> </head> <body> <input type="button" value="Button" id="button" /> <input type="button" value="Toggle" id="toggle" /> </body> </html> If you test this code, the Toggle button will successfully enable and disable the other button. However, un-commenting the btn.watch() line will somehow always set the disabled tag to true. Any ideas?

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  • Class Design - Returning a List<Object> From <Object>

    - by Mike
    Given a simple class: public class Person { public string FirstName; public string LastName; public string GetFullName() { return FirstName + LastName; } } The user of this class will populate a List<Person> object by reading an Xml file or some other data source. Should the logic for populating the List be in the Person class or should it just remain in the calling class? In other words, should there be a public List<Persons> GetPersons() method in the Person class or in the calling class? Or should the data accessor be in another class altogether? I know this is a rather simplistic question but I'm just curious how others typically do it.

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  • WPF ComboBox Object Binding - not updating DataContext Object

    - by Jaysen
    Hello, I have the following scenario: 1 class called 'Widget' with the properties: ID, Code, Description 1 class called 'MyWidget' with a property: m_Widget As Widget 1 ComboBox The ComboBox has a List(Of Widget) set as the ItemSource. I create an instance of 'MyWidget' named MyWidget1 and I set the property values of the m_Widget to match one of the items in the 'ComboBox List(Of Widget)'. I then set the DataContext of the ComboBox to MyWidget1.Widget. When I change the ComboBox selected item, only the ID property of 'MyWidget1.Widget' gets updated... How do I get the object 'Widget' on 'MyWidget1' to be updated instead of just 'MyWidget1.Widget.ID'? Here is a link to a sample project demonstrating this scenario: http://www.webpersona.com/ObjectBinding.zip Thanks in advance for any help :)

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  • How to determine whether a dependency object implements a given dependency property (C# / WPF)

    - by Tim Coulter
    I am working with the classes in the System.Windows.Documents namespace, trying to write some generic code that will conditionally set the value of certain dependency properties, depending on whether these properties exist on a given class. For example, the following method assigns an arbitrary value to the Padding property of the passed FrameworkContentElement: void SetElementPadding(FrameworkContentElement element) { element.SetValue(Block.PaddingProperty, new Thickness(155d)); } However, not all concrete implementations of FrameworkContentElement have a Padding property (Paragraph does but Span does not) so I would expect the property assignment to succeed for types that implement this property and to be silently ignored for types that do not. But it seems that the above property assignment succeeds for instances of all derivatives of FrameworkContentElement, regardless of whether they implement the Padding property. I make this assumption because I have always been able to read back the assigned value. I assume there is some flaw in the way I am assigning property values. What should I do to ensure that a given dependency property assignment is ignored by classes that do not implement that property? Many thanks for your advice. Tim

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  • Object declaration in Objective-C

    - by Sahat
    Is there any difference in declaring objects in Objective-C between (1) and (2), besides the style and personal preference? (1) One-line declaration, allocation, initialization. Student *myStudent = [[Student alloc] init]; (2) Multi-line declaration, allocation, initialization. Student *myStudent; myStudent = [Student alloc]; myStudent = [myStudent init];

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  • find(:all) and then add data from another table to the object

    - by Koning Baard XIV
    I have two tables: create_table "friendships", :force => true do |t| t.integer "user1_id" t.integer "user2_id" t.boolean "hasaccepted" t.datetime "created_at" t.datetime "updated_at" end and create_table "users", :force => true do |t| t.string "email" t.string "password" t.string "phone" t.boolean "gender" t.datetime "created_at" t.datetime "updated_at" t.string "firstname" t.string "lastname" t.date "birthday" end I need to show the user a list of Friendrequests, so I use this method in my controller: def getfriendrequests respond_to do |format| case params[:id] when "to_me" @friendrequests = Friendship.find(:all, :conditions => { :user2_id => session[:user], :hasaccepted => false }) when "from_me" @friendrequests = Friendship.find(:all, :conditions => { :user1_id => session[:user], :hasaccepted => false }) end format.xml { render :xml => @friendrequests } format.json { render :json => @friendrequests } end end I do nearly everything using AJAX, so to fetch the First and Last name of the user with UID user2_id (the to_me param comes later, don't worry right now), I need a for loop which make multiple AJAX calls. This sucks and costs much bandwidth. So I'd rather like that getfriendrequests also returns the First and Last name of the corresponding users, so, e.g. the JSON response would not be: [ { "friendship": { "created_at": "2010-02-19T13:51:31Z", "user1_id": 2, "updated_at": "2010-02-19T13:51:31Z", "hasaccepted": false, "id": 11, "user2_id": 3 } }, { "friendship": { "created_at": "2010-02-19T16:31:23Z", "user1_id": 2, "updated_at": "2010-02-19T16:31:23Z", "hasaccepted": false, "id": 12, "user2_id": 4 } } ] but rather: [ { "friendship": { "created_at": "2010-02-19T13:51:31Z", "user1_id": 2, "updated_at": "2010-02-19T13:51:31Z", "hasaccepted": false, "id": 11, "user2_id": 3, "firstname": "Jon", "lastname": "Skeet" } }, { "friendship": { "created_at": "2010-02-19T16:31:23Z", "user1_id": 2, "updated_at": "2010-02-19T16:31:23Z", "hasaccepted": false, "id": 12, "user2_id": 4, "firstname": "Mark", "lastname": "Gravell" } } ] I thought of a for loop in the getfriendrequests method, but I don't know how to implement this, and maybe there is an easier way. It must also work for XML. Can anyone help me? Thanks

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  • copying the request header from request object to urlConnection object

    - by Bunny Rabbit
    protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { // TODO Auto-generated method stub URL url = new URL("http://localhost:8080/testy/Out"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setDoOutput(true); connection.setRequestMethod("POST"); PrintWriter out=response.getWriter(); for(Enumeration e=request.getHeaderNames();e.hasMoreElements();){ Object o=e.nextElement(); String value=request.getHeader(o.toString()); out.println(o+"--is--"+value+"<br>"); connection.setRequestProperty((String) o, value); } connection.connect(); } i wrote the above code in a servlet to post form so some alternate locations than this servlet,but its not working.is it okay to use connection.setRequestProperty to set the header fields to what they are in the incoming request to servlet.

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  • wpf c# databinding on object

    - by Enriquev
    Hello, say I have this control: public partial class bloc999 : UserControl { bloc999Data mainBlock = new bloc999Data(); public bloc999() { InitializeComponent(); mainBlock.txtContents = "100"; base.DataContext = mainBlock; } } in the xaml: <TextBox Margin="74,116,106,0" Name="txtContents" Text="{Binding Path=txtContents, UpdateSourceTrigger=PropertyChanged,Mode = TwoWay}" /> <TextBox Margin="74,145,106,132" Name="txtContents2" Text="{Binding Path=txtContents2, UpdateSourceTrigger=PropertyChanged,Mode = TwoWay}" /> Then I have this class: public class bloc999Data : INotifyPropertyChanged { string _txtContents; string _txtContents2; public event PropertyChangedEventHandler PropertyChanged; void NotifyPropertyChanged(string propName) { if (this.PropertyChanged != null) this.PropertyChanged( this, new PropertyChangedEventArgs(propName)); } public string txtContents2 { get { return this._txtContents2; } set { if (int.Parse(value) > int.Parse(this._txtContents)) { this._txtContents2 = "000"; } else this._txtContents2 = value; NotifyPropertyChanged("txtContents2"); } } public string txtContents { get { return this._txtContents; } set { this._txtContents = value; NotifyPropertyChanged("txtContents"); } } } Ok now say I have A button on the form and I do this in the code: mainBlock.txtContents2 = "7777777"; It puts 000 in the textbox, but If i just type in manually, in the textbox (txtContents2, the setter code is called but for some reason the textboxes value does not change, the instance value does change. help?

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  • how does object programming work?

    - by venom
    Hello, I am not sure about some things in oop. If I have Class1, which has some private field, for example private Field field1, and make getField1(){return field1;} then I have some class with constructor public Class2(Field field){someMethod(field);} And then I call constructor of Class2 in Class3 like: Class2 cl = new Class2(instanceOfClass1.getField1()); And now the question: Am I working with field1 of instanceOfClass1 in "someMethod(field)"?

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  • Returning new object, overwrite the existing one in Java

    - by lupin
    Note: This is an assignment. Hi, Ok I have this method that will create a supposedly union of 2 sets. i mport java.io.*; class Set { public int numberOfElements; public String[] setElements; public int maxNumberOfElements; // constructor for our Set class public Set(int numberOfE, int setE, int maxNumberOfE) { this.numberOfElements = numberOfE; this.setElements = new String[setE]; this.maxNumberOfElements = maxNumberOfE; } // Helper method to shorten/remove element of array since we're using basic array instead of ArrayList or HashSet from collection interface :( static String[] removeAt(int k, String[] arr) { final int L = arr.length; String[] ret = new String[L - 1]; System.arraycopy(arr, 0, ret, 0, k); System.arraycopy(arr, k + 1, ret, k, L - k - 1); return ret; } int findElement(String element) { int retval = 0; for ( int i = 0; i < setElements.length; i++) { if ( setElements[i] != null && setElements[i].equals(element) ) { return retval = i; } retval = -1; } return retval; } void add(String newValue) { int elem = findElement(newValue); if( numberOfElements < maxNumberOfElements && elem == -1 ) { setElements[numberOfElements] = newValue; numberOfElements++; } } int getLength() { if ( setElements != null ) { return setElements.length; } else { return 0; } } String[] emptySet() { setElements = new String[0]; return setElements; } Boolean isFull() { Boolean True = new Boolean(true); Boolean False = new Boolean(false); if ( setElements.length == maxNumberOfElements ){ return True; } else { return False; } } Boolean isEmpty() { Boolean True = new Boolean(true); Boolean False = new Boolean(false); if ( setElements.length == 0 ) { return True; } else { return False; } } void remove(String newValue) { for ( int i = 0; i < setElements.length; i++) { if ( setElements[i] != null && setElements[i].equals(newValue) ) { setElements = removeAt(i,setElements); } } } int isAMember(String element) { int retval = -1; for ( int i = 0; i < setElements.length; i++ ) { if (setElements[i] != null && setElements[i].equals(element)) { return retval = i; } } return retval; } void printSet() { for ( int i = 0; i < setElements.length; i++) { if (setElements[i] != null) { System.out.println("Member elements on index: "+ i +" " + setElements[i]); } } } String[] getMember() { String[] tempArray = new String[setElements.length]; for ( int i = 0; i < setElements.length; i++) { if(setElements[i] != null) { tempArray[i] = setElements[i]; } } return tempArray; } Set union(Set x, Set y) { String[] newXtemparray = new String[x.getLength()]; String[] newYtemparray = new String[y.getLength()]; int len = newYtemparray.length + newXtemparray.length; Set temp = new Set(0,len,len); newXtemparray = x.getMember(); newYtemparray = x.getMember(); for(int i = 0; i < newYtemparray.length; i++) { temp.add(newYtemparray[i]); } for(int j = 0; j < newXtemparray.length; j++) { temp.add(newXtemparray[j]); } return temp; } Set difference(Set x, Set y) { String[] newXtemparray = new String[x.getLength()]; String[] newYtemparray = new String[y.getLength()]; int len = newYtemparray.length + newXtemparray.length; Set temp = new Set(0,len,len); newXtemparray = x.getMember(); newYtemparray = x.getMember(); for(int i = 0; i < newXtemparray.length; i++) { temp.add(newYtemparray[i]); } for(int j = 0; j < newYtemparray.length; j++) { int retval = temp.findElement(newYtemparray[j]); if( retval != -1 ) { temp.remove(newYtemparray[j]); } } return temp; } } // This is the SetDemo class that will make use of our Set class class SetDemo { public static void main(String[] args) { //get input from keyboard BufferedReader keyboard; InputStreamReader reader; String temp = ""; reader = new InputStreamReader(System.in); keyboard = new BufferedReader(reader); try { System.out.println("Enter string element to be added" ); temp = keyboard.readLine( ); System.out.println("You entered " + temp ); } catch (IOException IOerr) { System.out.println("There was an error during input"); } /* ************************************************************************** * Test cases for our new created Set class. * ************************************************************************** */ Set setA = new Set(0,10,10); setA.add(temp); setA.add("b"); setA.add("b"); setA.add("hello"); setA.add("world"); setA.add("six"); setA.add("seven"); setA.add("b"); int size = setA.getLength(); System.out.println("Set size is: " + size ); Boolean isempty = setA.isEmpty(); System.out.println("Set is empty? " + isempty ); int ismember = setA.isAMember("sixb"); System.out.println("Element sixb is member of setA? " + ismember ); Boolean output = setA.isFull(); System.out.println("Set is full? " + output ); //setA.printSet(); int index = setA.findElement("world"); System.out.println("Element b located on index: " + index ); setA.remove("b"); //setA.emptySet(); int resize = setA.getLength(); System.out.println("Set size is: " + resize ); //setA.printSet(); Set setB = new Set(0,10,10); setB.add("b"); setB.add("z"); setB.add("x"); setB.add("y"); Set setC = setA.union(setB,setA); System.out.println("Elements of setA"); setA.printSet(); System.out.println("Union of setA and setB"); setC.printSet(); } } The union method works a sense that somehow I can call another method on it but it doesn't do the job, i supposedly would create and union of all elements of setA and setB but it only return element of setB. Sample output follows: java SetDemo Enter string element to be added hello You entered hello Set size is: 10 Set is empty? false Element sixb is member of setA? -1 Set is full? true Element b located on index: 2 Set size is: 9 Elements of setA Member elements on index: 0 hello Member elements on index: 1 world Member elements on index: 2 six Member elements on index: 3 seven Union of setA and setB Member elements on index: 0 b Member elements on index: 1 z Member elements on index: 2 x Member elements on index: 3 y thanks, lupin

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  • property not updating in object when page is posted

    - by Jared
    Hi I have set a property in a constructor like so function __construct() { $this->count = count(@$_SESSION['filearray']); //count how many files in array } and using it in condition statements if($this->count > 10) //then do something but it appears the count isn't being updated when I use another method of injecting values into this 'filearray' until I refresh the page. am I doing something wrong? I thought that my constructor would detect a change had been made in the session and whenever I call $this-count I would get the current count value but it seems to be 1 step behind until I refresh the page. If this is all vague I can include my form page that has all the method calls, but this is the jist of my question, why is my property not updating and how do I fix it :) TIA

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  • Copy mdf file and use it in run time

    - by Anibas
    After I copy mdf file (and his log file) I tries to Insert data. I receive the following message: "An attempt to attach an auto-named database for file [fileName].mdf failed. A database with the same name exists, or specified file cannot be opened, or it is located on UNC share. When I copied the file manual everything worked normally. Is it correct the order File.Copy leaves the file engaged?

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  • getting an error on jslint while creating a new object using javascript

    - by user3712689
    For some reason this code is giving a lint. I can't really figure out why. It says: 'was expecting a assignment or function call, and instead saw an expression.' What does that mean? window.onload = function (){ function SuspectOne (naam, leeftijd, wie){ this.naam = Spencer Hawes; this.leeftijd = 22; this.wie = zoon van de man; } function SuspectTwo (naam, leeftijd, wie){ this.naam = Tyrone Biggums; this.leeftijd = 28; this.wie = lokale herionejunk; } function SuspectThree (naam, leeftijd, wie){ this.naam = Ellie Campbell Hawes; this.leeftijd = 40; this.wie = vrouw van de man; } var verdachten = new Array[]; verdachten[0] = new Verdachte("Spencer Hawes", 22, "zoon van de man"); verdachten[1] = new Verdachte("Tyrone Biggums", 28, "lokale herionejunk"); verdachten[2] = new Verdachte("Ellie Spencer Hawes", 40, "vrouw van de man"); for(x=0; x<verdachten.length; x++){ console.log("De verdachte is de " + verdachten[x].leeftijd + "jaar oud " + verdachten[x].naam + ", de " + verdachten[x].wie); } }; Can someone help me with this? I would really like a lint free code.

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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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