Merge pull request #176 from SanojPunchihewa/dev

Rename package name to genopo
SanojPunchihewa · May 21, 2020 · 65478bf · 65478bf
2 parents 3753fb4 + 2a0b857
commit 65478bf
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Showing 56 changed files with 213 additions and 215 deletions.
diff --git a/app/build.gradle b/app/build.gradle
@@ -14,7 +14,7 @@ android {
 
     compileSdkVersion 28
     defaultConfig {
-        applicationId "com.mobilegenomics.f5n"
+        applicationId "com.mobilegenomics.genopo"
         minSdkVersion 21
         targetSdkVersion 28
         versionCode gitVersionCode
@@ -25,7 +25,7 @@ android {
             versionName "${gitBranch}-${gitCommitHash}"
         }
 
-        setProperty("archivesBaseName", "mobilegenomics-f5n-v$versionName")
+        setProperty("archivesBaseName", "mobilegenomics-genopo-v$versionName")
         testInstrumentationRunner "androidx.test.runner.AndroidJUnitRunner"
         externalNativeBuild {
             cmake {

diff --git a/...genomics/f5n/ExampleInstrumentedTest.java → ...omics/genopo/ExampleInstrumentedTest.java b/...genomics/f5n/ExampleInstrumentedTest.java → ...omics/genopo/ExampleInstrumentedTest.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n;
+package com.mobilegenomics.genopo;
 
 import static org.junit.Assert.*;
 

diff --git a/app/src/main/AndroidManifest.xml b/app/src/main/AndroidManifest.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="utf-8"?>
 <manifest xmlns:android="http://schemas.android.com/apk/res/android"
     xmlns:tools="http://schemas.android.com/tools"
-    package="com.mobilegenomics.f5n">
+    package="com.mobilegenomics.genopo">
 
     <uses-permission android:name="android.permission.WRITE_EXTERNAL_STORAGE" />
     <uses-permission android:name="android.permission.READ_EXTERNAL_STORAGE" />
     <uses-permission android:name="android.permission.INTERNET" />
     <uses-permission android:name="android.permission.WRITE_SETTINGS" />
 
     <application
-        android:name=".Application"
+        android:name="com.mobilegenomics.genopo.Application"
         android:allowBackup="true"
         android:icon="@mipmap/launcher"
         android:label="@string/app_name"
@@ -18,55 +18,55 @@
         android:usesCleartextTraffic="true"
         tools:ignore="GoogleAppIndexingWarning">
         <activity
-            android:name=".activity.SettingsActivity"
+            android:name="com.mobilegenomics.genopo.activity.SettingsActivity"
             android:label="@string/title_activity_settings" />
-        <activity android:name=".activity.MainActivity">
+        <activity android:name="com.mobilegenomics.genopo.activity.MainActivity">
             <intent-filter>
                 <action android:name="android.intent.action.MAIN" />
 
                 <category android:name="android.intent.category.LAUNCHER" />
             </intent-filter>
         </activity>
         <activity
-            android:name=".activity.PipelineActivity"
+            android:name="com.mobilegenomics.genopo.activity.PipelineActivity"
             android:label="Select Steps" />
 
         <activity
-            android:name=".activity.StepActivity"
+            android:name="com.mobilegenomics.genopo.activity.StepActivity"
             android:label="Configure tool GUI Mode" />
 
         <activity
-            android:name=".activity.ConfirmationActivity"
+            android:name="com.mobilegenomics.genopo.activity.ConfirmationActivity"
             android:label="Pipeline Execution" />
 
         <activity
-            android:name=".activity.DownloadActivity"
+            android:name="com.mobilegenomics.genopo.activity.DownloadActivity"
             android:label="Download and Extract" />
 
         <activity
-            android:name=".activity.MinITActivity"
+            android:name="com.mobilegenomics.genopo.activity.MinITActivity"
             android:label="Connect to F5N Server" />
 
         <activity
-            android:name=".activity.TerminalActivity"
+            android:name="com.mobilegenomics.genopo.activity.TerminalActivity"
             android:label="Configure tool Terminal Mode" />
 
         <activity
-            android:name=".activity.HelpActivity"
+            android:name="com.mobilegenomics.genopo.activity.HelpActivity"
             android:label="Help" />
 
         <activity
-            android:name=".activity.TutorialActivity"
+            android:name="com.mobilegenomics.genopo.activity.TutorialActivity"
             android:label="How To" />
 
         <activity
-            android:name=".activity.DemoActivity"
+            android:name="com.mobilegenomics.genopo.activity.DemoActivity"
             android:label="Demo Mode" />
         <activity
-            android:name=".activity.ChoosePipelineActivity"
+            android:name="com.mobilegenomics.genopo.activity.ChoosePipelineActivity"
             android:label="Choose a Pipeline" />
         <activity
-            android:name=".activity.ArticPipelineActivity"
+            android:name="com.mobilegenomics.genopo.activity.ArticPipelineActivity"
             android:label="Artic Pipeline" />
     </application>
 

diff --git a/...a/com/mobilegenomics/f5n/Application.java → ...om/mobilegenomics/genopo/Application.java b/...a/com/mobilegenomics/f5n/Application.java → ...om/mobilegenomics/genopo/Application.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n;
+package com.mobilegenomics.genopo;
 
 import android.content.Context;
 import android.util.Log;

diff --git a/.../mobilegenomics/f5n/GUIConfiguration.java → ...bilegenomics/genopo/GUIConfiguration.java b/.../mobilegenomics/f5n/GUIConfiguration.java → ...bilegenomics/genopo/GUIConfiguration.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n;
+package com.mobilegenomics.genopo;
 
 import android.content.Context;
 import android.util.Log;
@@ -7,17 +7,17 @@
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
-import com.mobilegenomics.f5n.core.AppMode;
-import com.mobilegenomics.f5n.core.Argument;
-import com.mobilegenomics.f5n.core.ArticPipelineArgument;
-import com.mobilegenomics.f5n.core.PipelineComponent;
-import com.mobilegenomics.f5n.core.PipelineStep;
-import com.mobilegenomics.f5n.core.PipelineType;
-import com.mobilegenomics.f5n.core.Step;
-import com.mobilegenomics.f5n.support.JSONFileHelper;
-import com.mobilegenomics.f5n.support.PipelineState;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
-import com.mobilegenomics.f5n.support.TimeFormat;
+import com.mobilegenomics.genopo.core.AppMode;
+import com.mobilegenomics.genopo.core.Argument;
+import com.mobilegenomics.genopo.core.ArticPipelineArgument;
+import com.mobilegenomics.genopo.core.PipelineComponent;
+import com.mobilegenomics.genopo.core.PipelineStep;
+import com.mobilegenomics.genopo.core.PipelineType;
+import com.mobilegenomics.genopo.core.Step;
+import com.mobilegenomics.genopo.support.JSONFileHelper;
+import com.mobilegenomics.genopo.support.PipelineState;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
+import com.mobilegenomics.genopo.support.TimeFormat;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;

diff --git a/...s/f5n/activity/ArticPipelineActivity.java → ...enopo/activity/ArticPipelineActivity.java b/...s/f5n/activity/ArticPipelineActivity.java → ...enopo/activity/ArticPipelineActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.annotation.SuppressLint;
 import android.content.ClipData;
@@ -26,13 +26,13 @@
 import android.widget.Toast;
 import androidx.annotation.Nullable;
 import androidx.appcompat.app.AppCompatActivity;
-import com.mobilegenomics.f5n.GUIConfiguration;
-import com.mobilegenomics.f5n.R;
-import com.mobilegenomics.f5n.core.ArticPipelineArgument;
-import com.mobilegenomics.f5n.core.PipelineType;
-import com.mobilegenomics.f5n.core.Step;
-import com.mobilegenomics.f5n.support.PipelineState;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
+import com.mobilegenomics.genopo.GUIConfiguration;
+import com.mobilegenomics.genopo.R;
+import com.mobilegenomics.genopo.core.ArticPipelineArgument;
+import com.mobilegenomics.genopo.core.PipelineType;
+import com.mobilegenomics.genopo.core.Step;
+import com.mobilegenomics.genopo.support.PipelineState;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
 import com.obsez.android.lib.filechooser.ChooserDialog;
 import java.io.File;
 import java.util.ArrayList;

diff --git a/.../f5n/activity/ChoosePipelineActivity.java → ...nopo/activity/ChoosePipelineActivity.java b/.../f5n/activity/ChoosePipelineActivity.java → ...nopo/activity/ChoosePipelineActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.content.DialogInterface;
 import android.content.Intent;
@@ -10,11 +10,11 @@
 import androidx.annotation.Nullable;
 import androidx.appcompat.app.AlertDialog;
 import androidx.appcompat.app.AppCompatActivity;
-import com.mobilegenomics.f5n.GUIConfiguration;
-import com.mobilegenomics.f5n.R;
-import com.mobilegenomics.f5n.core.AppMode;
-import com.mobilegenomics.f5n.core.PipelineType;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
+import com.mobilegenomics.genopo.GUIConfiguration;
+import com.mobilegenomics.genopo.R;
+import com.mobilegenomics.genopo.core.AppMode;
+import com.mobilegenomics.genopo.core.PipelineType;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
 
 public class ChoosePipelineActivity extends AppCompatActivity {
 

diff --git a/...cs/f5n/activity/ConfirmationActivity.java → ...genopo/activity/ConfirmationActivity.java b/...cs/f5n/activity/ConfirmationActivity.java → ...genopo/activity/ConfirmationActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.content.ContentResolver;
 import android.content.DialogInterface;
@@ -30,16 +30,16 @@
 import androidx.appcompat.app.AlertDialog;
 import androidx.appcompat.app.AppCompatActivity;
 import androidx.core.widget.NestedScrollView;
-import com.mobilegenomics.f5n.GUIConfiguration;
-import com.mobilegenomics.f5n.R;
-import com.mobilegenomics.f5n.core.AppMode;
-import com.mobilegenomics.f5n.core.NativeCommands;
-import com.mobilegenomics.f5n.core.PipelineComponent;
-import com.mobilegenomics.f5n.support.FileUtil;
-import com.mobilegenomics.f5n.support.PipelineState;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
-import com.mobilegenomics.f5n.support.ScreenDimUtil;
-import com.mobilegenomics.f5n.support.TimeFormat;
+import com.mobilegenomics.genopo.GUIConfiguration;
+import com.mobilegenomics.genopo.R;
+import com.mobilegenomics.genopo.core.AppMode;
+import com.mobilegenomics.genopo.core.NativeCommands;
+import com.mobilegenomics.genopo.core.PipelineComponent;
+import com.mobilegenomics.genopo.support.FileUtil;
+import com.mobilegenomics.genopo.support.PipelineState;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
+import com.mobilegenomics.genopo.support.ScreenDimUtil;
+import com.mobilegenomics.genopo.support.TimeFormat;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;

diff --git a/...legenomics/f5n/activity/DemoActivity.java → ...enomics/genopo/activity/DemoActivity.java b/...legenomics/f5n/activity/DemoActivity.java → ...enomics/genopo/activity/DemoActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.content.Intent;
 import android.content.res.ColorStateList;
@@ -19,19 +19,19 @@
 import androidx.annotation.Nullable;
 import androidx.appcompat.app.AppCompatActivity;
 import com.liulishuo.okdownload.core.cause.EndCause;
-import com.mobilegenomics.f5n.GUIConfiguration;
-import com.mobilegenomics.f5n.R;
-import com.mobilegenomics.f5n.core.MethylationPipelineStep;
-import com.mobilegenomics.f5n.core.PipelineStep;
-import com.mobilegenomics.f5n.core.PipelineType;
-import com.mobilegenomics.f5n.core.VariantPipelineStep;
-import com.mobilegenomics.f5n.support.DownloadListener;
-import com.mobilegenomics.f5n.support.FileUtil;
-import com.mobilegenomics.f5n.support.PipelineState;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
-import com.mobilegenomics.f5n.support.TimeFormat;
-import com.mobilegenomics.f5n.support.ZipListener;
-import com.mobilegenomics.f5n.support.ZipManager;
+import com.mobilegenomics.genopo.GUIConfiguration;
+import com.mobilegenomics.genopo.R;
+import com.mobilegenomics.genopo.core.MethylationPipelineStep;
+import com.mobilegenomics.genopo.core.PipelineStep;
+import com.mobilegenomics.genopo.core.PipelineType;
+import com.mobilegenomics.genopo.core.VariantPipelineStep;
+import com.mobilegenomics.genopo.support.DownloadListener;
+import com.mobilegenomics.genopo.support.FileUtil;
+import com.mobilegenomics.genopo.support.PipelineState;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
+import com.mobilegenomics.genopo.support.TimeFormat;
+import com.mobilegenomics.genopo.support.ZipListener;
+import com.mobilegenomics.genopo.support.ZipManager;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -175,8 +175,8 @@ private void downloadDataSet(String url) {
 
         writeToLogFile("Downloading data set...\n");
 
-        com.mobilegenomics.f5n.support.DownloadManager
-                downloadManager = new com.mobilegenomics.f5n.support.DownloadManager(url,
+        com.mobilegenomics.genopo.support.DownloadManager
+                downloadManager = new com.mobilegenomics.genopo.support.DownloadManager(url,
                 Environment.getExternalStorageDirectory() + "/" + folderName, statusTextView,
                 progressBar,
                 new DownloadListener() {

diff --git a/...nomics/f5n/activity/DownloadActivity.java → ...ics/genopo/activity/DownloadActivity.java b/...nomics/f5n/activity/DownloadActivity.java → ...ics/genopo/activity/DownloadActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.annotation.SuppressLint;
 import android.content.res.ColorStateList;
@@ -20,14 +20,14 @@
 import androidx.annotation.Nullable;
 import androidx.appcompat.app.AppCompatActivity;
 import com.liulishuo.okdownload.core.cause.EndCause;
-import com.mobilegenomics.f5n.GUIConfiguration;
-import com.mobilegenomics.f5n.R;
-import com.mobilegenomics.f5n.core.AppMode;
-import com.mobilegenomics.f5n.support.DownloadListener;
-import com.mobilegenomics.f5n.support.DownloadManager;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
-import com.mobilegenomics.f5n.support.ZipListener;
-import com.mobilegenomics.f5n.support.ZipManager;
+import com.mobilegenomics.genopo.GUIConfiguration;
+import com.mobilegenomics.genopo.R;
+import com.mobilegenomics.genopo.core.AppMode;
+import com.mobilegenomics.genopo.support.DownloadListener;
+import com.mobilegenomics.genopo.support.DownloadManager;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
+import com.mobilegenomics.genopo.support.ZipListener;
+import com.mobilegenomics.genopo.support.ZipManager;
 import com.obsez.android.lib.filechooser.ChooserDialog;
 import java.io.File;
 

diff --git a/...legenomics/f5n/activity/HelpActivity.java → ...enomics/genopo/activity/HelpActivity.java b/...legenomics/f5n/activity/HelpActivity.java → ...enomics/genopo/activity/HelpActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.content.Intent;
 import android.graphics.Typeface;
@@ -13,7 +13,7 @@
 import android.widget.TextView;
 import androidx.annotation.Nullable;
 import androidx.appcompat.app.AppCompatActivity;
-import com.mobilegenomics.f5n.R;
+import com.mobilegenomics.genopo.R;
 
 public class HelpActivity extends AppCompatActivity {
 

diff --git a/...legenomics/f5n/activity/MainActivity.java → ...enomics/genopo/activity/MainActivity.java b/...legenomics/f5n/activity/MainActivity.java → ...enomics/genopo/activity/MainActivity.java
@@ -1,4 +1,4 @@
-package com.mobilegenomics.f5n.activity;
+package com.mobilegenomics.genopo.activity;
 
 import android.Manifest;
 import android.content.DialogInterface;
@@ -20,13 +20,13 @@
 import androidx.appcompat.app.AppCompatActivity;
 import androidx.core.app.ActivityCompat;
 import com.google.android.material.snackbar.Snackbar;
-import com.mobilegenomics.f5n.GUIConfiguration;
-import com.mobilegenomics.f5n.R;
-import com.mobilegenomics.f5n.core.AppMode;
-import com.mobilegenomics.f5n.core.PipelineType;
-import com.mobilegenomics.f5n.support.PermissionResultCallback;
-import com.mobilegenomics.f5n.support.PermissionUtils;
-import com.mobilegenomics.f5n.support.PreferenceUtil;
+import com.mobilegenomics.genopo.GUIConfiguration;
+import com.mobilegenomics.genopo.R;
+import com.mobilegenomics.genopo.core.AppMode;
+import com.mobilegenomics.genopo.core.PipelineType;
+import com.mobilegenomics.genopo.support.PermissionResultCallback;
+import com.mobilegenomics.genopo.support.PermissionUtils;
+import com.mobilegenomics.genopo.support.PreferenceUtil;
 import java.util.ArrayList;
 import java.util.Objects;