package jalview.hmmer;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Preferences;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.util.MessageManager;

import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Map;

public class HMMBuildThread implements Runnable
{

  AlignFrame af;
  AlignmentI alignment;

  long barID;

  Map<Integer, SequenceI> hmmSeqs;
  
  public HMMBuildThread(AlignFrame af)
  {
    this.af = af;
    alignment = af.getViewport().getAlignment();
  }

  @Override
  public void run()
  {
    barID = System.currentTimeMillis();
    af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
            barID);
    HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);

    try
    {
    try
    {
        hmmSeqs = alignment.getHMMConsensusSequences(true);
        HMMERCommands.exportData(alignment, true, false,
                new HiddenMarkovModel());
    } catch (FileNotFoundException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();

    }
    try
    {
      runCommand();
    } catch (IOException | InterruptedException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
    try
    {
      importData();
    } catch (IOException | InterruptedException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
    } catch (Exception e)
    {

    } finally
    {
      af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
              barID);
    }
  }

  

  
  private void runCommand() throws IOException, InterruptedException
  {
    final String command = HMMERCommands.HMMERFOLDER
            + HMMERCommands.HMMBUILD + HMMERCommands.NAME
            + af.getName() + HMMERCommands.SPACE
            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
    HMMERCommands.runCommand(command);
  }
  
  private void importData() throws IOException, InterruptedException
  {
    af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
            FileFormat.HMMER3, null);
    for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
    {
      SequenceI seq = entry.getValue();
      Integer pos = entry.getKey();
      HMMERCommands.addHMMConsensusSequence(af, seq, pos);
    }
    af.alignPanel.alignmentChanged();
  }
  
  
  
 
}