740 lines
24 KiB
Java
740 lines
24 KiB
Java
package com.smi.SickleCell;
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import androidx.annotation.MainThread;
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import androidx.annotation.NonNull;
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import androidx.appcompat.app.AppCompatActivity;
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import androidx.appcompat.app.AppCompatDelegate;
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import androidx.core.app.ActivityCompat;
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import androidx.core.content.ContextCompat;
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import android.Manifest;
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import android.content.ContentValues;
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import android.content.Intent;
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import android.content.SharedPreferences;
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import android.content.pm.PackageManager;
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import android.graphics.Color;
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import android.net.Uri;
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import android.os.Bundle;
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import android.os.Environment;
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import android.provider.Settings;
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import android.util.Log;
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import android.view.Gravity;
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import android.view.View;
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import android.widget.AdapterView;
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import android.widget.ArrayAdapter;
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import android.widget.Button;
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import android.widget.RelativeLayout;
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import android.widget.Spinner;
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import android.widget.TableLayout;
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import android.widget.TableRow;
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import android.widget.TextView;
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import android.widget.Toast;
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import com.google.android.gms.tasks.OnCompleteListener;
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import com.google.android.gms.tasks.Task;
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import com.google.firebase.database.DatabaseReference;
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import com.google.firebase.database.FirebaseDatabase;
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import com.opencsv.CSVReader;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.FileReader;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.text.SimpleDateFormat;
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import java.util.Calendar;
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import java.util.HashMap;
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public class MainActivity extends AppCompatActivity implements AdapterView.OnItemSelectedListener {
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private Button confirmatory, screening;
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private static final int REQUEST_CODE_PICK_FILE = 300;
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String FilePath;
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private TextView result;
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float number1;
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float number2;
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private String TestRandomKey, saveCurrentDate, saveCurrentTime;
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private DatabaseReference TestRef;
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private TextView result_confirmatory;
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String device;
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String result_test;
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String result_test1;
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String targetUri;
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TextView Type;
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String line;
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TableLayout table;
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RelativeLayout relativeLayout1;
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String Extension;
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String directory_path;
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float value;
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int columnCount = 0;
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int flag = 0;
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String serial_no, sample_name, numbers1, numbers2, ratios, resultsamp;
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File file = null;
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@Override
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protected void onCreate(Bundle savedInstanceState) {
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super.onCreate(savedInstanceState);
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setContentView(R.layout.activity_main);
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String directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
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screening = findViewById(R.id.screening);
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confirmatory = findViewById(R.id.confirmatory);
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relativeLayout1 = findViewById(R.id.RelativeLayout1);
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table = findViewById(R.id.table_main);
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TestRef = FirebaseDatabase.getInstance().getReference().child("Test_Data");
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Type = findViewById(R.id.type);
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AppCompatDelegate.setDefaultNightMode(AppCompatDelegate.MODE_NIGHT_YES);
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Spinner Spinner_type = findViewById(R.id.spinner_device);
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ArrayAdapter<CharSequence> adapter = ArrayAdapter.createFromResource(this,
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R.array.instrument, android.R.layout.simple_spinner_item);
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adapter.setDropDownViewResource(android.R.layout.simple_spinner_dropdown_item);
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Spinner_type.setAdapter(adapter);
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Spinner_type.setOnItemSelectedListener(this);
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result = findViewById(R.id.result);
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result_confirmatory = findViewById(R.id.result_confirmatory);
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if (android.os.Build.VERSION.SDK_INT > android.os.Build.VERSION_CODES.Q) {
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if (!Environment.isExternalStorageManager()) {
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Intent intent = new Intent();
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intent.setAction(Settings.ACTION_MANAGE_APP_ALL_FILES_ACCESS_PERMISSION);
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Uri uri = Uri.fromParts("package", this.getPackageName(), null);
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intent.setData(uri);
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startActivity(intent);
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}
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}
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if (ContextCompat.checkSelfPermission(this, Manifest.permission.WRITE_EXTERNAL_STORAGE) != PackageManager.PERMISSION_GRANTED) {
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ActivityCompat.requestPermissions(this, new String[]{Manifest.permission.WRITE_EXTERNAL_STORAGE}, 23);
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directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
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File file = new File(directory_path);
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if (!file.exists()) {
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file.mkdirs();
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}
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}
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if (ContextCompat.checkSelfPermission(this, Manifest.permission.READ_EXTERNAL_STORAGE) == PackageManager.PERMISSION_GRANTED) {
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directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
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File file = new File(directory_path);
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if (!file.exists()) {
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file.mkdirs();
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}
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} else {
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// Request permission from the user
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ActivityCompat.requestPermissions(this,
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new String[]{Manifest.permission.READ_EXTERNAL_STORAGE}, 0);
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}
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directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
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File file = new File(directory_path);
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if (!file.exists()) {
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file.mkdirs();
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}
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directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
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file = new File(directory_path);
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if (!file.exists()) {
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file.mkdirs();
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}
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screening.setOnClickListener(new View.OnClickListener() {
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@Override
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public void onClick(View v) {
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flag = 1;
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createfolder();
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selectCSVFile();
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}
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});
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confirmatory.setOnClickListener(new View.OnClickListener() {
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@Override
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public void onClick(View v) {
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flag = 2;
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createfolder();
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selectCSVFile();
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}
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});
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}
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private void selectCSVFile() {
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if (ContextCompat.checkSelfPermission(MainActivity.this, Manifest.permission.WRITE_EXTERNAL_STORAGE) != PackageManager.PERMISSION_GRANTED) {
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ActivityCompat.requestPermissions(MainActivity.this, new String[]{Manifest.permission.WRITE_EXTERNAL_STORAGE}, 23);
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}
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Uri uri = Uri.parse((Environment.getExternalStorageDirectory().getPath() + "/SickleCell/"));
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Intent intent = new Intent(Intent.ACTION_GET_CONTENT);
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intent.setDataAndType(uri, "*/*");
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// intent.setType("*/*");
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startActivityForResult(intent, REQUEST_CODE_PICK_FILE);
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}
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@Override
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protected void onActivityResult(int requestCode, int resultCode, Intent data) {
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super.onActivityResult(requestCode, resultCode, data);
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switch (requestCode) {
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case REQUEST_CODE_PICK_FILE: {
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if (resultCode == RESULT_OK) {
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Log.e("file", data.getData().getPath());
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FilePath = data.getData().getPath();
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Log.e("Filepath", FilePath);
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String filename1 = FilePath.substring(FilePath.lastIndexOf("/") + 1);
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Log.e("file", filename1);
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Extension = FilePath.substring(FilePath.lastIndexOf("."));
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Log.e("Entension ", Extension);
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String s = FilePath;
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directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
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targetUri = directory_path + filename1;
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if (!Extension.contains("csv")) {
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Type.setText("Wrong file Format");
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result.setText("");
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Type.setTextColor(Color.RED);
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result_confirmatory.setText("");
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} else if (flag == 1) {
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ImportCSV(new File(targetUri));
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} else if (flag == 2) {
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ImportCSV2(new File(targetUri));
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}
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}
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}
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}
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}
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private void ImportCSV(File from) {
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result_confirmatory.setText("");
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result.setText("");
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value = 0;
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number1 = 0;
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number2 = 0;
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resultsamp = "";
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table.removeAllViews();
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try {
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CSVReader reader = new CSVReader(new FileReader(from));
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String[] line;
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InputStream inputStream = new FileInputStream(from);
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BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
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String[] header = reader.readNext(); // assuming first read
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if (header != null) { // and there is a (header) line
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columnCount = header.length; // get the column count
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}
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Log.e("columc", String.valueOf(columnCount));
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if (device.equals("TestRight")) {
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result_confirmatory.setText("");
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result.setText("");
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resultsamp = "";
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Type.setText(" Select Test Type * ");
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Type.setTextColor(Color.WHITE);
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if (columnCount > 100) {
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Type.setText("Wrong File");
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Type.setTextColor(Color.RED);
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} else {
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Log.e("device", "Test right");
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while ((line = reader.readNext()) != null) {
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String[] values = line;
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if (values[0].equals("427.084")) {
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number1 = Float.parseFloat(String.valueOf(values[1]));
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Log.e("number1", String.valueOf(number1));
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} else if (values[0].equals("555.035")) {
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number2 = Float.parseFloat(String.valueOf(values[1]));
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Log.e("number2", String.valueOf(number2));
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}
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}
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if (number1 != 0 || number2 != 0) {
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value = number2 / number1;
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Log.e("value", String.valueOf(value));
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if (value < 0.16 || value == 0.0) {
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result.setText("Negative");
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result_test = result.getText().toString();
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result_test1 = result_confirmatory.getText().toString();
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} else {
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result.setText("Positive");
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result_test = result.getText().toString();
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result_test1 = result_confirmatory.getText().toString();
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}
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} else {
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result_confirmatory.setText("");
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result.setText("");
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Type.setText("Wrong File");
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Type.setTextColor(Color.RED);
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value = 0;
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}
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}
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} else if (device.equals("Denovix")) {
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result_confirmatory.setText("");
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result.setText("");
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result_confirmatory.setText("");
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result.setText("");
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Type.setText(" Select Test Type * ");
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Type.setTextColor(Color.WHITE);
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resultsamp = "";
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Log.e("device", "denovix");
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if (columnCount < 100) {
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result_confirmatory.setText("");
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result.setText("");
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Type.setText("Wrong file");
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Type.setTextColor(Color.RED);
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} else {
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init1();
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while ((line = reader.readNext()) != null) {
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String[] values = line;
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if (values[1].equals("Blank")) {
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continue;
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}
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if ((values[262].replaceAll("[^\\d.]", "")).equals("427") || (values[390].replaceAll("[^\\d.]", "")).equals("555")) {
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continue; //just skip the rows if row number is 0 or 1
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} else {
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number1 = Float.parseFloat(String.valueOf(values[262].replaceAll("[^\\d.]", "")));
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Log.e("number1", String.valueOf(number1));
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number2 = Float.parseFloat(String.valueOf(values[390]).replaceAll("[^\\d.]", ""));
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Log.e("number2", String.valueOf(number2));
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}
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if (number1 != 0 || number2 != 0) {
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value = number2 / number1;
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Log.e("value", String.valueOf(value));
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if (value < 0.16 || value == 0.0) {
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resultsamp = "Negative";
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} else {
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resultsamp = "Positive";
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}
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} else if (columnCount < 100) {
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result_confirmatory.setText("");
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result.setText("");
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Type.setText("Wrong file");
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Type.setTextColor(Color.RED);
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}
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serial_no = values[0];
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sample_name = values[1];
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numbers1 = values[262];
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numbers2 = values[390];
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ratios = String.valueOf(value);
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init(serial_no, sample_name, ratios, resultsamp);
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}
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}
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}
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} catch (IOException ex) {
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throw new RuntimeException("Error in reading CSV file: " + ex);
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}
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}
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private void ImportCSV2(File from) {
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result_confirmatory.setText("");
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result.setText("");
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value = 0;
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number1 = 0;
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number2 = 0;
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table.removeAllViews();
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try {
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CSVReader reader = new CSVReader(new FileReader(from));
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String[] line;
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InputStream inputStream = new FileInputStream(from);
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BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
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String[] header = reader.readNext(); // assuming first read
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if (header != null) { // and there is a (header) line
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columnCount = header.length; // get the column count
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}
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Log.e("columc", String.valueOf(columnCount));
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if (device.equals("TestRight")) {
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resultsamp = "";
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result_confirmatory.setText("");
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result.setText("");
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Type.setText(" Select Test Type * ");
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Type.setTextColor(Color.WHITE);
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if (columnCount > 100) {
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Type.setText("Wrong File");
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Type.setTextColor(Color.RED);
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} else {
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Log.e("device", "Test right");
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while ((line = reader.readNext()) != null) {
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String[] values = line;
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if (values[0].equals("427.084")) {
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number1 = Float.parseFloat(String.valueOf(values[1]));
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Log.e("number1", String.valueOf(number1));
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} else if (values[0].equals("555.035")) {
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number2 = Float.parseFloat(String.valueOf(values[1]));
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Log.e("number2", String.valueOf(number2));
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}
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}
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if (number1 != 0 || number2 != 0) {
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value = number2 / number1;
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Log.e("value", String.valueOf(value));
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if (value < 0.16 || value == 0.0) {
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result.setText("Negative");
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result_test = result.getText().toString();
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result_test1 = result_confirmatory.getText().toString();
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} else {
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result.setText("Positive");
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result_test = result.getText().toString();
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result_test1 = result_confirmatory.getText().toString();
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}
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if (value >= 0.16 && value < 0.24) {
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result_confirmatory.setText("Sickle Cell Trait");
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result_test = result.getText().toString();
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result_test1 = result_confirmatory.getText().toString();
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} else if (value >= 0.24) {
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result_confirmatory.setText("Sickle-Cell Disease");
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result_test = result.getText().toString();
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result_test1 = result_confirmatory.getText().toString();
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}
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} else {
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result_confirmatory.setText("");
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result.setText("");
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Type.setText("Wrong File");
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Type.setTextColor(Color.RED);
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value = 0;
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}
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}
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} else if (device.equals("Denovix")) {
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resultsamp = "";
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result_confirmatory.setText("");
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result.setText("");
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result_confirmatory.setText("");
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result.setText("");
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Type.setText(" Select Test Type * ");
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Type.setTextColor(Color.WHITE);
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Log.e("device", "denovix");
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if (columnCount < 100) {
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result_confirmatory.setText("");
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result.setText("");
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Type.setText("Wrong file");
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Type.setTextColor(Color.RED);
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} else {
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init1();
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while ((line = reader.readNext()) != null) {
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String[] values = line;
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if (values[1].equals("Blank")) {
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continue;
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}
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if ((values[262].replaceAll("[^\\d.]", "")).equals("427") || (values[390].replaceAll("[^\\d.]", "")).equals("555")) {
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continue; //just skip the rows if row number is 0 or 1
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} else {
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number1 = Float.parseFloat(String.valueOf(values[262].replaceAll("[^\\d.]", "")));
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Log.e("number1", String.valueOf(number1));
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number2 = Float.parseFloat(String.valueOf(values[390]).replaceAll("[^\\d.]", ""));
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Log.e("number2", String.valueOf(number2));
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}
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if (number1 != 0 || number2 != 0) {
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value = number2 / number1;
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Log.e("value", String.valueOf(value));
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if (value < 0.16 || value == 0.0) {
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resultsamp = "Negative";
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} else {
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resultsamp = "Positive";
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}
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if (value >= 0.16 && value < 0.24) {
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resultsamp = "Sickle Cell Trait ";
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} else if (value > 0.24) {
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resultsamp = "Sickle-Cell Disease";
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}
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} else if (columnCount < 100) {
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result_confirmatory.setText("");
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result.setText("");
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Type.setText("Wrong file");
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Type.setTextColor(Color.RED);
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}
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serial_no = values[0];
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sample_name = values[1];
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numbers1 = values[262];
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numbers2 = values[390];
|
|
ratios = String.valueOf(value);
|
|
init(serial_no, sample_name, ratios, resultsamp);
|
|
|
|
|
|
}
|
|
}
|
|
|
|
}
|
|
} catch (IOException ex) {
|
|
|
|
throw new RuntimeException("Error in reading CSV file: " + ex);
|
|
}
|
|
|
|
|
|
}
|
|
|
|
@Override
|
|
public void onItemSelected(AdapterView<?> parent, View view, int position, long id) {
|
|
if (parent.getId() == R.id.spinner_device) {
|
|
device = parent.getItemAtPosition(position).toString();
|
|
|
|
}
|
|
|
|
}
|
|
|
|
@Override
|
|
public void onNothingSelected(AdapterView<?> parent) {
|
|
|
|
}
|
|
|
|
private void createfolder() {
|
|
directory_path = Environment.getExternalStorageDirectory().getPath() + "/SickleCell/";
|
|
file = new File(directory_path);
|
|
if (!file.exists()) {
|
|
file.mkdirs();
|
|
}
|
|
|
|
}
|
|
|
|
|
|
private void SaveTestInfoToDatabase() {
|
|
HashMap<String, Object> productMap = new HashMap<>();
|
|
productMap.put("Value", String.valueOf(value));
|
|
productMap.put("number1", String.valueOf(number1));
|
|
productMap.put("number2", String.valueOf(number2));
|
|
productMap.put("Device", device);
|
|
productMap.put("Result", result_test);
|
|
productMap.put("Result Confirmatory", result_test1);
|
|
productMap.put("Directory Path", directory_path);
|
|
productMap.put("Full Path", targetUri);
|
|
|
|
|
|
// productMap("Result",String.valueOf(result.getText().toString()));
|
|
|
|
|
|
Calendar calendar = Calendar.getInstance();
|
|
|
|
SimpleDateFormat currentDate = new SimpleDateFormat("MMM dd, yyyy");
|
|
|
|
saveCurrentDate = currentDate.format(calendar.getTime());
|
|
saveCurrentDate = saveCurrentDate.replaceAll("[^A-Za-z0-9 ]", "");
|
|
|
|
|
|
SimpleDateFormat currentTime = new SimpleDateFormat("h:mm a");
|
|
saveCurrentTime = currentTime.format(calendar.getTime());
|
|
|
|
TestRandomKey = saveCurrentDate + saveCurrentTime + String.valueOf(Math.random());
|
|
TestRandomKey = TestRandomKey.replaceAll("[^A-Za-z0-9 ]", "");
|
|
|
|
|
|
TestRef.child(TestRandomKey).updateChildren(productMap)
|
|
.addOnCompleteListener(new OnCompleteListener<Void>() {
|
|
@Override
|
|
public void onComplete(@NonNull Task<Void> task) {
|
|
if (task.isSuccessful()) {
|
|
|
|
|
|
Toast.makeText(MainActivity.this, "Test Result added in backend successfully ", Toast.LENGTH_SHORT).show();
|
|
|
|
|
|
} else {
|
|
|
|
String message = task.getException().toString();
|
|
Toast.makeText(MainActivity.this, "Error: " + message, Toast.LENGTH_SHORT).show();
|
|
}
|
|
}
|
|
});
|
|
}
|
|
|
|
|
|
public void init1() {
|
|
|
|
TableLayout stk = (TableLayout) findViewById(R.id.table_main);
|
|
|
|
|
|
TableRow tbrow0 = new TableRow(this);
|
|
tbrow0.setBackgroundResource(R.color.purple_700);
|
|
|
|
TextView tv0 = new TextView(this);
|
|
tv0.setText(" S.No ");
|
|
tbrow0.addView(tv0);
|
|
TextView tv1 = new TextView(this);
|
|
tv1.setText(" Name sample ");
|
|
tbrow0.addView(tv1);
|
|
|
|
|
|
TextView tv2 = new TextView(this);
|
|
tv2.setText(" Ratio ");
|
|
tbrow0.addView(tv2);
|
|
|
|
|
|
TextView tv3 = new TextView(this);
|
|
tv3.setText("Result ");
|
|
tbrow0.addView(tv3);
|
|
stk.addView(tbrow0);
|
|
|
|
|
|
}
|
|
|
|
|
|
public void init(String sno, String samplename, String ratio, String result) {
|
|
|
|
TableLayout stk = (TableLayout) findViewById(R.id.table_main);
|
|
TableRow tbrow = new TableRow(this);
|
|
TextView t1v = new TextView(this);
|
|
t1v.setText("" + sno + " ");
|
|
t1v.setBackgroundResource(R.drawable.cellshape);
|
|
|
|
t1v.setGravity(Gravity.CENTER);
|
|
tbrow.addView(t1v);
|
|
TextView t2v = new TextView(this);
|
|
t2v.setText(samplename + " ");
|
|
t2v.setBackgroundResource(R.drawable.cellshape);
|
|
|
|
t2v.setGravity(Gravity.CENTER);
|
|
tbrow.addView(t2v);
|
|
|
|
|
|
TextView t5v = new TextView(this);
|
|
t5v.setText(ratio + " ");
|
|
t5v.setGravity(Gravity.CENTER);
|
|
tbrow.addView(t5v);
|
|
t5v.setBackgroundResource(R.drawable.cellshape);
|
|
|
|
|
|
TextView t6v = new TextView(this);
|
|
t6v.setText(" " + result);
|
|
t6v.setGravity(Gravity.LEFT);
|
|
t6v.setBackgroundResource(R.drawable.cellshape);
|
|
|
|
tbrow.addView(t6v);
|
|
|
|
|
|
stk.addView(tbrow);
|
|
|
|
|
|
}
|
|
|
|
|
|
} |