package jalview.io;

import jalview.datamodel.*;
import jalview.util.*;

import java.io.*;
import java.util.*;

public class MSFfile extends AlignFile {

  public MSFfile()
  {}

  public MSFfile(String inStr) {
    super(inStr);
  }

  public MSFfile(String inFile, String type) throws IOException {
    super(inFile,type);
  }

  private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~","-");
  private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex("["+jalview.util.Comparison.GapChars+"]","\\~");

  public void parse() {
    int       i       = 0;
    boolean   seqFlag = false;
    String    key     = new String();
    Vector    headers = new Vector();
    Hashtable seqhash = new Hashtable();
    String    line;

    try {
    while ((line = nextLine()) != null) {

      StringTokenizer str = new StringTokenizer(line);

      while (str.hasMoreTokens()) {

        String inStr = str.nextToken();

        //If line has header information add to the headers vector
        if (inStr.indexOf("Name:") != -1) {
          key = str.nextToken();
          headers.addElement(key);
        }

        //if line has // set SeqFlag to 1 so we know sequences are coming
        if (inStr.indexOf("//") != -1) {
          seqFlag = true;
        }

        //Process lines as sequence lines if seqFlag is set
        if (( inStr.indexOf("//") == -1) && (seqFlag == true)) {
          //seqeunce id is the first field
          key = inStr;
          StringBuffer tempseq;

          //Get sequence from hash if it exists
          if (seqhash.containsKey(key)) {
            tempseq = (StringBuffer)seqhash.get(key);
          } else {
	    tempseq = new StringBuffer();
	    seqhash.put(key,tempseq);
	  }

          //loop through the rest of the words
          while (str.hasMoreTokens()) {
            //append the word to the sequence
            tempseq.append(str.nextToken());
          }
        }
      }
    }
    } catch (IOException e) {
      System.err.println("Exception parsing MSFFile " + e);
      e.printStackTrace();
    }

    this.noSeqs = headers.size();

    //Add sequences to the hash
    for (i = 0; i < headers.size(); i++ ) {

      if ( seqhash.get(headers.elementAt(i)) != null) {
        String head =  headers.elementAt(i).toString();
        String seq  =  seqhash.get(head).toString();

        int start = 1;
        int end = seq.length();

        if (maxLength <  head.length() ) {
          maxLength =  head.length();
        }

        if (head.indexOf("/") > 0 ) {

          StringTokenizer st = new StringTokenizer(head,"/");

          if (st.countTokens() == 2) {

            head = st.nextToken();
            String tmp = st.nextToken();
            st = new StringTokenizer(tmp,"-");
            if (st.countTokens() == 2) {
              start = Integer.valueOf(st.nextToken()).intValue();
              end = Integer.valueOf(st.nextToken()).intValue();
            }
          }
        }
        // Replace ~ with a sensible gap character
        seq = gapre.replaceAll(seq);
        Sequence newSeq = new Sequence(head,seq,start,end);

        seqs.addElement(newSeq);

      } else {
        System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));
      }
    }

  }

  public static int checkSum(String seq) {
    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
    int check = 0;

    String index =  "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
    index += "--------------------------------------------------------------------------------------------------------------------------------";

    for(int i = 0; i < seq.length(); i++) {
      try {
        if (i <seq.length()) {
          int pos = index.indexOf(seq.substring(i,i+1));
          if (!index.substring(pos,pos+1).equals("_")) {
            check += ((i % 57) + 1) * pos;
          }
        }
      } catch (Exception e) {
        System.err.println("Exception during MSF Checksum calculation");
        e.printStackTrace();
      }
    }
    return check % 10000;
  }

  public static String print(SequenceI[] s) {
    return print(s, false);
  }
  public static String print(SequenceI[] s, boolean is_NA) {
    StringBuffer out = new StringBuffer("!!"+(is_NA ? "NA":"AA")+"_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.

    int max = 0;
    int maxid = 0;
    int i = 0;
    String big = "";

    while (i < s.length && s[i] != null) {
      String sq;
      big += (sq=s[i].getSequence());
      if (sq.length() > max) {
        max = sq.length();
      }
      i++;
    }
    Format maxLenpad = new Format("%"+(new String(""+max)).length()+"d");
    Format maxChkpad = new Format("%"+(new String("1"+max)).length()+"d");
    i = 0;
    long bigcheck = checkSum(big);
    long maxNB=0;
    out.append("   MSF: " + s[0].getSequence().length() + "   Type: "+(is_NA?"N":"P")+"    Check:  " + bigcheck + "   ..\n\n\n");
    String nameBlock[] = new String[s.length];
    String idBlock[] = new String[s.length];
    while (i < s.length && s[i] != null) {
      String seq = s[i].getSequence();
      String name =  s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd();
      int check = checkSum(s[i].getSequence());
      nameBlock[i]=new String("  Name: "+name+" ");
      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length()) + "  Check:" + maxChkpad.form(check) + "  Weight: 1.00\n");

      if (name.length() > maxid) {
        maxid = name.length();
      }
      if (nameBlock[i].length()>maxNB) {
        maxNB=nameBlock[i].length();
      }

      i++;
    }
    if (maxid < 10) {
      maxid = 10;
    }
    if (maxNB<15) {
      maxNB=15;
    }
    Format nbFormat = new Format("%-"+maxNB+"s");
    for (i=0;i<s.length && s[i]!=null;i++) {
      out.append(nbFormat.form(nameBlock[i])+idBlock[i]);
    }
    maxid++;
    out.append( "\n\n//\n\n");

    int len = 50;

    int nochunks =  max / len + 1;
    if (max%len == 0) {
      nochunks--;
    }
    for (i = 0; i < nochunks; i++) {
      int j = 0;
      while (j < s.length && s[j] != null) {
        String name =  s[j].getName();
        out.append( new Format("%-" + maxid + "s").form(name + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
        for (int k = 0; k < 5; k++) {

          int start = i*50 + k*10;
          int end = start + 10;

          if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
            out.append(re2gap.replaceAll(s[j].getSequence().substring(start,end)));
            if (k < 4) {
              // out.append(" ");
            } else {
              out.append("\n");
            }
          } else {
            if (start < s[j].getSequence().length()) {
              out.append(re2gap.replaceAll(s[j].getSequence().substring(start)));
              out.append("\n");
            } else {
              if (k == 0) {
                out.append("\n");
              }
            }
          }
        }
        j++;
      }
      out.append("\n");

    }
    return out.toString();
  }
  public String print() {
    return print(getSeqsAsArray());
  }
}