package jalview.hmmer;

import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.HiddenMarkovModel;
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 jalview.ws.params.simple.BooleanOption;
import jalview.ws.params.simple.Option;

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

import javax.swing.JOptionPane;

public class HMMSearch extends Search
{

  boolean realign = false;

  boolean trim = false;

  boolean returnNoOfNewSeqs = false;

  int seqsToReturn = Integer.MAX_VALUE;


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

  /**
   * Runs the HMMSearchThread: 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()
  {
    HiddenMarkovModel hmm = getHmmProfile();
    if (hmm == null)
    {
      // shouldn't happen if we got this far
      Cache.log.error("Error: no hmm for hmmsearch");
      return;
    }

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

    try
    {
      File hmmFile = FileUtils.createTempFile("hmm", ".hmm");
      File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
              ".sto");
      File searchOutputFile = FileUtils.createTempFile("searchOutput",
              ".sto");

      exportHmm(hmm, hmmFile.getAbsoluteFile());

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

      importData(hmmSeq, hitsAlignmentFile, hmmFile, 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 hmmsearch with the given hmm 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 hmmFile
   * 
   * @return
   * @throws IOException
   */
  private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
          File hmmFile) throws IOException
  {
    String command = getCommandPath(HMMSEARCH);
    if (command == null)
    {
      return false;
    }

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

    return runCommand(args);
  }


  /**
   * Imports the data from the temporary file to which the output of hmmsearch
   * was directed. The results are optionally realigned using hmmalign.
   * 
   * @param hmmSeq
   */
  private void importData(SequenceI hmmSeq, File inputAlignmentTemp,
          File hmmTemp, 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, false);

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

      // look for PP cons and ref seq in alignment only annotation
      AlignmentAnnotation modelpos = null, ppcons = null;
      for (AlignmentAnnotation aa : file.getAnnotations())
      {
        if (aa.sequenceRef == null)
        {
          if (aa.label.equals("Reference Positions")) // RF feature type in
                                                      // stockholm parser
          {
            modelpos = aa;
          }
          if (aa.label.equals("Posterior Probability"))
          {
            ppcons = aa;
          }
        }
      }


      int seqCount = Math.min(seqs.length, seqsToReturn);
      SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
      hmmSeq = hmmSeq.deriveSequence(); // otherwise all bad things happen
      hmmAndSeqs[0] = hmmSeq;
      System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
      if (modelpos != null)
      {
        // TODO need - get ungapped sequence method
        hmmSeq.setSequence(
                hmmSeq.getDatasetSequence().getSequenceAsString());
        Annotation[] refpos = modelpos.annotations;
        // insert gaps to match with refseq positions
        int gc = 0, lcol = 0;
        for (int c = 0; c < refpos.length; c++)
        {
          if (refpos[c] != null && ("x".equals(refpos[c].displayCharacter)))
          {
            if (gc > 0)
            {
              hmmSeq.insertCharAt(lcol + 1, gc, '-');
            }
            gc = 0;
            lcol = c;
          }
          else
          {
            gc++;
          }
        }
      }

      if (realign)
      {
        realignResults(hmmAndSeqs);
      }
      else
      {
        AlignmentI al = new Alignment(hmmAndSeqs);
        if (ppcons != null)
        {
          al.addAnnotation(ppcons);
        }
        if (modelpos != null)
        {
          al.addAnnotation(modelpos);
        }
        AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
                AlignFrame.DEFAULT_HEIGHT);
        String ttl = "hmmSearch of " + databaseName + " using "
                + hmmSeq.getName();
        Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
                AlignFrame.DEFAULT_HEIGHT);

        if (returnNoOfNewSeqs)
        {
          int nNew = checkForNewSequences();
          JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
                  + MessageManager.getString("label.new_returned"));
        }

      }


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

  private int checkForNewSequences()
  {
    int nNew = seqs.length;

    for (SequenceI resultSeq : seqs)
    {
      for (SequenceI aliSeq : alignment.getSequencesArray())
      {
        if (resultSeq.getName().equals(aliSeq.getName()))
        {
          nNew--;
          break;
        }
      }
    }

    return nNew;

  }

  /**
   * Realigns the given sequences using hmmalign, to the HMM profile sequence
   * which is the first in the array, and opens the results in a new frame
   * 
   * @param hmmAndSeqs
   */
  protected void realignResults(SequenceI[] hmmAndSeqs)
  {
    /*
     * and align the search results to the HMM profile
     */
    AlignmentI al = new Alignment(hmmAndSeqs);
    AlignFrame frame = new AlignFrame(al, 1, 1);
    List<ArgumentI> alignArgs = new ArrayList<>();
    String alignTo = hmmAndSeqs[0].getName();
    List<String> options = Collections.singletonList(alignTo);
    Option option = new Option(MessageManager.getString("label.use_hmm"),
            "", true, alignTo, alignTo, options, null);
    alignArgs.add(option);
    if (trim)
    {
      alignArgs.add(new BooleanOption(
              MessageManager.getString(TRIM_TERMINI_KEY),
              MessageManager.getString("label.trim_termini_desc"), true,
              true, true, null));
    }
    HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
    hmmalign.run();

    if (returnNoOfNewSeqs)
    {
      int nNew = checkForNewSequences();
      JvOptionPane.showMessageDialog(frame.alignPanel,
              nNew + " " + MessageManager.getString("label.new_returned"));
    }
  }

}