package jalview.gui.structurechooser;

import java.util.Collection;
import java.util.List;
import java.util.Objects;
import java.util.Vector;

import javax.swing.JTable;
import javax.swing.table.TableModel;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.jbgui.FilterOption;

/**
 * logic for querying sources of structural data for structures of sequences
 * 
 * @author jprocter
 *
 * @param <T>
 */
public abstract class StructureChooserQuerySource
{

  protected FTSDataColumnPreferences docFieldPrefs;

  /**
   * max length of a GET URL (probably :( )
   */
  protected static int MAX_QLENGTH = 7820;

  public StructureChooserQuerySource()
  {
  }

  public static StructureChooserQuerySource getPDBfts()
  {
          return new PDBStructureChooserQuerySource();
  }

  public static StructureChooserQuerySource getTDBfts()
  {
    return new ThreeDBStructureChooserQuerySource();
  }

  public FTSDataColumnPreferences getDocFieldPrefs()
  {
    return docFieldPrefs;
  }

  public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
  {
    this.docFieldPrefs = docFieldPrefs;
  }

  public FTSDataColumnPreferences getInitialFieldPreferences()
  {
    return docFieldPrefs;
  }


  /**
   * Builds a query string for a given sequences using its DBRef entries
   * 
   * @param seq
   *          the sequences to build a query for
   * @return the built query string
   */

  public abstract String buildQuery(SequenceI seq);
  

  /**
   * Remove the following special characters from input string +, -, &, !, (, ),
   * {, }, [, ], ^, ", ~, *, ?, :, \
   * 
   * @param seqName
   * @return
   */
  public static String sanitizeSeqName(String seqName)
  {
    Objects.requireNonNull(seqName);
    return seqName.replaceAll("\\[\\d*\\]", "")
            .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
  }

  /**
   * Ensures sequence ref names are not less than 3 characters and does not
   * contain a database name
   * 
   * @param seqName
   * @return
   */
  static boolean isValidSeqName(String seqName)
  {
    // System.out.println("seqName : " + seqName);
    String ignoreList = "pdb,uniprot,swiss-prot";
    if (seqName.length() < 3)
    {
      return false;
    }
    if (seqName.contains(":"))
    {
      return false;
    }
    seqName = seqName.toLowerCase();
    for (String ignoredEntry : ignoreList.split(","))
    {
      if (seqName.contains(ignoredEntry))
      {
        return false;
      }
    }
    return true;
  }

  static String getDBRefId(DBRefEntry dbRef)
  {
    String ref = dbRef.getAccessionId().replaceAll("GO:", "");
    return ref;
  }

  static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
  {
    Objects.requireNonNull(id);
    Objects.requireNonNull(pdbEntries);
    PDBEntry foundEntry = null;
    for (PDBEntry entry : pdbEntries)
    {
      if (entry.getId().equalsIgnoreCase(id))
      {
        return entry;
      }
    }
    return foundEntry;
  }

  /**
   * FTSRestClient specific query builder to recover associated structure data
   * records for a sequence
   * 
   * @param seq
   *          - seq to generate a query for
   * @param wantedFields
   *          - fields to retrieve
   * @param selectedFilterOpt
   *          - criterion for ranking results (e.g. resolution)
   * @param b
   *          - sort ascending or descending
   * @return
   * @throws Exception
   */
  public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq,
          Collection<FTSDataColumnI> wantedFields,
          FilterOption selectedFilterOpt, boolean b) throws Exception;

  /**
   * FTSRestClient specific query builder to pick top ranked entry from a
   * fetchStructuresMetaData query
   * 
   * @param seq
   *          - seq to generate a query for
   * @param discoveredStructuresSet - existing set of entries - allows client side selection
   * @param wantedFields
   *          - fields to retrieve
   * @param selectedFilterOpt
   *          - criterion for ranking results (e.g. resolution)
   * @param b
   *          - sort ascending or descending
   * @return
   * @throws Exception
   */
  public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
          Collection<FTSData> discoveredStructuresSet, Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
          boolean b) throws Exception;

  /**
   * 
   * @param discoveredStructuresSet
   * @return the table model for the given result set for this engine
   */
  public TableModel getTableModel(
          Collection<FTSData> discoveredStructuresSet)
  {
    return FTSRestResponse.getTableModel(getLastFTSRequest(),
            discoveredStructuresSet);
  }

  protected abstract FTSRestRequest getLastFTSRequest();

  public abstract PDBEntry[] collectSelectedRows(JTable restable,
          int[] selectedRows, List<SequenceI> selectedSeqsToView);

  /**
   * @param VIEWS_FILTER
   *          - a String key that can be used by the caller to tag the returned filter
   *          options to distinguish them in a collection
   * @return list of FilterOption - convention is that the last one in the list
   *         will be constructed with 'addSeparator==true'
   */
  public abstract List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER);

  /**
   * construct a structure chooser query source for the given set of sequences
   * @param selectedSeqs
   * @return PDBe or 3DB query source
   */
  public static StructureChooserQuerySource getQuerySourceFor(
          SequenceI[] selectedSeqs)
  {
    ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
    boolean hasUniprot=false;
    boolean hasNA=false,hasProtein=false;
    for (SequenceI seq:selectedSeqs)
    {
      hasNA|=!seq.isProtein();
      hasProtein |= seq.isProtein();
      if (seq.isProtein())
      {
        String query = tdbSource.buildQuery(seq);
        if (query!=null && query.length()>0)
        {
          hasUniprot=true;
        }
      }
    }
    if (hasProtein && hasUniprot && !hasNA)
    {
      return tdbSource;
    }
    return new PDBStructureChooserQuerySource();
  }

  /**
   * some filter options may mean the original query needs to be executed again. 
   * @param selectedFilterOpt
   * @return true if the fetchStructuresMetadata method needs to be called again
   */
  public abstract boolean needsRefetch(FilterOption selectedFilterOpt);

}