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I don't understand how to organise my fragments

I have realised an NFC reader application
So i have 3 activities :
MainActivity, which is an activity who contains a Button. If button is clicked, the scan is activated and the user can put his NFC tag against the device to detect it.
WebActivity, who is launched if the NFC tag contains and URL (and open a WebView) or if the user want to launch WebActivity by himself
HistoryActivity, who gonna contains a list of every scans.
Now, I would like to swipe activity with a finger gesture. according to my research on Internet. I need fragments and ViewPager.
But every example that I saw is bases on ONE activity and multiple fragments.
But in my case, I have to create 3 fragments (one per activity), right ?
And I really don't know how to manage my fragment. I mean, what to put inside ?
All I want to do is create a transition/animation while changing activity... That's crazy

This is too broad of a question but hopefully my answer will steer you in right direction.
You should definitely go with single activity/multiple fragments model. Aside of recommendations by Google, you could use navigation components, deep linking much easier then without single activity.
Yes you should be using ViewPager for the purpose (and likely your implementation of FragmentPagerAdapter as well) however I do not understand what kind of swiping will you be doing
Reading your setup, I would suggest to use bottom view with 2 items (good example is here https://github.com/android/architecture-components-samples/tree/master/NavigationAdvancedSample/app/src/main/java/com/example/android/navigationadvancedsample). 2nd one would show history, first one would offer a button that activates your action, and then displays fragment with your WebView.
As a side effect of such implementation, you'd be able to go back from 2nd bottom view item to whatever first one holds - by pressing system back button - which I think is nice touch.
UPDATE to "swiping takes place anytime. " comment:
You could have single activity, ViewPager with 2 fragments. First fragment would display a button, 2nd fragment would display a history. You could freely swipe between them, as you want to. However to me it does not make sense to put WebView screen into this. WebView screen is result of action (NFC detection) and it should probably display as full screen, without any chance of swiping between main/history and itself. Hope it helps or I'm missing some important piece of info you did not share.

How should I structure bottom navigation in Android coming from iOS background?

Some background:
Coming from an iOS background, using UITabbarController is very common and straight forward. Each Tab in the tab controller will change the current view to another UIViewController, and each of these UIViewControllers can have its own NavigationController (which kind of acts as a back stack). So whenever I switch tab, I would resume to the state where I left off.
Now I want to implement the same thing in Android, but it seems like the use of ViewController is different in Android. After digging around, I read that instead of using Activity like UIViewController, I should use Activity to act more like NavigationController, and use Fragments (which is deprecated)
to act as UIViewController instead.
However my question is:
Should I be implementing multiple Activities for Bottom Navigation? When I click on each item in the Bottom Navigation should I use an Intent to change Activity? Because from my understanding, using Intent to change Activity will add the new Activity to an Activity back stack, which would prevent me from switching back to whichever Activity I want. If someone could, Please tell me what is the "right" way (if there is one) to structure Bottom Navigation. Thank you all in advance.

You can use fragments as UIs, And Use a BottomNavigationView in your activity or you can use some libraries.
Here is a library for better customization: https://github.com/ittianyu/BottomNavigationViewEx
Native Method:
https://medium.com/#hitherejoe/exploring-the-android-design-support-library-bottom-navigation-drawer-548de699e8e0

In Android you should use Viewpager, tablayout and Fragments. Just search for its tutorials. there are lots of them on internet

Connection between activity and layout? How to change layout? How to start and destroy an activity?

I'm a total beginner with Android and Eclipse and I have few questions that will help me understand the philosophy of Android:
The activity does all the work "behind the scenes". Activities are connected to a layout in the XML file. When the activity is started, if declared in setContentView method, the connected layout will be shown. Activity can be independent, without any layout, it can be invoked by another activity and will do all the work without showing any layout.
Activity is something like a php file which is invoked by my submit button in HTML, and the layout is .HTML which shows elements.
Am I right with this one?
For example, if I want to change the layout of my app, I want to show Layout2.xml when clicking button in Layout1.xml. Then I have to destroy the activity which is connected with Layout1.xml and start the activity which is connected with Layout2.xml? Is this correct? Is there any better way to do this?
How can I (by which method) destroy/stop a certain activity?
Thank you in an advance.

The best bet is to read the Android documentation regarding activites at http://developer.android.com/reference/android/app/Activity.html
I will answer your specific questions here though
An Activity is a window that the user can see (or a hidden window if there is no layout defined). It deals with the logic of a part of the app that the user can see and interact with. If we take the MVC model (Model View Controller), the Activity is the controller, in terms of it controls which data from the Model is shown on the View (the xml layout).
If you want to show a new window/screen/activity you do not need to destroy the current one. You can open a new activity whilst keeping the old one in the background (in the back stack). With the use of fragments, you can have multiple fragments in an activity so rather than changing activities, you can change fragments in a single activity. For more information about fragments take a look at http://developer.android.com/reference/android/app/Fragment.html.
This point relies heavily on the activity lifecycle. When an activity is destroyed, it means it is finishing and this can be done by the user pressing the back button whilst on the activity, the activity calling finish() on itself or by the Android operating system destroying the activity because memory is required elsewhere (this can happen when the app is in the background).
When we say an activity is stopped, it means that the activity is no longer visible to the user. This can be the case where the activity is in the back stack (another activity is in front of it) or if the app has been put into the background.
This is a brief answer to your questions but I highly recommend you read the Android documentation to gain better knowledge.

Android application design help, How to control which activity shows

Hello I require some advice on how to approach this problem,
bear with me as I am still new to android.
I have an activity that opens on application start and requires some information from the user, but next time the user opens the app, i want the application to open a different activity that will display the various information.
Kind of like facebooks app, where when you first run it, you have to login, and only then next time you run the app you are guided straight to the feed.
Any ideas how one could do this efficiently?
UPDATE: Ive stored the information via shared preferences and am now using a controller activity that decides which step to take.
So, Controller activity runs on start up, and decides whether to show a log in screen or whether to go straight to the information. But now im encountering a problem where i end up opening a blank activity (the controller) and then another ontop of that ( the decided activtiy). I dont want the blank activity to show, so its kinda of like a background process, any ideas?

Ideally you would have a main activity like a controller. Use a SharedPreference object to keep track of whether the user is logged in or not. So back in your main activity, read this value and if it is set go to your news feed activity else show a login screen activity. (as you do the check and redirection, you can show a progress dialog)
links for SharedPreferences
MobTuts
Android Developer

Saving Android application state

I understand how to save an application's state by using SharedPreferences, onSavedInstanceState() & onRestoreInstanceState(), etc as outlined in a similar post ( Saving Android Activity state using Save Instance State ), but how do I save the last activity?
To be more specific, my application starts up and goes to a login screen. Once a user logs in and navigates through several activities, lets say he or she leaves the app using the home button or in some other way. Next time the user starts the app, it will go back to the login screen and do a login again. Instead, I want the app to start up and go to the last activity that was on top of the stack when the user left the app in the previous session.
How is the last activity saved so that it can be restored on app startup?

I believe Android does this automatically. We have an app that we are working on. When I click the home button and them come back to the app, it starts in the activity where I left off. We have not written any code to make this happen. It just seems to work.

My colleague has written an article on Android application state including details on getLastNonConfigurationInstance() which retrieves the instance that was last stored. Take a look here: http://www.eigo.co.uk/Managing-State-in-an-Android-Activity.aspx

Please note that the above answer is correct only on one case: If your process does not get killed by android because the resources (memory, ...) are needed for a different reason.
To get what you describe, I would write a custom parent activity and override the correct life-cycle methods to store your application state and read it and act accordingly. Then let all your activities inherit from MyActivity (instead of android.app.Activity)
public MyActivity extends android.app.Activity {
...
#Override
public onCreate(...) {
// Read the Application state,
// check if the currently launching Activity is the right one,
// if not, start the last Activity and finish the current one.
}
#Override
public onDestroy(...) {
// Store the current Activity ID in the SharedPreferences
}
...
}
Take care to call the super.onDestroy and super.onCreate methods in all your Activites (like you should do anyways).
Happy coding and have fun with Android!