/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ws.jws2;

import jalview.api.AlignCalcWorkerI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;

import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.TreeSet;
import java.util.regex.Pattern;

import compbio.data.sequence.RNAStructReader.AlifoldResult;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;

/**
 * Client for the JABA RNA Alifold Service
 * 
 * @author daluke - Daniel Barton
 * 
 */

public class RNAalifoldClient extends JabawsCalcWorker implements
        AlignCalcWorkerI
{

  String methodName;

  AlignFrame af;

  // keeps track of whether the RNAalifold result includes base contact
  // probabilities
  boolean bpScores;

  public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
          WsParamSetI preset, List<Argument> paramset)
  {
    super(sh, alignFrame, preset, paramset);
    af = alignFrame;
    methodName = sh.serviceType;
    alignedSeqs = true;
    submitGaps = true;
    nucleotidesAllowed = true;
    proteinAllowed = false;
    initViewportParams();
  }

  public String getCalcId()
  {
    return CALC_ID;
  }

  private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";

  public static AlignAnalysisUIText getAlignAnalysisUITest()
  {
    return new AlignAnalysisUIText(
            compbio.ws.client.Services.RNAalifoldWS.toString(),
            jalview.ws.jws2.RNAalifoldClient.class,
            CALC_ID,
            true,
            false,
            true,
            "RNAAliFold Prediction",
            "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.",
            "Change RNAAliFold settings...",
            "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters");

  }

  @Override
  public String getServiceActionText()
  {
    return "Submitting RNA alignment for Secondary Structure prediction using "
            + "RNAalifold Service";
  }

  @Override
  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
  {
    return (seqs.size() > 1);
  }

  @Override
  public void updateResultAnnotation(boolean immediate)
  {

    if (immediate || !calcMan.isWorking(this) && scoremanager != null)
    {

      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();

      // Unpack the ScoreManager
      List<String> structs = ((RNAStructScoreManager) scoremanager)
              .getStructs();
      List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
              .getData();

      // test to see if this data object contains base pair contacts
      Score fscore = data.get(0).first();
      this.bpScores = (fscore.getMethod()
              .equals(AlifoldResult.contactProbabilities.toString()));

      // add annotation for the consensus sequence alignment
      createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
              structs.get(0), null, null);

      // Add annotations for the mfe Structure
      createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
              structs.get(1), data.get(1), null);

      // decide whether to add base pair contact probability histogram
      int count = 2;
      if (bpScores)
      {
        createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
                structs.get(2), data.get(0), data.get(2));
        count++;
      }

      // Now loop for the rest of the Annotations (if there it isn't stochastic
      // output
      // only the centroid and MEA structures remain anyway)
      for (int i = count; i < structs.size(); i++)
      {
        // The ensemble values should be displayed in the description of the
        // first (or all?) Stochastic Backtrack Structures.
        if (!data.get(i).first().getMethod()
                .equals(AlifoldResult.ensembleValues.toString()))
        {

          createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
                  structs.get(i), data.get(i), null);
        }
      }

      if (ourAnnot.size() > 0)
      {

        updateOurAnnots(ourAnnot);
        ap.adjustAnnotationHeight();
      }
    }
  }

  protected void createAnnotationRowforScoreHolder(
          List<AlignmentAnnotation> ourAnnot, String calcId, String struct,
          TreeSet<Score> data, TreeSet<Score> descriptionData)
  {
    /*
     * If contactProbability information is returned from RNAalifold it is
     * stored in the first TreeSet<Score> object corresponding to the String Id
     * which holds the consensus alignment. The method enumeration is then
     * updated to AlifoldResult.contactProbabilties. This line recreates the
     * same data object as was overwritten with the contact probabilites data.
     */
    if (data == null)
      data = compbio.data.sequence.RNAStructReader
              .newEmptyScore(AlifoldResult.consensusAlignment);

    if (descriptionData == null)
      descriptionData = data;

    String[] typenameAndDescription = constructTypenameAndDescription(descriptionData
            .first());
    String typename = typenameAndDescription[0];
    String description = typenameAndDescription[1];

    AlignmentAnnotation annotation = alignViewport.getAlignment()
            .findOrCreateAnnotation(typename, calcId, false, null, null);

    constructAnnotationFromScoreHolder(annotation, struct, data);

    /*
     * update annotation description with the free Energy, frequency in ensemble
     * or other data where appropriate.
     * 
     * Doesnt deal with AlifoldResult.ensembleValues, the free energy of
     * ensemble and frequency of mfe structure in ensemble. How to deal with
     * these?
     */
    annotation.description = description;

    annotation.belowAlignment = false;
    // annotation.showAllColLabels = true;

    alignViewport.getAlignment().validateAnnotation(annotation);
    af.setMenusForViewport();

    ourAnnot.add(annotation);
  }

  private AlignmentAnnotation constructAnnotationFromScoreHolder(
          AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
  {
    Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
            : struct.length()];

    if (data != null
            && data.size() > 1
            && data.first().getMethod()
                    .equals(AlifoldResult.contactProbabilities.toString()))
    {

      // The base pair probabilities are stored in a set in scoreholder. we want
      // a map
      LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<Range, Float>();
      for (Score score : data)
      {
        // The Score objects contain a set of size one containing the range and
        // an ArrayList<float> of size one containing the probabilty
        basePairs.put(score.getRanges().first(), new Float(score
                .getScores().get(0)));
      }

      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
      {
        if (gapMap != null)
        {
          // skip any gapped columns in the input data
          while (!gapMap[ri])
          {
            ri++;
          }
        }
        // Return all the contacts associated with position i
        LinkedHashMap<Range, Float> contacts = isContact(basePairs, i + 1);

        String description = "";
        float prob = 0f;

        if (contacts.size() == 0)
        {
          description = "No Data";
        }
        else
        {
          for (Range contact : contacts.keySet())
          {
            float t = contacts.get(contact);
            if (t > prob)
              prob = t;
            description += Integer.toString(contact.from) + "->"
                    + Integer.toString(contact.to) + ": "
                    + Float.toString(t) + "%  |  ";
          }
        }

        anns[ri] = new Annotation(struct.substring(i, i + 1), description,
                isSS(struct.charAt(i)), prob);
      }
    }
    else if (data == null || data.size() == 1)
    {
      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
      {
        if (gapMap != null)
        {
          // skip any gapped columns in the input data
          while (!gapMap[ri] && ri < gapMap.length)
          {
            ri++;
          }
          if (ri == gapMap.length)
          {
            break;
          }
        }
        anns[ri] = new Annotation(struct.substring(i, i + 1), "",
                isSS(struct.charAt(i)), Float.NaN);
      }

      annotation.graph = 0; // No graph
    }

    annotation.annotations = anns;

    return annotation;
  }

  private String[] constructTypenameAndDescription(Score score)
  {
    String description = "";
    String typename = "";
    String datatype = score.getMethod();

    // Look up java switch syntax and use one here
    if (datatype.equals(AlifoldResult.mfeStructure.toString()))
    {

      description = MessageFormat.format(
              "Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
              score.getScores().get(0), score.getScores().get(1), score
                      .getScores().get(2));
      typename = "MFE Structure";
    }
    else if (datatype.equals(AlifoldResult.contactProbabilityStructure
            .toString()))
    {
      description = MessageFormat
              .format("Base Pair Contact Probabilities. "
                      + "Energy of Ensemble: {0}  Frequency of Ensemble: {1}",
                      score.getScores().get(0), score.getScores().get(1));
      typename = "Contact Probabilities";
    }
    else if (datatype.equals(AlifoldResult.centroidStructure.toString()))
    {
      description = MessageFormat.format(
              "Centroid Structure. Energy: {0} = {1} + {2}", score
                      .getScores().get(0), score.getScores().get(1), score
                      .getScores().get(2));
      typename = "Centroid Structure";
    }
    else if (datatype.equals(AlifoldResult.stochBTStructure.toString()))
    {
      if (score.getScores().size() > 0)
      {
        description = MessageFormat.format("Probability: {0}  Energy: {1}",
                score.getScores().get(0), score.getScores().get(1));
      }
      else
        description = "Stochastic Backtrack Structure";
    }
    else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
    {
      description = MessageFormat.format(
              "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}", score
                      .getScores().get(0), score.getScores().get(1));
      typename = "MEA Structure";
    }
    else if (datatype.equals(AlifoldResult.consensusAlignment.toString()))
    {
      typename = "RNAalifold Consensus";
      description = "Consensus Alignment Produced by RNAalifold";
    }
    else
    {
      typename = datatype;
      description = typename;
    }

    return new String[]
    { typename, description };
  }

  // Check whether, at position i there is a base contact and return all the
  // contacts at this position. Should be in order of descending probability.
  private LinkedHashMap<Range, Float> isContact(
          LinkedHashMap<Range, Float> basePairs, int i)
  {
    LinkedHashMap<Range, Float> contacts = new LinkedHashMap<Range, Float>();

    for (Range contact : basePairs.keySet())
    {
      // finds the contacts associtated with position i ordered by the natural
      // ordering of the Scores TreeSet in ScoreManager which is, descending
      // probability
      if (contact.from == i || contact.to == i)
        contacts.put(contact, basePairs.get(contact));
    }

    return contacts;
  }

  private char isSS(char chr)
  {
    String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
    char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
    return ss;
  }
}