package jalview.controller;

import java.awt.Color;
import java.util.BitSet;
import java.util.List;

import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;

public class AlignViewController implements AlignViewControllerI
{
  AlignViewportI viewport=null;
  AlignmentViewPanel alignPanel=null;
  /**
   * the GUI container that is handling interactions with the user
   */
  private AlignViewControllerGuiI avcg;
  @Override
  protected void finalize() throws Throwable {
    viewport = null;
    alignPanel = null;
    avcg = null;
  };
  
  public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
          AlignmentViewPanel alignPanel)
  {
    this.avcg = alignFrame;
    this.viewport=viewport;
    this.alignPanel = alignPanel;
  }
  @Override
  public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
  {
    this.alignPanel = alignPanel;
    this.viewport = viewport;
    
  }
  @Override
  public boolean makeGroupsFromSelection()
  {

    if (viewport.getSelectionGroup() != null)
    {
      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
              viewport.getSequenceSelection(),
              viewport.getAlignmentView(true).getSequenceStrings(
                      viewport.getGapCharacter()), viewport.getAlignment()
                      .getGroups());
      viewport.getAlignment().deleteAllGroups();
      viewport.clearSequenceColours();
      viewport.setSelectionGroup(null);
      // set view properties for each group
      for (int g = 0; g < gps.length; g++)
      {
        // gps[g].setShowunconserved(viewport.getShowUnconserved());
        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
        viewport.getAlignment().addGroup(gps[g]);
        Color col = new Color((int) (Math.random() * 255),
                (int) (Math.random() * 255), (int) (Math.random() * 255));
        col = col.brighter();
        for (SequenceI sq : gps[g].getSequences(null))
          viewport.setSequenceColour(sq, col);
      }
      return true;
    }
    return false;
}
  @Override
  public boolean createGroup()
  {

    SequenceGroup sg = viewport.getSelectionGroup();
    if (sg!=null)
    {
        viewport.getAlignment().addGroup(sg);
        return true;
      } 
    return false;
  }
  @Override
  public boolean unGroup()
  {
    SequenceGroup sg = viewport.getSelectionGroup();
    if (sg!=null)
    {
        viewport.getAlignment().deleteGroup(sg);
        return true;
    }
    return false;
  }
  @Override
  public boolean deleteGroups()
  {
    if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
    {
    viewport.getAlignment().deleteAllGroups();
    viewport.clearSequenceColours();
    viewport.setSelectionGroup(null);
    return true;
    }
    return false;
  }
   
  @Override
  public boolean markColumnsContainingFeatures(boolean invert,
          String featureType)
  {
    // JBPNote this routine could also mark rows, not just columns.
    // need a decent query structure to allow all types of feature searches
    BitSet bs = new BitSet();
    List<SequenceI> seqs = viewport.getAlignment().getSequences();
    int alw = viewport.getAlignment().getWidth();
    int nseq = 0;
    for (SequenceI sq : seqs)
    {
      int tfeat = 0;
      if (sq != null)
      {
        SequenceI dsq = sq.getDatasetSequence();
        while (dsq.getDatasetSequence() != null)
        {
          dsq = dsq.getDatasetSequence();
        }
        ;
        SequenceFeature[] sf = dsq.getSequenceFeatures();
        if (sf != null)
        {
          for (SequenceFeature sfpos : sf)
          {
            // future functionalty - featureType == null means mark columns
            // containing all displayed features
            if (sfpos != null && (featureType.equals(sfpos.getType())))
            {
              tfeat++;
              // optimisation - could consider 'spos,apos' like cursor argument
              // - findIndex wastes time by starting from first character and
              // counting

              int i = sq.findIndex(sfpos.getBegin());
              int ist = sq.findIndex(sq.getStart());
              if (i < ist)
              {
                i = ist;
              }
              int j = sq.findIndex(sfpos.getEnd());
              if (j > alw)
              {
                j = alw;
              }
              for (; i <= j; i++)
              {
                bs.set(i - 1);
              }
            }
          }
        }

        if (tfeat > 0)
        {
          nseq++;
        }
      }
    }
    if (bs.cardinality() > 0 || invert)
    {
      ColumnSelection cs = viewport.getColumnSelection();
      if (cs == null)
      {
        cs = new ColumnSelection();
      }
      if (invert)
      {
        for (int i = bs.nextClearBit(0), ibs = bs.nextSetBit(0); i >= 0
                && i < alw;)
        {
          if (ibs < 0 || i < ibs)
          {
            cs.addElement(i++);
          }
          else
          {
            i = bs.nextClearBit(ibs);
            ibs = bs.nextSetBit(i);
          }
        }
      }
      else
      {
        for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
        {
          cs.addElement(i);
        }
      }
      viewport.setColumnSelection(cs);
      alignPanel.paintAlignment(true);
      avcg.setStatus("Marked "
              + (invert ? alw - bs.cardinality() : bs.cardinality())
              + " columns containing features of type " + featureType
              + " across " + nseq);
      return true;
    }
    else
    {
      avcg.setStatus("No features of type " + featureType + " found.");
      return false;
    }
  }
}