package jalview.datamodel;


import java.awt.*;

public class Sequence implements SequenceI {
  protected String   name;
  protected String   sequence;
  protected int      start;
  protected int      end;
  protected String   description;
  protected int      charHeight;
  protected String   displayId;
  protected Color    color = Color.black;

  public Sequence(String name, String sequence, int start, int end)
  {

    this.name     = name;
    this.sequence = sequence;
    this.start    = start;
    this.end      = end;

    setDisplayId();

  }

  public Sequence(String name,String sequence) {
    this(name,sequence,1,sequence.length());
  }
  public Sequence(SequenceI seq) {
    this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
  }
  public String getDisplayId() {
    return displayId;
  }
  public void setDisplayId() {
    displayId = name + "/" + start + "-" + end;
  }
  public void setName(String name) {
    this.name = name;
    setDisplayId();
  }
  public String getName() {
    return this.name;
  }
  public void setStart(int start) {
    this.start = start;
    setDisplayId();
  }
  public int getStart() {
    return this.start;
  }
  public void setEnd(int end) {
    this.end = end;
    setDisplayId();
  }
  public int getEnd() {
    return this.end;
  }
  public int getLength() {
    return this.sequence.length();
  }
  public void setSequence(String seq) {
    this.sequence = seq;
  }
  public String getSequence() {
    return this.sequence;
  }
  public String getSequence(int start,int end) {
    return this.sequence.substring(start,end);
  }

  public char getCharAt(int i) {
    if (i < sequence.length()) {
      return sequence.charAt(i);
    } else {
      return ' ';
    }
  }
  public void setDescription(String desc) {
    this.description = desc;
  }
  public String getDescription() {
    return this.description;
  }

  public int findIndex(int pos) {
    // returns the alignment position for a residue
    int j = start;
    int i = 0;

    while (i< sequence.length() && j <= end && j <= pos) {

      String s = sequence.substring(i,i+1);

      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
        j++;
      }
      i++;
    }
    if (j == end && j < pos) {
      return end+1;
    } else {

      return i;
    }
  }

  public int findPosition(int i) {
    // Returns the sequence position for an alignment position
    int j   = 0;
    int pos = start;

    while (j < i) {
      String s = sequence.substring(j,j+1);

      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
        pos++;
      }
      j++;
    }
    return pos;
  }
  public void deleteCharAt(int i)
  {
    StringBuffer sbuffer = new StringBuffer(sequence);
    sbuffer.deleteCharAt(i);
    sequence = sbuffer.toString();
  }

  public void insertCharAt(int i, char c)
  {
    insertCharAt(i,c,true);
  }

  public void insertCharAt(int i,char c,boolean chop) {

    String tmp = new String(sequence);

    if (i < sequence.length()) {
      sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);
    } else {
      sequence = tmp + String.valueOf(c);
    }

  }

  public void        setColor(Color c) {
    this.color = c;
  }

  public Color       getColor() {
    return color;
  }

}