/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 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;

public class AlignmentAnnotation
{
  public String label;
  public String description;
  public Annotation  [] annotations;
  public boolean isGraph = false;
  public float graphMin, graphMax;
  public int windowLength;

  // Graphical hints and tips
  public boolean editable = false;
  public boolean hasIcons; //
  public boolean hasText;
  public boolean visible = true;
  public int height=0;

  public AlignmentAnnotation(String label, String description, Annotation [] annotations)
  {
    // always editable?
    editable = true;
    this.label = label;
    this.description = description;
    this.annotations = annotations;
    for(int i=0; i<annotations.length; i++)
    {
      if (annotations[i]!=null &&(
          annotations[i].secondaryStructure == 'H' ||
          annotations[i].secondaryStructure == 'E'))
        hasIcons = true;

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

  public AlignmentAnnotation(String label, String description, Annotation [] annotations, float min, float max, int winLength)
  {
    // graphs are not editable
    this.label = label;
    this.description = description;
    this.annotations = annotations;
    isGraph = true;
    if(min==max)
    {
      for(int i=0; i<annotations.length; i++)
      {
        if(annotations[i]==null)
          continue;
        if(annotations[i].value>max)
          max = annotations[i].value;
        if(annotations[i].value<min)
          min = annotations[i].value;
      }
    }

    graphMin = min;
    graphMax = max;
    windowLength = winLength;
    for(int i=0; i<annotations.length; i++)
    {
      if (annotations[i]!=null &&(
          annotations[i].secondaryStructure == 'H' ||
          annotations[i].secondaryStructure == 'E'))
        hasIcons = true;

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

  public String toString()
  {
    StringBuffer buffer = new StringBuffer();
    for(int i=0; i<annotations.length; i++)
   {
     if(annotations[i]!=null)
     {
       if(isGraph)
         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();
  }

}