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.Hashtable;
import java.util.List;
import java.util.Scanner;

import javax.swing.JOptionPane;

public class HMMSearch extends HmmerCommand
{
  static final String HMMSEARCH = "hmmsearch";

  boolean realign = false;

  boolean trim = false;

  boolean returnNoOfNewSeqs = false;

  int seqsToReturn = Integer.MAX_VALUE;

  boolean searchAlignment = true;

  SequenceI[] seqs;

  private String databaseName;

  Hashtable sequencesHash;

  /**
   * 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);
  }

  /**
   * Appends command line arguments to the given list, to specify input and
   * output files for the search, and any additional options that may have been
   * passed from the parameters dialog
   * 
   * @param args
   * @param searchOutputFile
   * @param hitsAlignmentFile
   * @param hmmFile
   * @throws IOException
   */
  protected void buildArguments(List<String> args, File searchOutputFile,
          File hitsAlignmentFile, File hmmFile) throws IOException
  {
    args.add("-o");
    args.add(getFilePath(searchOutputFile, true));
    args.add("-A");
    args.add(getFilePath(hitsAlignmentFile, true));

    boolean dbFound = false;
    String dbPath = "";
    File databaseFile = null;

    boolean useEvalueCutoff = false;
    boolean useScoreCutoff = false;
    String seqEvalueCutoff = null;
    String domEvalueCutoff = null;
    String seqScoreCutoff = null;
    String domScoreCutoff = null;
    databaseName = "Alignment";

    if (params != null)
    {
      for (ArgumentI arg : params)
      {
        String name = arg.getName();
        if (MessageManager.getString(NUMBER_OF_RESULTS_KEY)
                .equals(name))
        {
          seqsToReturn = Integer.parseInt(arg.getValue());
        }
        else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
                .equals(name))
        {
          realign = true;
        }
        else if (MessageManager.getString(USE_ACCESSIONS_KEY)
                .equals(name))
        {
          args.add("--acc");
        }
        else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
                .equals(name))
        {
          if (CUTOFF_EVALUE.equals(arg.getValue()))
          {
            useEvalueCutoff = true;
          }
          else if (CUTOFF_SCORE.equals(arg.getValue()))
          {
            useScoreCutoff = true;
          }
        }
        else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
        {
          seqEvalueCutoff = arg.getValue();
        }
        else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
        {
          seqScoreCutoff = arg.getValue();
        }
        else if (MessageManager.getString(DOM_EVALUE_KEY)
                .equals(name))
        {
          domEvalueCutoff = arg.getValue();
        }
        else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
        {
          domScoreCutoff = arg.getValue();
        }
        else if (MessageManager.getString(TRIM_TERMINI_KEY)
                .equals(name))
        {
          trim = true;
        }
        else if (MessageManager.getString(DATABASE_KEY).equals(name))
        {
          dbFound = true;
          dbPath = arg.getValue();
          if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
                  .equals(dbPath))
          {
            int pos = dbPath.lastIndexOf(File.separator);
            databaseName = dbPath.substring(pos + 1);
            databaseFile = new File(dbPath);
          }
          searchAlignment = false;
        }
        else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
        {
          returnNoOfNewSeqs = true;
        }
      }
    }

    if (useEvalueCutoff)
    {
      args.add("-E");
      args.add(seqEvalueCutoff);
      args.add("--domE");
      args.add(domEvalueCutoff);
    }
    else if (useScoreCutoff)
    {
      args.add("-T");
      args.add(seqScoreCutoff);
      args.add("--domT");
      args.add(domScoreCutoff);
    }

//    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
//            .equals(dbPath))
      if (searchAlignment)
    {
      /*
       * no external database specified for search, so
       * export current alignment as 'database' to search,
       * excluding any HMM consensus sequences it contains
       */
      databaseFile = FileUtils.createTempFile("database", ".sto");
      AlignmentI al = af.getViewport().getAlignment();
      AlignmentI copy = new Alignment(al);
      deleteHmmSequences(copy);

      sequencesHash = stashSequences(copy.getSequencesArray());

      exportStockholm(copy.getSequencesArray(), databaseFile, null);

    }

    args.add(getFilePath(hmmFile, true));
    args.add(getFilePath(databaseFile, true));
  }

  /**
   * 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();

      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;
          }
        }
      }
      readTable(searchOutputFile);

      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"));
    }
  }

  /**
   * Reads in the scores table output by hmmsearch and adds annotation to
   * sequences for E-value and bit score
   * 
   * @param inputTableTemp
   * @throws IOException
   */
  void readTable(File inputTableTemp) throws IOException
  {
    BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
    String line = "";
    while (!line.startsWith("Query:"))
    {
      line = br.readLine();
    }
    while (!line.contains("-------"))
    {
      line = br.readLine();
    }
    line = br.readLine();

    int index = 0;
    while (!"  ------ inclusion threshold ------".equals(line)
            && !"".equals(line))
    {
      SequenceI seq = seqs[index];
      Scanner scanner = new Scanner(line);
      String evalue = scanner.next();
      String score = scanner.next();
      addScoreAnnotations(evalue, score, seq);
      scanner.close();
      line = br.readLine();
      index++;
    }

    br.close();
  }


  protected void addScoreAnnotations(String eValue, String bitScore,
          SequenceI seq)
  {
    String label = "Search Scores";
    String description = "Full sequence bit score and E-Value";

    try
    {
      AlignmentAnnotation annot = new AlignmentAnnotation(label,
              description, null);

      annot.label = label;
      annot.description = description;

      annot.setCalcId(HMMSEARCH);

      double dEValue = Double.parseDouble(eValue);
      annot.setEValue(dEValue);

      double dBitScore = Double.parseDouble(bitScore);
      annot.setBitScore(dBitScore);

      annot.setSequenceRef(seq);
      seq.addAlignmentAnnotation(annot);
    } catch (NumberFormatException e)
    {
      System.err.println("Error parsing " + label + " from " + eValue
              + " & " + bitScore);
    }
  }

}