package jalview.ws.phyre2;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.fts.core.DecimalFormatTableCellRenderer;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingClient;
import jalview.structures.models.MappingOutputModel;
import jalview.util.Comparison;
import jalview.util.Format;

import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;

import javax.swing.JTable;
import javax.swing.table.DefaultTableModel;

import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
import org.jsoup.select.Elements;

public class Phyre2Client extends StructureMappingClient
{
  private final static String NEWLINE = System.lineSeparator();

  public static final int UNASSIGNED = -1;

  private final static String PATH_SEPARATOR = File.separator;

  public Phyre2Client(StructureFile structureFile)
  {
    this.structureFile = structureFile;
  }

  @Override
  public StructureMapping getStructureMapping(SequenceI seq,
          String pdbFile, String chain)
  {
    final StringBuilder mappingDetails = new StringBuilder(128);
    PrintStream ps = new PrintStream(System.out)
    {
      @Override
      public void print(String x)
      {
        mappingDetails.append(x);
      }

      @Override
      public void println()
      {
        mappingDetails.append(NEWLINE);
      }
    };
    HashMap<Integer, int[]> mapping = getPhyre2FastaMapping(seq, ps);

    String mappingOutput = mappingDetails.toString();
    StructureMapping phyre2ModelMapping = new StructureMapping(seq,
            pdbFile, structureFile.getId(), chain, mapping, mappingOutput);
    return phyre2ModelMapping;
  }

  public HashMap<Integer, int[]> getPhyre2FastaMapping(SequenceI inputSeq,
          java.io.PrintStream os)
  {
    HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
    AlignmentI seq2Phyre2ModelFastaMapping = null;
    try
    {
      seq2Phyre2ModelFastaMapping = new FormatAdapter().readFile(
              getFastaMappingFile(), DataSourceType.FILE, FileFormat.Fasta);
    } catch (IOException e1)
    {
      e1.printStackTrace();
    }
    SequenceI[] seqs = seq2Phyre2ModelFastaMapping.getSequencesArray();
    SequenceI tSequenceRes = seqs[0];
    SequenceI tStructureRes = seqs[1];

    // Essential to resolve fastaAlignment to input sequence and model sequence
    // coordinates
    tSequenceRes.setStart(inputSeq.getStart());
    tSequenceRes.setEnd(inputSeq.getEnd());

    tStructureRes.setStart(structureFile.getSeqsAsArray()[0].getStart());
    tStructureRes.setEnd(structureFile.getSeqsAsArray()[0].getEnd());
    try
    {
      int sequenceResLenght = tSequenceRes.getLength();
      int structureResLenght = tStructureRes.getLength();
      if (sequenceResLenght == structureResLenght)
      {
        int prevStructResNum = -1;
        int alignmentLenght = sequenceResLenght + tSequenceRes.getStart();
        for (int x = 0; x < alignmentLenght; x++)
        {
          int alignSeqResidueIndex = tSequenceRes.findIndex(x);
          int structResNum = tStructureRes
                  .findPosition(alignSeqResidueIndex);
          int sequenceResNum = tSequenceRes
                  .findPosition(alignSeqResidueIndex - 1);
          boolean sameResNum = (structResNum == prevStructResNum);
          // System.out.println(sequenceResNum + " : "
          // + (sameResNum ? -1 : prevStructResNum));
          mapping.put(sequenceResNum, new int[] {
              sameResNum ? -1 : prevStructResNum, -1 });
          prevStructResNum = structResNum;
        }
      }
    } catch (Exception e)
    {
      e.printStackTrace();
    }

    try
    {
      populateAtomPositions(" ", mapping);
    } catch (IllegalArgumentException e)
    {
      e.printStackTrace();
    } catch (StructureMappingException e)
    {
      e.printStackTrace();
    }

    if (os != null)
    {
      MappingOutputModel mop = new MappingOutputModel();
      mop.setSeqStart(tSequenceRes.getStart());
      mop.setSeqEnd(tSequenceRes.getEnd());
      mop.setSeqName(tSequenceRes.getName());
      mop.setSeqResidue(tSequenceRes.getSequenceAsString());

      mop.setStrStart(tStructureRes.getStart());
      mop.setStrEnd(tStructureRes.getEnd());
      mop.setStrName(tStructureRes.getName());
      mop.setStrResidue(tStructureRes.getSequenceAsString());

      mop.setType("pep");
      try
      {
        os.print(getMappingOutput(mop).toString());
      } catch (Exception e)
      {
        e.printStackTrace();
      }
      os.println();
    }
    return mapping;
  }

  private String getFastaMappingFile()
  {
    File phyre2ModelFile = new File(structureFile.getDataName());
    String phyre2ModelResultDir = phyre2ModelFile.getParent();
    String modelId = structureFile.getId().substring(0,
            structureFile.getId().lastIndexOf(".pdb"));
    return phyre2ModelResultDir + PATH_SEPARATOR + modelId + ".fasta";
  }

  @Override
  public StringBuffer getMappingOutput(MappingOutputModel mp)
          throws StructureMappingException
  {
    String seqRes = mp.getSeqResidue();
    String seqName = mp.getSeqName();
    int sStart = mp.getSeqStart();
    int sEnd = mp.getSeqEnd();

    String strRes = mp.getStrResidue();
    String strName = mp.getStrName();
    int pdbStart = mp.getStrStart();
    int pdbEnd = mp.getStrEnd();

    String type = mp.getType();

    int maxid = (seqName.length() >= strName.length()) ? seqName.length()
            : strName.length();
    int len = 72 - maxid - 1;

    int nochunks = ((seqRes.length()) / len)
            + ((seqRes.length()) % len > 0 ? 1 : 0);
    // output mappings
    StringBuffer output = new StringBuffer();
    output.append(NEWLINE);
    output.append("Sequence \u27f7 Structure mapping details").append(
            NEWLINE);
    output.append("Method: Phyre2 Alignment");
    output.append(NEWLINE).append(NEWLINE);

    output.append(new Format("%" + maxid + "s").form(seqName));
    output.append(" :  ");
    output.append(String.valueOf(sStart));
    output.append(" - ");
    output.append(String.valueOf(sEnd));
    output.append(" Maps to ");
    output.append(NEWLINE);
    output.append(new Format("%" + maxid + "s").form(strName));
    output.append(" :  ");
    output.append(String.valueOf(pdbStart));
    output.append(" - ");
    output.append(String.valueOf(pdbEnd));
    output.append(NEWLINE).append(NEWLINE);

    int matchedSeqCount = 0;
    for (int j = 0; j < nochunks; j++)
    {
      // Print the first aligned sequence
      output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
              " ");

      for (int i = 0; i < len; i++)
      {
        if ((i + (j * len)) < seqRes.length())
        {
          output.append(seqRes.charAt(i + (j * len)));
        }
      }

      output.append(NEWLINE);
      output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");

      // Print out the matching chars
      for (int i = 0; i < len; i++)
      {
        try
        {
          if ((i + (j * len)) < seqRes.length())
          {
            boolean sameChar = Comparison.isSameResidue(
                    seqRes.charAt(i + (j * len)),
                    strRes.charAt(i + (j * len)), false);
            if (sameChar
                    && !jalview.util.Comparison.isGap(seqRes.charAt(i
                            + (j * len))))
            {
              matchedSeqCount++;
              output.append("|");
            }
            else if (type.equals("pep"))
            {
              if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
                      strRes.charAt(i + (j * len))) > 0)
              {
                output.append(".");
              }
              else
              {
                output.append(" ");
              }
            }
            else
            {
              output.append(" ");
            }
          }
        } catch (IndexOutOfBoundsException e)
        {
          continue;
        }
      }
      // Now print the second aligned sequence
      output = output.append(NEWLINE);
      output = output.append(new Format("%" + (maxid) + "s").form(strName))
              .append(" ");
      for (int i = 0; i < len; i++)
      {
        if ((i + (j * len)) < strRes.length())
        {
          output.append(strRes.charAt(i + (j * len)));
        }
      }
      output.append(NEWLINE).append(NEWLINE);
    }
    float pid = (float) matchedSeqCount / seqRes.length() * 100;
    // if (pid < SiftsSettings.getFailSafePIDThreshold())
    // {
    // throw new Exception(">>> Low PID detected for Phyre2 mapping...");
    // }
    output.append("Length of alignment = " + seqRes.length()).append(
            NEWLINE);
    output.append(new Format("Percentage ID = %2.2f").form(pid));
    return output;
  }



  public static List<Phyre2SummaryPojo> parsePhyre2ResultSummaryTable(
          String html)
  {
    List<Phyre2SummaryPojo> phyre2Results = new ArrayList<Phyre2SummaryPojo>();
    try
    {
      File in = new File(html);
      Document doc = Jsoup.parse(in, null);
      // Document doc = Jsoup.connect(html).get();
      Elements tableElements = doc.select("table.midshade");
      for (Element table : tableElements)
      {
        System.out.println();
        Elements tableRowElements = table.select(":not(thead) tr");
        for (int i = 0; i < tableRowElements.size(); i++)
        {
          Element row = tableRowElements.get(i);
          Elements rowItems = row.select("td");
          if (rowItems.size() > 11)
          {
            // for (int j = 0; j < rowItems.size(); j++)
            // {
            // System.out.println(">>> r:" + j + "  =  "
            // + rowItems.get(j).text());
            // }

            String c = rowItems.get(6).select("input").attr("onmouseover");
            String alignedRange = c.substring(c.indexOf("Residues ") + 9,
                    c.indexOf(" of your sequence aligned "));
            String coverage = c.substring(c.lastIndexOf(" (") + 2,
                    c.lastIndexOf(" coverage). Click to view detailed"));
            // System.out.println("coverage" + coverage);
            try
            {
              Phyre2SummaryPojo psp = new Phyre2SummaryPojo();
              String sn = rowItems.get(0).text();
              psp.setSerialNo(Integer.valueOf(sn));
              psp.setTemplateId(rowItems.get(1).text());
              psp.setCoverage(coverage);
              psp.setAlignedRange(alignedRange);
              psp.setConfidence(Double.valueOf(rowItems.get(8).text()));
              psp.setPid(Integer.valueOf(rowItems.get(9).text()));
              psp.setTemplateSummary(rowItems.get(10).text());
              // System.out.println("row  >>>> " + psp.toString());
              // System.out.println();
              phyre2Results.add(psp);
            } catch (NumberFormatException e)
            {
              e.printStackTrace();
            } catch (IndexOutOfBoundsException e)
            {
              e.printStackTrace();
            } catch (Exception e)
            {
              e.printStackTrace();
            }
          }
        }
      }
      return phyre2Results;

    } catch (Exception e)
    {
      e.printStackTrace();
      return null;
    }
  }

  public static DefaultTableModel getTableModel(
          List<Phyre2SummaryPojo> phyreResults)
  {
    if (phyreResults == null)
    {
      return null;
    }
    DefaultTableModel tableModel = new DefaultTableModel()
    {
      @Override
      public boolean isCellEditable(int row, int column)
      {
        return false;
      }

      @Override
      public Class<?> getColumnClass(int columnIndex)
      {
        switch (columnIndex)
        {
        case 0:
          return Integer.class;
        case 1:
          return String.class;
        case 2:
          return String.class;
        case 3:
          return String.class;
        case 4:
          return Double.class;
        case 5:
          return Integer.class;
        case 6:
          return String.class;
        default:
          return String.class;
        }
      }

    };

    tableModel.addColumn("#");
    tableModel.addColumn("Template");
    tableModel.addColumn("Aligned Range");
    tableModel.addColumn("Coverage");
    tableModel.addColumn("Confidence");
    tableModel.addColumn("%.i.d");
    tableModel.addColumn("Template Information");

    for (Phyre2SummaryPojo res : phyreResults)
    {
      tableModel.addRow(new Object[] { res.getSerialNo(),
          res.getTemplateId(), res.getAlignedRange(), res.getCoverage(),
          res.getConfidence(), res.getPid(), res.getTemplateSummary() }); 
    }
    return tableModel;
  }

  public static void configurePhyreResultTable(JTable phyreResultTable)
  {

    DecimalFormatTableCellRenderer idCellRender = new DecimalFormatTableCellRenderer(
            true, 0);
    DecimalFormatTableCellRenderer pidCellRender = new DecimalFormatTableCellRenderer(
            true, 1);
    DecimalFormatTableCellRenderer confidenceCellRender = new DecimalFormatTableCellRenderer(
            true, 1);

    phyreResultTable.getColumn("#").setMinWidth(20);
    phyreResultTable.getColumn("#").setPreferredWidth(30);
    phyreResultTable.getColumn("#").setMaxWidth(40);
    phyreResultTable.getColumn("#").setCellRenderer(idCellRender);

    phyreResultTable.getColumn("Template").setMinWidth(60);
    phyreResultTable.getColumn("Template").setPreferredWidth(60);
    phyreResultTable.getColumn("Template").setMaxWidth(90);

    phyreResultTable.getColumn("Aligned Range").setMinWidth(80);
    phyreResultTable.getColumn("Aligned Range").setPreferredWidth(80);
    phyreResultTable.getColumn("Aligned Range").setMaxWidth(120);

    phyreResultTable.getColumn("Coverage").setMinWidth(60);
    phyreResultTable.getColumn("Coverage").setPreferredWidth(60);
    phyreResultTable.getColumn("Coverage").setMaxWidth(90);

    phyreResultTable.getColumn("Confidence").setMinWidth(60);
    phyreResultTable.getColumn("Confidence").setPreferredWidth(60);
    phyreResultTable.getColumn("Confidence").setMaxWidth(90);
    phyreResultTable.getColumn("Confidence").setCellRenderer(
            confidenceCellRender);

    phyreResultTable.getColumn("%.i.d").setMinWidth(45);
    phyreResultTable.getColumn("%.i.d").setPreferredWidth(450);
    phyreResultTable.getColumn("%.i.d").setMaxWidth(65);
    phyreResultTable.getColumn("%.i.d").setCellRenderer(pidCellRender);

    phyreResultTable.getColumn("Template Information").setMinWidth(400);
    phyreResultTable.getColumn("Template Information").setPreferredWidth(
            600);
    phyreResultTable.getColumn("Template Information").setMaxWidth(1500);
  }
}