package jalview.hmmer;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.HMMFile;
import jalview.io.StockholmFile;

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.Hashtable;
import java.util.List;

/**
 * Contains multiple commands and methods frequently used to run hmmbuild,
 * hmmalign and hmmsearch
 * 
 * @author TZVanaalten
 *
 */
public class HMMERCommands
{
  // Path of hmmer binaries directory
  String HMMERFOLDER = "/Documents/";

  public String JALVIEWDIRECTORY = System.getProperty("user.dir")
          + "/";

  public final String HMMALIGN = "/hmmalign ";

  public final String HMMBUILD = "/hmmbuild ";

  public final String HMMSEARCH = "/hmmsearch ";

  public String OUTPUTALIGNMENT;

  public final String NAME = "-n ";

  public final String SPACE = " ";

  public final String ALLCOL = "--allcol ";

  public final String TRIM = "--trim ";

  public final String FORCEAMINO = "--amino ";

  public final String FORCEDNA = "--dna ";

  public final String FORCERNA = "--rna ";

  Hashtable hash = new Hashtable();

  List<SequenceI> hmmSeqs;

  /**
   * Uniquifies the sequences when exporting and stores their details in a
   * hashtable.
   * 
   * @param seqs
   */
  public void uniquifySequences(SequenceI[] seqs)
  {
    hash = jalview.analysis.SeqsetUtils.uniquify(seqs, true);
  }

  /**
   * Recover the sequence data lost by uniquifying.
   * 
   * @param seqs
   */
  public void recoverSequenceNames(SequenceI[] seqs)
  {
    jalview.analysis.SeqsetUtils.deuniquify(hash, seqs);
  }

  /**
   * Runs a command in the command line.
   * 
   * @param command
   * @throws IOException
   * @throws InterruptedException
   */
  public boolean runCommand(String command)
          throws IOException, InterruptedException
  {
    try
    {
    final Process p = Runtime.getRuntime().exec(command);

    new Thread(new Runnable()
    {
      @Override
      public void run()
      {
        BufferedReader input = new BufferedReader(
                new InputStreamReader(p.getInputStream()));
        String line = null;

        try
        {
          while ((line = input.readLine()) != null)
          {
            System.out.println(line);
          }
        } catch (IOException e)
        {
          e.printStackTrace();
        }
      }
    }).start();

    p.waitFor();
    } catch (Exception e)
    {
      e.printStackTrace();
      return false;
    }
    return true;
  }

  /**
   * Exports an alignment and/or HMM to the specified file.
   * 
   * @param alignment
   * @throws IOException
   */
  public void exportData(SequenceI[] seqs,
          File stoLocation, HiddenMarkovModel hmm, File hmmLocation)
          throws IOException
  {
    if (seqs != null)
    {
      StockholmFile file = new StockholmFile(new Alignment(seqs));
      String output = file.print(seqs, false);
      PrintWriter writer = new PrintWriter(stoLocation);
      writer.println(output);
      writer.close();
    }

    if (hmm != null)
    {
      HMMFile file = new HMMFile(hmm);
      PrintWriter writer = new PrintWriter(hmmLocation);
      writer.print(file.print());
      writer.close();
    }
  }

  /**
   * Adds any HMM sequences removed before submitting the alignment as a job
   * back into the alignment.
   * 
   * @param af
   */
  public void addHMMConsensusSequences(AlignFrame af)
  {
    AlignmentI al = af.getViewport().getAlignment();
    if (hmmSeqs == null || hmmSeqs.size() < 1)
    {
      return;
    }
    for (SequenceI seq : hmmSeqs)
    {
      Integer position = seq.getPreviousPosition();
      al.getSequences().add(position, seq);
    }
    af.getViewport().setAlignment(al);
    af.alignPanel.adjustAnnotationHeight();
    af.getViewport().updateSequenceIdColours();
    af.buildSortByAnnotationScoresMenu();
    af.getViewport().initInformation();
  }

  /**
   * Returns the list of HMM sequences removed
   * 
   * @return
   */
  public List<SequenceI> getHmmSeqs()
  {
    return hmmSeqs;
  }

  /**
   * Sets the list of removed HMM sequences
   * 
   * @param hmmSeqs
   */
  public void setHmmSeqs(List<SequenceI> hmmSeqs)
  {
    this.hmmSeqs = hmmSeqs;
  }
}