package jalview.io.vamsas;

import java.io.IOException;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Vector;

import jalview.analysis.NJTree;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.Entry;
import uk.ac.vamsas.objects.core.Input;
import uk.ac.vamsas.objects.core.Newick;
import uk.ac.vamsas.objects.core.Param;
import uk.ac.vamsas.objects.core.Provenance;
import uk.ac.vamsas.objects.core.Seg;
import uk.ac.vamsas.objects.core.Treenode;
import uk.ac.vamsas.objects.core.Vref;

public class Tree extends DatastoreItem
{
  AlignmentI jal;
  TreePanel tp;
  uk.ac.vamsas.objects.core.Tree tree;
  uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
                                                  // other kind of tree
  private NewickFile ntree;
  private String title;
  private AlignmentView inputData = null;
  public static void updateFrom(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree) {
    Tree toTree = new Tree(datastore, alignFrame, vtree);
    
  }
  public Tree(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree)
  {
    super(datastore);
    tree = vtree;
    TreePanel tp = (TreePanel) getvObj2jv(tree);
    if (tp != null) {
      if (tree.isUpdated())
      {
        Cache.log.info(
                "Update from vamsas document to alignment associated tree not implemented yet.");
      }
    }
    else
    {
      // make a new tree
      Object[] idata = this.recoverInputData(tree.getProvenance());
      try
      {
        if (idata != null && idata[0] != null)
        {
          inputData = (AlignmentView) idata[0];
        }
        ntree = getNtree();
        title = tree.getNewick(0).getTitle();
        if (title==null || title.length()==0)
        {
          title = tree.getTitle(); // hack!!!!
        }
      }
      catch (Exception e)
      {
        Cache.log.warn("Problems parsing treefile '" +
                       tree.getNewick(0).getContent() + "'", e);
      }
    }
  }
  private NewickFile getNtree() throws IOException
  {
    return new jalview.io.NewickFile(tree.getNewick(0).getContent());
  }
  public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2)
  {
    super(datastore);

    jal = jal2;
    tp = tp2;
    alignment = alignment2;
    
    tree = (uk.ac.vamsas.objects.core.Tree) getjv2vObj(tp);
    if (tree == null)
    {
      add();
    }
    else
    {
      if (isModifiable(tree.getModifiable()))
      {
        // synchronize(); // update();
        // verify any changes.
        System.out.println("Update tree in document.");
      }
      else
      {
        // handle conflict
        System.out
            .println("Add modified tree as new tree in document.");
      }
    }
  }
  /**
   * correctly creates provenance for trees calculated on an alignment by
   * jalview.
   * 
   * @param jal
   * @param tp
   * @return
   */
  private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
  {
    Cache.log.debug("Making Tree provenance for "+tp.getTitle());
    Provenance prov = new Provenance();
    prov.addEntry(new Entry());
    prov.getEntry(0).setAction("imported " + tp.getTitle());
    prov.getEntry(0).setUser(provEntry.getUser());
    prov.getEntry(0).setApp(provEntry.getApp());
    prov.getEntry(0).setDate(provEntry.getDate());
    if (tp.getTree().hasOriginalSequenceData())
    {
      Input vInput = new Input();
      // LATER: check to see if tree input data is contained in this alignment -
      // or just correctly resolve the tree's seqData to the correct alignment
      // in
      // the document.
      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp.getTree().seqData.getSequences()));
      Object[] alsqs = new Object[alsqrefs.size()];
      alsqrefs.copyInto(alsqs);
      vInput.setObjRef(alsqs);
      // now create main provenance data
      prov.getEntry(0).setAction("created " + tp.getTitle());
      prov.getEntry(0).addInput(vInput);
      // jalview's special input parameter for distance matrix calculations
      vInput.setName("jalview:seqdist");
      prov.getEntry(0).addParam(new Param());
      prov.getEntry(0).getParam(0).setName("treeType");
      prov.getEntry(0).getParam(0).setType("utf8");
      prov.getEntry(0).getParam(0).setContent("NJ");
      int ranges[] = tp.getTree().seqData.getVisibleContigs();
      // VisibleContigs are with respect to alignment coordinates. Still need
      // offsets
      int start = tp.getTree().seqData.getAlignmentOrigin();
      for (int r = 0; r < ranges.length; r += 2)
      {
        Seg visSeg = new Seg();
        visSeg.setStart(1 + start + ranges[r]);
        visSeg.setEnd(start + ranges[r + 1]);
        visSeg.setInclusive(true);
        vInput.addSeg(visSeg);
      }
    }
    Cache.log.debug("Finished Tree provenance for "+tp.getTitle());
    return prov;
  }
  /**
   * look up SeqCigars in an existing alignment.
   * 
   * @param jal
   * @param sequences
   * @return vector of alignment sequences in order of SeqCigar array (but
   *         missing unfound seqcigars)
   */
  private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
  {
    SeqCigar[] tseqs = new SeqCigar[sequences.length];
    System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
    Vector alsq = new Vector();
    Enumeration as = jal.getSequences().elements();
    while (as.hasMoreElements())
    {
      SequenceI asq = (SequenceI) as.nextElement();
      for (int t = 0; t<sequences.length; t++)
      {
        if (tseqs[t]!=null 
                && (tseqs[t].getRefSeq()==asq || tseqs[t].getRefSeq() == asq.getDatasetSequence()))
                // && tseqs[t].getStart()>=asq.getStart() && tseqs[t].getEnd()<=asq.getEnd())
        {
          tseqs[t] = null;
          alsq.add(asq);
        }
      }
    }
    if (alsq.size()<sequences.length)
      Cache.log.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
    return alsq;
  }
  /**
   * construct treenode mappings for mapped sequences
   * 
   * @param ntree
   * @return
   */
  public Treenode[] makeTreeNodes(NJTree ntree) {
    Vector leaves = new Vector();
    ntree.findLeaves(ntree.getTopNode(), leaves);
    Vector tnv = new Vector();
    Enumeration l = leaves.elements();
    int i=0;
    Hashtable nodespecs = new Hashtable();
    while (l.hasMoreElements())
    {
      jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l.nextElement();
      if (tnode instanceof jalview.datamodel.SequenceNode)
      {
        if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
        {
          Object assocseq = ((jalview.datamodel.SequenceNode) tnode).element();
          if (assocseq instanceof SequenceI)
          {
            Vobject vobj = this.getjv2vObj(assocseq);
            if (vobj!=null)
            {
              Treenode node = new Treenode();
              node.setNodespec(makeNodeSpec(nodespecs, tnode));
              node.setName(tnode.getName());
              Vref vr = new Vref();
              vr.addRefs(vobj);
              node.addVref(vr);
              tnv.addElement(node);
            }
            else
            {
              System.err.println("WARNING: Unassociated treeNode "+tnode.element().toString()+" "
                      +((tnode.getName()!=null) ? " label "+tnode.getName() : ""));
            }
          }
        }
      }
    }
    if (tnv.size()>0)
    {
      Treenode[] tn = new Treenode[tnv.size()];
      tnv.copyInto(tn);  
      return tn;
    }
    return new Treenode[] {};
  }
  private String makeNodeSpec(Hashtable nodespecs, jalview.datamodel.BinaryNode tnode)
  { 
    String nname = new String(tnode.getName());
    Integer nindx = (Integer) nodespecs.get(nname);
    if (nindx==null)
    {
      nindx = new Integer(1);
    }
    nname = nindx.toString()+" "+nname;
    return nname;
  }
  /**
   * call to match up Treenode specs to NJTree parsed from document object.
   * 
   * @param nodespec
   * @param leaves
   *          as returned from NJTree.findLeaves( .., ..) ..
   * @return
   */
  private jalview.datamodel.BinaryNode findNodeSpec(String nodespec, Vector leaves)
  {
    int occurence=-1;
    String nspec = nodespec.substring(nodespec.indexOf(' ')+1);
    String oval = nodespec.substring(0, nodespec.indexOf(' '));
    try {
      occurence = new Integer(oval).intValue();
    }
    catch (Exception e)
    {
      System.err.println("Invalid nodespec '"+nodespec+"'");
      return null;
    }
    jalview.datamodel.BinaryNode bn = null;
    
    int nocc = 0;
    Enumeration en = leaves.elements();
    while (en.hasMoreElements() && nocc<occurence)
    {
      bn = (jalview.datamodel.BinaryNode) en.nextElement();
      if (bn instanceof jalview.datamodel.SequenceNode && bn.getName().equals(nspec))
      {
         --occurence;
      } else 
        bn=null;
    }
    return bn;
  }
  /**
   * add jalview object to vamsas document
   * 
   */
  public void add() {
    tree = new uk.ac.vamsas.objects.core.Tree();
    bindjvvobj(tp, tree);
    tree.setTitle(tp.getTitle());
    Newick newick = new Newick();
    newick.setContent(tp.getTree().toString());
    newick.setTitle(tp.getTitle());
    tree.addNewick(newick);
    tree.setProvenance(makeTreeProvenance(jal, tp));
    tree.setTreenode(makeTreeNodes(tp.getTree()));
    
    alignment.addTree(tree);
  }

  /**
   * note: this function assumes that all sequence and alignment objects
   * referenced in input data has already been associated with jalview objects.
   * 
   * @param tp
   * @return Object[] { AlignmentView, AlignmentI - reference alignment for
   *         input }
   */
  public Object[] recoverInputData(Provenance tp)
  {
    AlignViewport javport=null;
    jalview.datamodel.AlignmentI jal=null;
    jalview.datamodel.CigarArray view=null;
    for (int pe = 0; pe < tp.getEntryCount(); pe++)
    {
      if (tp.getEntry(pe).getInputCount() > 0)
      {
        if (tp.getEntry(pe).getInputCount() > 1)
        {
          Cache.log.warn("Ignoring additional input spec in provenance entry "
                         + tp.getEntry(pe).toString());
        }
        // LATER: deal sensibly with multiple inputs
        Input vInput = tp.getEntry(pe).getInput(0);
        // is this the whole alignment or a specific set of sequences ?
        if (vInput.getObjRefCount()==0)
          continue;
        if (vInput.getObjRefCount()==1 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
        {
          // recover an AlignmentView for the input data
          javport = (AlignViewport) getvObj2jv( (uk.ac.vamsas.
              client.Vobject) vInput
              .getObjRef(0));
          jal = javport.getAlignment();
          view = javport.getAlignment().
              getCompactAlignment();
        } else 
          if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence) {
            // recover an AlignmentView for the input data
            javport = (AlignViewport) getvObj2jv(((Vobject)vInput.getObjRef(0)).getV_parent());
            jal = javport.getAlignment();
            jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput.getObjRefCount()];
            for (int i=0,iSize=vInput.getObjRefCount(); i<iSize; i++)
            {
              SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput.getObjRef(i));
              seqs[i] = seq;
            }
            view = new jalview.datamodel.Alignment(seqs).getCompactAlignment();
              
            
        }
        int from = 1, to = jal.getWidth();
        int offset = 0; // deleteRange modifies its frame of reference
        for (int r = 0, s = vInput.getSegCount(); r < s; r++)
        {
          Seg visSeg = vInput.getSeg(r);
          int se[] = getSegRange(visSeg, true); // jalview doesn't do
                                                // bidirection alignments yet.
          if (to < se[1])
          {
            Cache.log.warn("Ignoring invalid segment in InputData spec.");
              }
            else
            {
              if (se[0] > from)
              {
                view.deleteRange(offset + from - 1, offset + se[0] - 2);
                offset -= se[0] - from;
              }
              from = se[1] + 1;
            }
          }
          if (from < to)
          {
            view.deleteRange(offset + from - 1, offset + to - 1); // final
                                                                  // deletion -
                                                                  // TODO: check
                                                                  // off by
            // one for to
          }
          return new Object[]{new AlignmentView(view), jal};
        }
    }
    Cache.log.debug("Returning null for input data recovery from provenance.");
    return null;
  }
  public NewickFile getNewickTree()
  {
    return ntree;
  }
  public String getTitle()
  {
    return title;
  }
  public AlignmentView getInputData()
  {
    return inputData;
  }
  public boolean isValidTree()
  {
    try {
      ntree.parse();
      if (ntree.getTree()!=null)
      {
        ntree = getNtree();
      }
        return true;
    }
    catch (Exception e)
    {
      Cache.log.debug("Failed to parse newick tree string",e);
    }
    return false;
  }

}