Android Open Source - DIYgenomics_Android Import Activity

From Project

Back to project page DIYgenomics_Android.
License

The source code is released under:
/** * Copyright (C) 2010 DIYgenomics diygenomics.org * Copyright (C) 2010 Melanie Swan mxswan@gmail * Copyright (C) 2010 Michael Kolb * Copyright (C) 2010 Lawrence S. Wong * All rights reserved. * * M...
If you think the Android project DIYgenomics_Android listed in this page is inappropriate, such as containing malicious code/tools or violating the copyright, please email info at java2s dot com, thanks.
Java Source Code

package org.diygenomics.pg;
/*from  w ww . j  a va 2s.c  om*/
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.util.StringTokenizer;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;

import org.diygenomics.pg.Data.LoaderCallback;
import org.diygenomics.pg.utils.MLog;

import android.app.Activity;
import android.content.Intent;
import android.net.Uri;
import android.os.AsyncTask;
import android.os.Bundle;
import android.util.Log;
import android.view.View;
import android.view.View.OnClickListener;
import android.widget.Button;
import android.widget.ProgressBar;


/**
 * the main activity show an initial graphic and a progress spinner while
 * loading the data load data in background
 */
public class ImportActivity extends Activity implements OnClickListener {

  private static final String TAG = "import";
  
  private Object lock;
  private Data mData;
  private ProgressBar mProgress;
  private Button mContinue;
  private Button mCancel;
  private View mLabel;
  private View mWarning;
  private View mButtons;
  
  @Override
  public void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);
    MLog.enable(TAG);
    View view = getLayoutInflater().inflate(R.layout.import_screen, null);
    mButtons = view.findViewById(R.id.buttons);
    mButtons.setVisibility(View.VISIBLE);
    mContinue = (Button) view.findViewById(R.id.cont);
    mCancel = (Button) view.findViewById(R.id.cancel);
    mContinue.setOnClickListener(this);
    mCancel.setOnClickListener(this);
    mWarning = view.findViewById(R.id.warning);
    mWarning.setVisibility(View.VISIBLE);
    mLabel = view.findViewById(R.id.label);
    mLabel.setVisibility(View.GONE);
    mProgress = (ProgressBar) view.findViewById(R.id.progress_bar);
    mProgress.setVisibility(View.GONE);
    mProgress.setProgress(0);
    lock = new Object();
    setContentView(view);
  }

  @Override
  public void onClick(View view) {
    if (view == mCancel) {
      finish();
    } else if (view == mContinue) {
      mButtons.setVisibility(View.GONE);
      mWarning.setVisibility(View.GONE);
      mLabel.setVisibility(View.VISIBLE);
      mProgress.setVisibility(View.VISIBLE);
      mProgress.setProgress(0);
      loadData(getIntent());
    }
  }

  private void loadData(final Intent intent) {
    AsyncTask<Void, Integer, Void> loader = new AsyncTask<Void, Integer, Void>() {

      @Override
      protected Void doInBackground(Void... arg0) {
        MLog.i(TAG, "import a zip file data: ",intent.getData());
        // make sure that the csv data is loaded
        // Main either has the data already loaded, in which case the data is returned
        // if the data is null, it is loaded asynchronously
        //   block this thread until the callback is called
        synchronized(lock) {
          try {
            mData = Main.loadData(ImportActivity.this, new LoaderCallback() {
              public void done(Data data) {
                mData = data;
                synchronized(lock) {
                  MLog.i(TAG,"got loader result");
                  lock.notifyAll();
                }
              }
            });
            if (mData == null) {
              MLog.i(TAG, "waiting for loader");
              lock.wait();
            }
          } catch (InterruptedException e) {
            e.printStackTrace();
          }
        }
        Uri uri = intent.getData();
        try {
          InputStream in = getContentResolver().openInputStream(uri);
          ZipInputStream zin = new ZipInputStream(in);
          ZipEntry entry = zin.getNextEntry();
          if (entry != null) {
            MLog.i(TAG, "found a zip entry: ",entry.getName()," size: ",entry.getSize());
            long total = entry.getSize();
            BufferedReader reader = new BufferedReader(new InputStreamReader(zin));
            BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(openFileOutput(Data.FILE_GENOME, MODE_APPEND)));
            int count = 0;
            int bread = 0;
            int lineCounter = 0;
            while (true) {
              String line = reader.readLine();
              if (line != null) {
                bread += line.length();
                lineCounter++;
                if ((total != -1) && (lineCounter % 100 == 0)) {
                  publishProgress((int)(bread * 100 / total));
                }
                if (!line.startsWith("#")) {
                  StringTokenizer st = new StringTokenizer(line);
                  String snip = st.nextToken();
                  st.nextToken();
                  st.nextToken();
                  String gtype = st.nextToken();
                  if (mData.getVariantMap().get(snip) != null) {
                    writer.append(snip);
                    writer.append(",");
                    writer.append(gtype);
                    writer.append("\n");
                    count++;
                  } else {
                  }
                }
              } else {
                break;
              }
            }
            reader.close();
            writer.close();
            mData.loadGenome(ImportActivity.this);
            MLog.i(TAG, "found ",count," relevant snips");
          }
          zin.close();
        } catch (FileNotFoundException e) {
          e.printStackTrace();
        } catch (IOException e) {
          Log.e(TAG,"ioerror: "+e);
          e.printStackTrace();
        }
        return null;
      }
      
        protected void onProgressUpdate(Integer... progress) {
          final ProgressBar p = mProgress;
          p.setProgress(progress[0]);
         }
      
      protected void onPostExecute(Void result) {
        done();
      }
    };
    loader.execute((Void) null);
  }

  public void done() {
    startActivity(new Intent(ImportActivity.this, CategoriesActivity.class));
  }


}
Java Source Code List
