/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program 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 2
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.datamodel;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class AlignmentAnnotation
{
    public SequenceI sequenceRef;

    /** DOCUMENT ME!! */
    public String label;

    /** DOCUMENT ME!! */
    public String description;

    /** DOCUMENT ME!! */
    public Annotation[] annotations;

    public java.util.Hashtable sequenceMapping;

    /** DOCUMENT ME!! */
    public float graphMin;

    /** DOCUMENT ME!! */
    public float graphMax;

    public GraphLine threshold;

    // Graphical hints and tips

    /** DOCUMENT ME!! */
    public boolean editable = false;

    /** DOCUMENT ME!! */
    public boolean hasIcons; //

    /** DOCUMENT ME!! */
    public boolean hasText;

    /** DOCUMENT ME!! */
    public boolean visible = true;

    public int graphGroup = -1;

    /** DOCUMENT ME!! */
    public int height = 0;

    public int graph = 0;

    public int graphHeight = 40;

    public static final int NO_GRAPH = 0;

    public static final int BAR_GRAPH = 1;

    public static final int LINE_GRAPH = 2;

    public static int getGraphValueFromString(String string)
    {
      if(string.equalsIgnoreCase("BAR_GRAPH"))
        return BAR_GRAPH;
      else if(string.equalsIgnoreCase("LINE_GRAPH"))
        return LINE_GRAPH;
      else
        return NO_GRAPH;
    }

    /**
     * Creates a new AlignmentAnnotation object.
     *
     * @param label DOCUMENT ME!
     * @param description DOCUMENT ME!
     * @param annotations DOCUMENT ME!
     */
    public AlignmentAnnotation(String label, String description,
        Annotation[] annotations)
    {
        // always editable?
        editable = true;
        this.label = label;
        this.description = description;
        this.annotations = annotations;

       areLabelsSecondaryStructure();
    }

    void areLabelsSecondaryStructure()
    {
      boolean nonSSLabel = false;
      for (int i = 0; i < annotations.length; i++)
      {
        if(annotations[i]==null)
          continue;

        if (annotations[i].secondaryStructure == 'H' ||
            annotations[i].secondaryStructure == 'E')
        {
          hasIcons = true;
        }

        if (annotations[i].displayCharacter.length()==1
            && !annotations[i].displayCharacter.equals("H")
            && !annotations[i].displayCharacter.equals("E")
            && !annotations[i].displayCharacter.equals("-"))
        {
          if(jalview.schemes.ResidueProperties.aaIndex
             [annotations[i].displayCharacter.charAt(0)]>0)
          {
            nonSSLabel = true;
          }
        }

        if (annotations[i].displayCharacter.length() > 0)
        {
          hasText = true;
        }
      }

      if(nonSSLabel)
      {
        hasIcons = false;
        for (int j = 0; j < annotations.length; j++)
        {
          if(annotations[j] !=null && annotations[j].secondaryStructure!=' ')
          {
            annotations[j].displayCharacter
                =String.valueOf(annotations[j].secondaryStructure);
            annotations[j].secondaryStructure = ' ';
          }

        }

      }

    }

    /**
     * Creates a new AlignmentAnnotation object.
     *
     * @param label DOCUMENT ME!
     * @param description DOCUMENT ME!
     * @param annotations DOCUMENT ME!
     * @param min DOCUMENT ME!
     * @param max DOCUMENT ME!
     * @param winLength DOCUMENT ME!
     */
    public AlignmentAnnotation(String label, String description,
        Annotation[] annotations, float min, float max, int graphType)
    {
        // graphs are not editable
        this.label = label;
        this.description = description;
        this.annotations = annotations;
        graph = graphType;

        boolean drawValues = true;

        if (min == max)
        {
            min = 999999999;
            for (int i = 0; i < annotations.length; i++)
            {
                if (annotations[i] == null)
                {
                    continue;
                }

                if(drawValues && annotations[i].displayCharacter.length() > 1 )
                {
                  drawValues = false;
                }

                if (annotations[i].value > max)
                {
                    max = annotations[i].value;
                }

                if (annotations[i].value < min)
                {
                    min = annotations[i].value;
                }
            }
        }

        graphMin = min;
        graphMax = max;

        areLabelsSecondaryStructure();

        if(!drawValues && graphType!=NO_GRAPH)
        {
          for (int i = 0; i < annotations.length; i++)
          {
            if (annotations[i] != null)
              annotations[i].displayCharacter = "";
          }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String toString()
    {
        StringBuffer buffer = new StringBuffer();

        for (int i = 0; i < annotations.length; i++)
        {
            if (annotations[i] != null)
            {
                if (graph!=0)
                {
                    buffer.append(annotations[i].value);
                }
                else if (hasIcons)
                {
                    buffer.append(annotations[i].secondaryStructure);
                }
                else
                {
                    buffer.append(annotations[i].displayCharacter);
                }
            }

            buffer.append(", ");
        }

        if (label.equals("Consensus"))
        {
            buffer.append("\n");

            for (int i = 0; i < annotations.length; i++)
            {
                if (annotations[i] != null)
                {
                    buffer.append(annotations[i].description);
                }

                buffer.append(", ");
            }
        }

        return buffer.toString();
      }

      public void setThreshold(GraphLine line)
      {
        threshold = line;
      }

      public GraphLine getThreshold()
      {
          return threshold;
      }

      /**
       * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
       * @param seqRef
       * @param startRes
       * @param alreadyMapped
       */
      public void createSequenceMapping(SequenceI seqRef,
                                        int startRes,
                                        boolean alreadyMapped)
      {
        if(seqRef == null)
          return;

        sequenceMapping = new java.util.Hashtable();

        sequenceRef = seqRef;
        int seqPos;

        for(int i = 0; i < annotations.length; i++)
        {
            if (annotations[i] != null)
            {
              if(alreadyMapped)
                seqPos = seqRef.findPosition(i);
              else
                seqPos = i+startRes;

              sequenceMapping.put(new Integer(seqPos), annotations[i]);
            }
         }

        adjustForAlignment();
      }

      public void adjustForAlignment()
      {
          int a=0, aSize = sequenceRef.getLength();

          if(aSize == 0)
          {
            //Its been deleted
            return;
          }

          int position;
          Annotation[] temp = new Annotation[aSize];
          Integer index;

          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
          {
              index = new Integer(a);
              if(sequenceMapping.containsKey(index))
              {
                position = sequenceRef.findIndex(a)-1;

                temp[position] = (Annotation)sequenceMapping.get(index);
              }
          }

          annotations = temp;
      }
}