package jalview.hmmer;

import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StockholmFile;
import jalview.util.FileUtils;
import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import javax.swing.JOptionPane;

public class JackHMMER extends Search
{

  SequenceI seq = null;

  /**
   * Constructor for the JackhmmerThread
   * 
   * @param af
   */
  public JackHMMER(AlignFrame af, List<ArgumentI> args)
  {
    super(af, args);
  }

  /**
   * Runs the JackhmmerThread: the data on the alignment or group is exported,
   * then the command is executed in the command line and then the data is
   * imported and displayed in a new frame. Call this method directly to execute
   * synchronously, or via start() in a new Thread for asynchronously.
   */
  @Override
  public void run()
  {
    seq = getSequence();
    if (seq == null)
    {
      // shouldn't happen if we got this far
      Cache.log.error("Error: no sequence for jackhmmer");
      return;
    }

    long msgId = System.currentTimeMillis();
    af.setProgressBar(MessageManager.getString("status.running_search"),
            msgId);

    try
    {
      File seqFile = FileUtils.createTempFile("seq", ".sto");
      File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
              ".sto");
      File searchOutputFile = FileUtils.createTempFile("searchOutput",
              ".txt");

      exportStockholm(new SequenceI[] { seq }, seqFile.getAbsoluteFile(),
              null);

      boolean ran = runCommand(searchOutputFile, hitsAlignmentFile,
              seqFile);
      if (!ran)
      {
        JvOptionPane.showInternalMessageDialog(af, MessageManager
                .formatMessage("warn.command_failed", "jackhmmer"));
        return;
      }

      importData(hitsAlignmentFile, seqFile, searchOutputFile);
      // TODO make realignment of search results a step at this level
      // and make it conditional on this.realign
    } catch (IOException | InterruptedException e)
    {
      e.printStackTrace();
    } finally
    {
      af.setProgressBar("", msgId);
    }
  }

  /**
   * Executes an jackhmmer search with the given sequence as input. The database
   * to be searched is a local file as specified by the 'Database' parameter, or
   * the current alignment (written to file) if none is specified.
   * 
   * @param searchOutputFile
   * @param hitsAlignmentFile
   * @param seqFile
   * 
   * @return
   * @throws IOException
   */
  private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
          File seqFile) throws IOException
  {
    String command = getCommandPath(JACKHMMER);
    if (command == null)
    {
      return false;
    }

    List<String> args = new ArrayList<>();
    args.add(command);
    buildArguments(args, searchOutputFile, hitsAlignmentFile, seqFile);

    return runCommand(args);
  }

  /**
   * Imports the data from the temporary file to which the output of jackhmmer was
   * directed.
   */
  private void importData(File inputAlignmentTemp, File seqTemp,
          File searchOutputFile) throws IOException, InterruptedException
  {
    BufferedReader br = new BufferedReader(
            new FileReader(inputAlignmentTemp));
    try
    {
      if (br.readLine() == null)
      {
        JOptionPane.showMessageDialog(af,
                MessageManager.getString("label.no_sequences_found"));
        return;
      }
      StockholmFile file = new StockholmFile(new FileParse(
              inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
      seqs = file.getSeqsAsArray();

      readDomainTable(searchOutputFile, true);

      if (searchAlignment)
      {
        recoverSequences(sequencesHash, seqs);
      }



      int seqCount = seqs.length;


      AlignmentI al = new Alignment(seqs);

      AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
              AlignFrame.DEFAULT_HEIGHT);
      String ttl = "jackhmmer search of " + databaseName + " using "
              + seqs[0].getName();
      Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
              AlignFrame.DEFAULT_HEIGHT);

      seqTemp.delete();
      inputAlignmentTemp.delete();
      searchOutputFile.delete();
    } finally
    {
      if (br != null)
      {
        br.close();
      }
    }
  }




}