package jalview.hmmer;

import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
import jalview.gui.SplitFrame;
import jalview.io.DataSourceType;
import jalview.io.StockholmFile;
import jalview.util.MessageManager;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;

public class HMMAlignThread implements Runnable
{

  /**
   * feature settings from view that job was associated with
   */
  protected FeatureRendererSettings featureSettings = null;

  HMMERCommands cmds = new HMMERCommands();

  AlignFrame af;

  AlignmentI alignment;

  AlignmentI dataset;

  List<AlignmentOrder> orders;

  AlignmentView msa;

  HiddenMarkovModel hmm;

  boolean newFrame;

  long barID;

  Map<Integer, SequenceI> hmmSeqs;

  File hmmTemp = null;

  File outTemp = null;

  File inputTemp = null;

  List<AlignmentOrder> allOrders;

  SequenceI[][] allResults;

  public HMMAlignThread(AlignFrame af, boolean createNewFrame)
  {
    this.af = af;
    alignment = af.getViewport().getAlignment();
    if (alignment.getDataset() != null)
    {
      dataset = alignment.getDataset();
    }
    newFrame = createNewFrame;
    featureSettings = af.getFeatureRenderer().getSettings();
  }

  @Override
  public void run()
  {
	  if (af.getViewport().getSelectedHMM() == null)
    {
      JOptionPane.showMessageDialog(af,
              MessageManager.getString("warn.no_selected_hmm"));
      return;
    }
    else
    {
    	hmm = af.getViewport().getSelectedHMM();
    }
    barID = System.currentTimeMillis();
    af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
            barID);
    cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);

    // if (!alignment.isAligned())
    // {
    // alignment.padGaps();
    // }
    prepareAlignment();
    SequenceI[][] subAlignments = msa.getVisibleContigs('-');
    allOrders = new ArrayList<>();
    allResults = new SequenceI[subAlignments.length][];
    int job = 0;
    for (SequenceI[] seqs : subAlignments)
    {
      cmds.uniquifySequences(seqs);
      try
      {
        createTemporaryFiles();
      } catch (IOException e2)
      {
        e2.printStackTrace();
      }
      try
      {
        cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
                hmmTemp.getAbsoluteFile());
      } catch (IOException e1)
      {
        e1.printStackTrace();
      }
      try
      {
        boolean ran = runCommand();
        if (!ran)
        {
          JvOptionPane.showInternalMessageDialog(af,
                  MessageManager.getString("warn.hmmalign_failed"));
          return;
        }
      } catch (IOException | InterruptedException e)
      {
        e.printStackTrace();
      }
      try
      {
        importData(job);
      } catch (IOException | InterruptedException e)
      {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }
      job++;
    }

    displayResults(newFrame);

    af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
            barID);

  }

  private void createTemporaryFiles() throws IOException
  {
    hmmTemp = File.createTempFile("hmm", ".hmm");
    hmmTemp.deleteOnExit();
    outTemp = File.createTempFile("output", ".sto");
    outTemp.deleteOnExit();
    inputTemp = File.createTempFile("input", ".sto");
    inputTemp.deleteOnExit();
  }

  private boolean runCommand() throws IOException, InterruptedException
  {
    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmalign.exe");
    if (!file.canExecute())
    {
      return false;
    }
    String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
    if (!hmm.getFileHeader().contains("HMMER3/f"))
    {
      command += cmds.ALLCOL;
    }
    boolean trim = true;
    String bool = Cache.getProperty("TRIM_TERMINI");
    if ("false".equals(bool))
    {
      trim = false;
    }
    if (trim)
    {
      command += cmds.TRIM;
    }
    command += " -o" + inputTemp.getAbsolutePath() + cmds.SPACE
            + hmmTemp.getAbsolutePath() + cmds.SPACE
            + outTemp.getAbsolutePath();
    return cmds.runCommand(command);
  }

  private void importData(int index)
          throws IOException, InterruptedException
  {
    StockholmFile file = new StockholmFile(inputTemp.getAbsolutePath(),
            DataSourceType.FILE);
    SequenceI[] result = file.getSeqsAsArray();
    AlignmentOrder msaorder = new AlignmentOrder(result);
    jalview.analysis.AlignmentSorter.recoverOrder(result);
    jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
    allOrders.add(msaorder);
    allResults[index] = result;
    hmmTemp.delete();
    outTemp.delete();
    inputTemp.delete();
  }

  private void prepareAlignment()
  {
    // hmmSeqs = alignment.getHMMConsensusSequences(true);
    msa = af.gatherSequencesForAlignment();
  }

  private void displayResults(boolean newFrame)
  {
    AlignmentOrder[] arrOrders = allOrders
            .toArray(new AlignmentOrder[allOrders.size()]);
    Object[] newview = msa.getUpdatedView(allResults,
            arrOrders, '-');
    SequenceI[] alignment = (SequenceI[]) newview[0];
    HiddenColumns hidden = (HiddenColumns) newview[1];
    Alignment al = new Alignment(alignment);
    al.setProperty("Alignment Program", "hmmalign");
    if (dataset != null)
    {
      al.setDataset(dataset);
    }

    if (newFrame)
    {
      displayInNewFrame(al, allOrders, hidden);
    }
  }

  private void displayInNewFrame(AlignmentI al,
          List<AlignmentOrder> alorders, HiddenColumns hidden)
  {
    AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
            AlignFrame.DEFAULT_HEIGHT);

    // initialise with same renderer settings as in parent alignframe.
    af.getFeatureRenderer().transferSettings(this.featureSettings);

    if (allOrders.size() > 0)
    {
      addSortByMenuItems(af, allOrders);
    }

    // TODO: refactor retrieve and show as new splitFrame as Desktop method

    /*
     * If alignment was requested from one half of a SplitFrame, show in a
     * SplitFrame with the other pane similarly aligned.
     */
    AlignFrame requestedBy = this.af;
    if (requestedBy != null && requestedBy.getSplitViewContainer() != null
            && requestedBy.getSplitViewContainer()
                    .getComplement(requestedBy) != null)
    {
      AlignmentI complement = requestedBy.getSplitViewContainer()
              .getComplement(requestedBy);
      String complementTitle = requestedBy.getSplitViewContainer()
              .getComplementTitle(requestedBy);
      // becomes null if the alignment window was closed before the alignment
      // job finished.
      AlignmentI copyComplement = new Alignment(complement);
      // todo should this be done by copy constructor?
      copyComplement.setGapCharacter(complement.getGapCharacter());
      // share the same dataset (and the mappings it holds)
      copyComplement.setDataset(complement.getDataset());
      copyComplement.alignAs(al);
      if (copyComplement.getHeight() > 0)
      {
        af.setTitle(this.af.getTitle());
        AlignFrame af2 = new AlignFrame(copyComplement,
                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
        af2.setTitle(complementTitle);
        String linkedTitle = MessageManager
                .getString("label.linked_view_title");
        JInternalFrame splitFrame = new SplitFrame(
                al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
        Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
        return;
      }
    }

    /*
     * Not from SplitFrame, or failed to created a complementary alignment
     */
    Desktop.addInternalFrame(af, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
            AlignFrame.DEFAULT_HEIGHT);
  }

  /**
   * Add sort order options to the AlignFrame menus.
   * 
   * @param af
   * @param alorders
   */
  protected void addSortByMenuItems(AlignFrame af,
          List<AlignmentOrder> alorders)
  {
    // update orders
    if (alorders.size() == 1)
    {
      af.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
    }
    else
    {
      // construct a non-redundant ordering set
      List<String> names = new ArrayList<>();
      for (int i = 0, l = alorders.size(); i < l; i++)
      {
        String orderName = " Region " + i;
        int j = i + 1;

        while (j < l)
        {
          if (alorders.get(i).equals(alorders.get(j)))
          {
            alorders.remove(j);
            l--;
            orderName += "," + j;
          }
          else
          {
            j++;
          }
        }

        if (i == 0 && j == 1)
        {
          names.add("");
        }
        else
        {
          names.add(orderName);
        }
      }
      for (int i = 0, l = alorders.size(); i < l; i++)
      {
        af.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
                alorders.get(i));
      }
    }
  }

  }