/*
 * 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.structures.models;

import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.AtomSpecModel;
import jalview.ext.rbvi.chimera.ChimeraCommands;
import jalview.io.DataSourceType;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;

import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Collections;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

/**
 * 
 * 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;

  /*
   * distinct PDB entries (pdb files) associated
   * with sequences
   */
  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
   */
  DataSourceType protocol = null;

  protected boolean colourBySequence = true;

  private boolean nucleotide;

  private boolean finishedInit = false;

  /**
   * current set of model filenames loaded in the Jmol instance
   */
  protected String[] modelFileNames = null;

  public String fileLoadingError;

  private boolean showAlignmentOnly;

  /*
   * a list of chains "pdbid:chainid" to show in the viewer;
   * empty means show all
   */
  // TODO make private once deprecated JalviewJmolBinding.centerViewer removed
  protected List<String> chainsToShow;

  private boolean hideHiddenRegions;

  protected List<String> chainNames = new ArrayList<>();

  /**
   * Data bean class to simplify parameterisation in superposeStructures
   */
  protected class SuperposeData
  {
    /**
     * Constructor with alignment width argument
     * 
     * @param width
     */
    public SuperposeData(int width)
    {
      pdbResNo = new int[width];
    }

    public String filename;

    public String pdbId;

    public String chain = "";

    public boolean isRna;

    /*
     * The pdb residue number (if any) mapped to each column of the alignment
     */
    public int[] pdbResNo;
  }

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

  /**
   * Constructor
   * 
   * @param ssm
   * @param pdbentry
   * @param sequenceIs
   * @param protocol
   */
  public AAStructureBindingModel(StructureSelectionManager ssm,
          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
          DataSourceType protocol)
  {
    this.ssm = ssm;
    this.sequence = sequenceIs;
    this.nucleotide = Comparison.isNucleotide(sequenceIs);
    this.pdbEntry = pdbentry;
    this.protocol = protocol;
    chainsToShow = new ArrayList<>();

    resolveChains();
  }

  private boolean resolveChains()
  {
    /**
     * final count of chain mappings discovered
     */
    int chainmaps = 0;
    // JBPNote: JAL-2693 - this should be a list of chain mappings per
    // [pdbentry][sequence]
    String[][] newchains = new String[pdbEntry.length][];
    int pe = 0;
    for (PDBEntry pdb : pdbEntry)
    {
      SequenceI[] seqsForPdb = sequence[pe];
      if (seqsForPdb != null)
      {
        newchains[pe] = new String[seqsForPdb.length];
        int se = 0;
        for (SequenceI asq : seqsForPdb)
        {
          String chain = (chains != null && chains[pe] != null)
                  ? chains[pe][se]
                  : null;
          SequenceI sq = (asq.getDatasetSequence() == null) ? asq
                  : asq.getDatasetSequence();
          if (sq.getAllPDBEntries() != null)
          {
            for (PDBEntry pdbentry : sq.getAllPDBEntries())
            {
              if (pdb.getFile() != null && pdbentry.getFile() != null
                      && pdb.getFile().equals(pdbentry.getFile()))
              {
                String chaincode = pdbentry.getChainCode();
                if (chaincode != null && chaincode.length() > 0)
                {
                  chain = chaincode;
                  chainmaps++;
                  break;
                }
              }
            }
          }
          newchains[pe][se] = chain;
          se++;
        }
        pe++;
      }
    }

    chains = newchains;
    return chainmaps > 0;
  }
  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;
  }

  /**
   * Answers true if this binding includes the given PDB id, else false
   * 
   * @param pdbId
   * @return
   */
  public boolean hasPdbId(String pdbId)
  {
    if (pdbEntry != null)
    {
      for (PDBEntry pdb : pdbEntry)
      {
        if (pdb.getId().equals(pdbId))
        {
          return true;
        }
      }
    }
    return false;
  }

  /**
   * 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 DataSourceType 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 pdbe = getPdbEntry(0);
    title.append(viewerName + " view for " + getSequence()[0][0].getName()
            + ":" + pdbe.getId());

    if (verbose)
    {
      String method = (String) pdbe.getProperty("method");
      if (method != null)
      {
        title.append(" Method: ").append(method);
      }
      String chain = (String) pdbe.getProperty("chains");
      if (chain != null)
      {
        title.append(" Chain:").append(chain);
      }
    }
    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<>();
    List<String> c = new ArrayList<>();
    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<>();
    List<int[]> rtn = new ArrayList<>();
    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);
      }
    }
  }

  @Override
  public abstract void highlightAtoms(List<AtomSpec> atoms);

  protected boolean isNucleotide()
  {
    return this.nucleotide;
  }

  /**
   * Returns a readable description of all mappings for the wrapped pdbfile to
   * any mapped sequences
   * 
   * @param pdbfile
   * @param seqs
   * @return
   */
  public String printMappings()
  {
    if (pdbEntry == null)
    {
      return "";
    }
    StringBuilder sb = new StringBuilder(128);
    for (int pdbe = 0; pdbe < getPdbCount(); pdbe++)
    {
      String pdbfile = getPdbEntry(pdbe).getFile();
      List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]);
      sb.append(getSsm().printMappings(pdbfile, seqs));
    }
    return sb.toString();
  }

  /**
   * Returns the mapped structure position for a given aligned column of a given
   * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
   * not mapped to structure.
   * 
   * @param seq
   * @param alignedPos
   * @param mapping
   * @return
   */
  protected int getMappedPosition(SequenceI seq, int alignedPos,
          StructureMapping mapping)
  {
    if (alignedPos >= seq.getLength())
    {
      return -1;
    }

    if (Comparison.isGap(seq.getCharAt(alignedPos)))
    {
      return -1;
    }
    int seqPos = seq.findPosition(alignedPos);
    int pos = mapping.getPDBResNum(seqPos);
    return pos;
  }

  /**
   * Helper method to identify residues that can participate in a structure
   * superposition command. For each structure, identify a sequence in the
   * alignment which is mapped to the structure. Identify non-gapped columns in
   * the sequence which have a mapping to a residue in the structure. Returns
   * the index of the first structure that has a mapping to the alignment.
   * 
   * @param alignment
   *          the sequence alignment which is the basis of structure
   *          superposition
   * @param matched
   *          a BitSet, where bit j is set to indicate that every structure has
   *          a mapped residue present in column j (so the column can
   *          participate in structure alignment)
   * @param structures
   *          an array of data beans corresponding to pdb file index
   * @return
   */
  protected int findSuperposableResidues(AlignmentI alignment,
          BitSet matched, SuperposeData[] structures)
  {
    int refStructure = -1;
    String[] files = getStructureFiles();
    if (files == null)
    {
      return -1;
    }
    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
    {
      StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
      int lastPos = -1;

      /*
       * Find the first mapped sequence (if any) for this PDB entry which is in
       * the alignment
       */
      final int seqCountForPdbFile = getSequence()[pdbfnum].length;
      for (int s = 0; s < seqCountForPdbFile; s++)
      {
        for (StructureMapping mapping : mappings)
        {
          final SequenceI theSequence = getSequence()[pdbfnum][s];
          if (mapping.getSequence() == theSequence
                  && alignment.findIndex(theSequence) > -1)
          {
            if (refStructure < 0)
            {
              refStructure = pdbfnum;
            }
            for (int r = 0; r < alignment.getWidth(); r++)
            {
              if (!matched.get(r))
              {
                continue;
              }
              int pos = getMappedPosition(theSequence, r, mapping);
              if (pos < 1 || pos == lastPos)
              {
                matched.clear(r);
                continue;
              }
              lastPos = pos;
              structures[pdbfnum].pdbResNo[r] = pos;
            }
            String chain = mapping.getChain();
            if (chain != null && chain.trim().length() > 0)
            {
              structures[pdbfnum].chain = chain;
            }
            structures[pdbfnum].pdbId = mapping.getPdbId();
            structures[pdbfnum].isRna = theSequence.getRNA() != null;

            /*
             * move on to next pdb file (ignore sequences for other chains
             * for the same structure)
             */
            s = seqCountForPdbFile;
            break;
          }
        }
      }
    }
    return refStructure;
  }

  /**
   * Returns true if the structure viewer has loaded all of the files of
   * interest (identified by the file mapping having been set up), or false if
   * any are still not loaded after a timeout interval.
   * 
   * @param files
   */
  protected boolean waitForFileLoad(String[] files)
  {
    /*
     * give up after 10 secs plus 1 sec per file
     */
    long starttime = System.currentTimeMillis();
    long endTime = 10000 + 1000 * files.length + starttime;
    String notLoaded = null;

    boolean waiting = true;
    while (waiting && System.currentTimeMillis() < endTime)
    {
      waiting = false;
      for (String file : files)
      {
        notLoaded = file;
        if (file == null)
        {
          continue;
        }
        try
        {
          StructureMapping[] sm = getSsm().getMapping(file);
          if (sm == null || sm.length == 0)
          {
            waiting = true;
          }
        } catch (Throwable x)
        {
          waiting = true;
        }
      }
    }

    if (waiting)
    {
      System.err.println(
              "Timed out waiting for structure viewer to load file "
                      + notLoaded);
      return false;
    }
    return true;
  }

  @Override
  public boolean isListeningFor(SequenceI seq)
  {
    if (sequence != null)
    {
      for (SequenceI[] seqs : sequence)
      {
        if (seqs != null)
        {
          for (SequenceI s : seqs)
          {
            if (s == seq || (s.getDatasetSequence() != null
                    && s.getDatasetSequence() == seq.getDatasetSequence()))
            {
              return true;
            }
          }
        }
      }
    }
    return false;
  }

  public boolean isFinishedInit()
  {
    return finishedInit;
  }

  public void setFinishedInit(boolean fi)
  {
    this.finishedInit = fi;
  }

  /**
   * Returns the Jalview panel hosting the structure viewer (if any)
   * 
   * @return
   */
  public JalviewStructureDisplayI getViewer()
  {
    return null;
  }

  public abstract void setJalviewColourScheme(ColourSchemeI cs);

  /**
   * Constructs and sends a command to align structures against a reference
   * structure, based on one or more sequence alignments. May optionally return
   * an error or warning message for the alignment command.
   * 
   * @param alignments
   *          an array of alignments to process
   * @param structureIndices
   *          an array of corresponding reference structures (index into pdb
   *          file array); if a negative value is passed, the first PDB file
   *          mapped to an alignment sequence is used as the reference for
   *          superposition
   * @param hiddenCols
   *          an array of corresponding hidden columns for each alignment
   * @return
   */
  public abstract String superposeStructures(AlignmentI[] alignments,
          int[] structureIndices, HiddenColumns[] hiddenCols);

  public abstract void setBackgroundColour(Color col);

  protected abstract String[] getColourBySequenceCommands(
          String[] files, AlignmentViewPanel avp);

  /**
   * returns the current sequenceRenderer that should be used to colour the
   * structures
   * 
   * @param alignment
   * 
   * @return
   */
  public abstract SequenceRenderer getSequenceRenderer(
          AlignmentViewPanel alignment);

  protected abstract void colourBySequence(
          String[] colourBySequenceCommands);

  public abstract void colourByChain();

  public abstract void colourByCharge();

  /**
   * Recolours the displayed structures, if they are coloured by sequence, or
   * 'show only visible alignment' is selected. This supports updating structure
   * colours on either change of alignment colours, or change to the visible
   * region of the alignment.
   */
  public void updateStructureColours(AlignmentViewPanel alignmentv)
  {
    if (!isLoadingFinished())
    {
      return;
    }

    /*
     * if structure is not coloured by sequence, but restricted to the alignment,
     * then redraw it (but don't recolour it) in case hidden regions have changed
     * (todo: specific messaging for change of hidden region only)
     */
    if (!colourBySequence)
    {
      if (isShowAlignmentOnly())
      {
        showStructures(alignmentv.getAlignViewport(), false);
      }
      return;
    }
    if (getSsm() == null)
    {
      return;
    }
    String[] files = getStructureFiles();

    String[] colourBySequenceCommands = getColourBySequenceCommands(
            files, alignmentv);
    colourBySequence(colourBySequenceCommands);
  }

  public boolean hasFileLoadingError()
  {
    return fileLoadingError != null && fileLoadingError.length() > 0;
  }

  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
          AlignmentViewPanel alignment);

  /**
   * Sets the flag for whether only mapped visible residues in the alignment
   * should be visible in the structure viewer
   * 
   * @param b
   */
  public void setShowAlignmentOnly(boolean b)
  {
    showAlignmentOnly = b;
  }

  /**
   * Answers true if only residues mapped to the alignment should be shown in the
   * structure viewer, else false
   * 
   * @return
   */
  public boolean isShowAlignmentOnly()
  {
    return showAlignmentOnly;
  }

  /**
   * Sets the flag for hiding regions of structure which are hidden in the
   * alignment (only applies when the structure viewer is restricted to the
   * alignment only)
   * 
   * @param b
   */
  public void setHideHiddenRegions(boolean b)
  {
    hideHiddenRegions = b;
  }

  /**
   * Answers true if regions hidden in the alignment should also be hidden in the
   * structure viewer, else false (only applies when the structure viewer is
   * restricted to the alignment only)
   * 
   * @return
   */
  public boolean isHideHiddenRegions()
  {
    return hideHiddenRegions;
  }

  /**
   * Shows the structures in the viewer, without changing their colouring. This is
   * to support toggling of whether the whole structure is shown, or only residues
   * mapped to visible regions of the alignment.
   * 
   * @param alignViewportI
   * @param refocus
   *                         if true, refit the display to the viewer
   */
  public void showStructures(AlignViewportI alignViewportI, boolean refocus)
  {
    // override with implementation
  }

  @Override
  public void updateColours(Object source)
  {
    AlignmentViewPanel ap = (AlignmentViewPanel) source;
    // ignore events from panels not used to colour this view
    if (!getViewer().isUsedforcolourby(ap))
    {
      return;
    }
    if (!isLoadingFromArchive())
    {
      updateStructureColours(ap);
    }
  }

  /**
   * Sets the list of chains to display (as "pdbid:chain"), where an empty list
   * means show all
   * 
   * @param chains
   */
  public void setChainsToShow(List<String> chains)
  {
    chainsToShow = chains;
  }

  /**
   * Answers true if the specified structure and chain are selected to be shown in
   * the viewer, else false
   * 
   * @param pdbId
   * @param chainId
   * @return
   */
  protected boolean isShowChain(String pdbId, String chainId)
  {
    if (chainsToShow.isEmpty())
    {
      return true;
    }
    return chainsToShow.contains(pdbId + ":" + chainId);
  }

  @Override
  public abstract String[] getStructureFiles();

  /**
   * Builds a model of residues mapped from sequences to show on structure, taking
   * into account user choices of
   * <ul>
   * <li>which chains are shown</li>
   * <li>whether all structure is shown, or only that mapped to the alignment</li>
   * <li>whether hidden regions of the alignment are hidden (excluded) or grayed
   * out (included)</li>
   * </ul>
   * 
   * @param av
   * @return
   */
  protected AtomSpecModel getShownResidues(AlignViewportI av)
  {
    AlignmentI alignment = av.getAlignment();
    final int width = alignment.getWidth();
  
    String[] files = getStructureFiles();
  
    AtomSpecModel model = new AtomSpecModel();
  
    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
    {
      StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
  
      /*
       * Find the first mapped sequence (if any) for this PDB entry which is in
       * the alignment
       */
      final int seqCountForPdbFile = getSequence()[pdbfnum].length;
      for (int s = 0; s < seqCountForPdbFile; s++)
      {
        for (StructureMapping mapping : mappings)
        {
          final SequenceI theSequence = getSequence()[pdbfnum][s];
          if (mapping.getSequence() == theSequence
                  && alignment.findIndex(theSequence) > -1)
          {
            String chainCd = mapping.getChain();
            if (!isShowChain(mapping.getPdbId(), chainCd))
            {
              continue;
            }
            Iterator<int[]> visible;
            if (isShowAlignmentOnly() && isHideHiddenRegions())
            {
              visible = alignment.getHiddenColumns()
                    .getVisContigsIterator(0, width, true);
            }
            else
            {
              visible = Collections.singletonList(new int[] { 0, width })
                      .iterator();
            }
            while (visible.hasNext())
            {
              int[] visibleRegion = visible.next();
              int seqStartPos = theSequence.findPosition(visibleRegion[0]);
              int seqEndPos = theSequence.findPosition(visibleRegion[1]);
              List<int[]> residueRanges = mapping
                      .getPDBResNumRanges(seqStartPos, seqEndPos);
              if (!residueRanges.isEmpty())
              {
                for (int[] range : residueRanges)
                {
                  model.addRange(pdbfnum, range[0], range[1], chainCd);
                }
              }
            }
          }
        }
      }
    }
  
    return model;
  }

  /**
   * Answers a default structure model specification which is simply the string
   * form of the model number. Override if needed to specify submodels.
   * 
   * @param model
   * @return
   */
  public String getModelSpec(int model)
  {
    return String.valueOf(model);
  }

  /**
   * Build a data structure which records contiguous subsequences for each colour.
   * From this we can easily generate the Chimera command for colour by sequence.
   * 
   * <pre>
   * Color
   *     Model number
   *         Chain
   *             list of start/end ranges
   * </pre>
   * 
   * Ordering is by order of addition (for colours and positions), natural
   * ordering (for models and chains)
   * 
   * @param viewPanel
   * @return
   */
  public Map<Object, AtomSpecModel> buildColoursMap(
          AlignmentViewPanel viewPanel)
  {
    FeatureRenderer fr = viewPanel.getFeatureRenderer();
    FeatureColourFinder finder = new FeatureColourFinder(fr);
    AlignViewportI viewport = viewPanel.getAlignViewport();
    HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
    AlignmentI al = viewport.getAlignment();
    SequenceRenderer sr = getSequenceRenderer(viewPanel);
    String[] files = getStructureFiles();
    
    Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
    Color lastColour = null;
  
    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
    {
      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  
      if (mapping == null || mapping.length < 1)
      {
        continue;
      }
  
      int startPos = -1, lastPos = -1;
      String lastChain = "";
      for (int s = 0; s < sequence[pdbfnum].length; s++)
      {
        for (int sp, m = 0; m < mapping.length; m++)
        {
          final SequenceI seq = sequence[pdbfnum][s];
          if (mapping[m].getSequence() == seq
                  && (sp = al.findIndex(seq)) > -1)
          {
            SequenceI asp = al.getSequenceAt(sp);
            for (int r = 0; r < asp.getLength(); r++)
            {
              // no mapping to gaps in sequence
              if (Comparison.isGap(asp.getCharAt(r)))
              {
                continue;
              }
              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  
              if (pos < 1 || pos == lastPos)
              {
                continue;
              }
  
              Color colour = sr.getResidueColour(seq, r, finder);
  
              /*
               * hidden regions are shown gray or, optionally, ignored
               */
              if (!cs.isVisible(r))
              {
                if (hideHiddenRegions)
                {
                  continue;
                }
                else
                {
                  colour = Color.GRAY;
                }
              }
  
              final String chain = mapping[m].getChain();
  
              /*
               * Just keep incrementing the end position for this colour range
               * _unless_ colour, PDB model or chain has changed, or there is a
               * gap in the mapped residue sequence
               */
              final boolean newColour = !colour.equals(lastColour);
              final boolean nonContig = lastPos + 1 != pos;
              final boolean newChain = !chain.equals(lastChain);
              if (newColour || nonContig || newChain)
              {
                if (startPos != -1)
                {
                  ChimeraCommands.addAtomSpecRange(colourMap, lastColour,
                          pdbfnum, startPos,
                          lastPos, lastChain);
                }
                startPos = pos;
              }
              lastColour = colour;
              lastPos = pos;
              lastChain = chain;
            }
            // final colour range
            if (lastColour != null)
            {
              ChimeraCommands.addAtomSpecRange(colourMap, lastColour,
                      pdbfnum,
                      startPos, lastPos, lastChain);
            }
            // break;
          }
        }
      }
    }
    return colourMap;
  }

  /**
   * Returns a list of chains mapped in this viewer. Note this list is not
   * currently scoped per structure.
   * 
   * @return
   */
  public List<String> getChainNames()
  {
    return chainNames;
  }
}