package jalview.structures.models;

import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;

import java.awt.event.ComponentEvent;
import java.util.ArrayList;
import java.util.List;

/**
 * A base class to hold common function for protein structure model binding.
 * Initial version created by refactoring JMol and Chimera binding models, but
 * other structure viewers could in principle be accommodated in future.
 * 
 * @author gmcarstairs
 *
 */
public abstract class AAStructureBindingModel extends
        SequenceStructureBindingModel implements StructureListener,
        StructureSelectionManagerProvider
{

  private StructureSelectionManager ssm;

  private PDBEntry[] pdbEntry;

  /*
   * sequences mapped to each pdbentry
   */
  private SequenceI[][] sequence;

  /*
   * array of target chains for sequences - tied to pdbentry and sequence[]
   */
  private String[][] chains;

  /*
   * datasource protocol for access to PDBEntrylatest
   */
  String protocol = null;

  protected boolean colourBySequence = true;

  /**
   * Constructor
   * 
   * @param ssm
   * @param seqs
   */
  public AAStructureBindingModel(StructureSelectionManager ssm,
          SequenceI[][] seqs)
  {
    this.ssm = ssm;
    this.sequence = seqs;
  }

  /**
   * Constructor
   * 
   * @param ssm
   * @param pdbentry
   * @param sequenceIs
   * @param chains
   * @param protocol
   */
  public AAStructureBindingModel(StructureSelectionManager ssm,
          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
          String protocol)
  {
    this.ssm = ssm;
    this.sequence = sequenceIs;
    this.chains = chains;
    this.pdbEntry = pdbentry;
    this.protocol = protocol;
    if (chains == null)
    {
      this.chains = new String[pdbentry.length][];
    }
  }

  public StructureSelectionManager getSsm()
  {
    return ssm;
  }

  /**
   * Returns the i'th PDBEntry (or null)
   * 
   * @param i
   * @return
   */
  public PDBEntry getPdbEntry(int i)
  {
    return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null;
  }

  /**
   * Returns the number of modelled PDB file entries.
   * 
   * @return
   */
  public int getPdbCount()
  {
    return pdbEntry == null ? 0 : pdbEntry.length;
  }

  public SequenceI[][] getSequence()
  {
    return sequence;
  }

  public String[][] getChains()
  {
    return chains;
  }

  public String getProtocol()
  {
    return protocol;
  }

  // TODO may remove this if calling methods can be pulled up here
  protected void setPdbentry(PDBEntry[] pdbentry)
  {
    this.pdbEntry = pdbentry;
  }

  protected void setSequence(SequenceI[][] sequence)
  {
    this.sequence = sequence;
  }

  protected void setChains(String[][] chains)
  {
    this.chains = chains;
  }

  /**
   * Construct a title string for the viewer window based on the data Jalview
   * knows about
   * @param viewerName TODO
   * @param verbose
   * 
   * @return
   */
  public String getViewerTitle(String viewerName, boolean verbose)
  {
    if (getSequence() == null || getSequence().length < 1
            || getPdbCount() < 1
            || getSequence()[0].length < 1)
    {
      return ("Jalview " + viewerName + " Window");
    }
    // TODO: give a more informative title when multiple structures are
    // displayed.
    StringBuilder title = new StringBuilder(64);
    final PDBEntry pdbEntry = getPdbEntry(0);
    title.append(viewerName + " view for " + getSequence()[0][0].getName()
            + ":"
            + pdbEntry.getId());
  
    if (verbose)
    {
      if (pdbEntry.getProperty() != null)
      {
        if (pdbEntry.getProperty().get("method") != null)
        {
          title.append(" Method: ");
          title.append(pdbEntry.getProperty().get("method"));
        }
        if (pdbEntry.getProperty().get("chains") != null)
        {
          title.append(" Chain:");
          title.append(pdbEntry.getProperty().get("chains"));
        }
      }
    }
    return title.toString();
  }

  /**
   * Called by after closeViewer is called, to release any resources and
   * references so they can be garbage collected. Override if needed.
   */
  protected void releaseUIResources()
  {

  }

  public boolean isColourBySequence()
  {
    return colourBySequence;
  }

  public void setColourBySequence(boolean colourBySequence)
  {
    this.colourBySequence = colourBySequence;
  }

  protected void addSequenceAndChain(int pe, SequenceI[] seq,
          String[] tchain)
  {
    if (pe < 0 || pe >= getPdbCount())
    {
      throw new Error(MessageManager.formatMessage(
              "error.implementation_error_no_pdbentry_from_index",
              new Object[]
              { Integer.valueOf(pe).toString() }));
    }
    final String nullChain = "TheNullChain";
    List<SequenceI> s = new ArrayList<SequenceI>();
    List<String> c = new ArrayList<String>();
    if (getChains() == null)
    {
      setChains(new String[getPdbCount()][]);
    }
    if (getSequence()[pe] != null)
    {
      for (int i = 0; i < getSequence()[pe].length; i++)
      {
        s.add(getSequence()[pe][i]);
        if (getChains()[pe] != null)
        {
          if (i < getChains()[pe].length)
          {
            c.add(getChains()[pe][i]);
          }
          else
          {
            c.add(nullChain);
          }
        }
        else
        {
          if (tchain != null && tchain.length > 0)
          {
            c.add(nullChain);
          }
        }
      }
    }
    for (int i = 0; i < seq.length; i++)
    {
      if (!s.contains(seq[i]))
      {
        s.add(seq[i]);
        if (tchain != null && i < tchain.length)
        {
          c.add(tchain[i] == null ? nullChain : tchain[i]);
        }
      }
    }
    SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
    getSequence()[pe] = tmp;
    if (c.size() > 0)
    {
      String[] tch = c.toArray(new String[c.size()]);
      for (int i = 0; i < tch.length; i++)
      {
        if (tch[i] == nullChain)
        {
          tch[i] = null;
        }
      }
      getChains()[pe] = tch;
    }
    else
    {
      getChains()[pe] = null;
    }
  }

  /**
   * add structures and any known sequence associations
   * 
   * @returns the pdb entries added to the current set.
   */
  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
          String[][] chns)
  {
    List<PDBEntry> v = new ArrayList<PDBEntry>();
    List<int[]> rtn = new ArrayList<int[]>();
    for (int i = 0; i < getPdbCount(); i++)
    {
      v.add(getPdbEntry(i));
    }
    for (int i = 0; i < pdbe.length; i++)
    {
      int r = v.indexOf(pdbe[i]);
      if (r == -1 || r >= getPdbCount())
      {
        rtn.add(new int[]
        { v.size(), i });
        v.add(pdbe[i]);
      }
      else
      {
        // just make sure the sequence/chain entries are all up to date
        addSequenceAndChain(r, seq[i], chns[i]);
      }
    }
    pdbe = v.toArray(new PDBEntry[v.size()]);
    setPdbentry(pdbe);
    if (rtn.size() > 0)
    {
      // expand the tied sequence[] and string[] arrays
      SequenceI[][] sqs = new SequenceI[getPdbCount()][];
      String[][] sch = new String[getPdbCount()][];
      System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
      System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
      setSequence(sqs);
      setChains(sch);
      pdbe = new PDBEntry[rtn.size()];
      for (int r = 0; r < pdbe.length; r++)
      {
        int[] stri = (rtn.get(r));
        // record the pdb file as a new addition
        pdbe[r] = getPdbEntry(stri[0]);
        // and add the new sequence/chain entries
        addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
      }
    }
    else
    {
      pdbe = null;
    }
    return pdbe;
  }

  /**
   * Add sequences to the pe'th pdbentry's sequence set.
   * 
   * @param pe
   * @param seq
   */
  public void addSequence(int pe, SequenceI[] seq)
  {
    addSequenceAndChain(pe, seq, null);
  }

  /**
   * add the given sequences to the mapping scope for the given pdb file handle
   * 
   * @param pdbFile
   *          - pdbFile identifier
   * @param seq
   *          - set of sequences it can be mapped to
   */
  public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
  {
    for (int pe = 0; pe < getPdbCount(); pe++)
    {
      if (getPdbEntry(pe).getFile().equals(pdbFile))
      {
        addSequence(pe, seq);
      }
    }
  }

}