(* Last edited on 1999-08-05 19:03:39 by hcgl *)



PROCEDURE TrimAndPackCandidate(
    READONLY cand: PZCandidate.T;
    READONLY match: PZMatch.T;
    mismatch: LONGREAL;
    length: LONGREAL;
    nMatched: CARDINAL;
    step: LONGREAL;
  ): PZCandidate.T =
  VAR t: ARRAY [0..1] OF PZSegment.T;  (* Matched segments *)
  BEGIN
    WITH
      nm = NUMBER(match),
      rpm = PZMatch.Pack(match)
    DO
      (* Trim the candidate "cand" to the matched part: *)
      FOR j := 0 TO 1 DO 
        WITH sj = cand.seg[j], tj = t[j] DO
          tj := sj;
          IF sj.rev THEN
            tj.ini := (sj.ini + sj.len - 1 - match[nm-1][j]) MOD sj.tot
          ELSE
            tj.ini := (sj.ini + match[0][j]) MOD sj.tot;
          END;
          tj.len := match[nm-1][j] - match[0][j] + 1;
        END;
      END;
      (* Output the trimmed candidate with the encoded matching: *)
      RETURN
        PZCandidate.T{
          seg := t,
          mismatch := mismatch,
          length := length,
          matched := FLOAT(nMatched, LONGREAL) * step,
          pm := PZMatch.AdjustPacked(rpm, cand.seg, t)
        }
    END
  END TrimAndPackCandidate;


PROCEDURE FmtMatchedRange(
    READONLY seg: PZSegment.T; 
    m: CARDINAL;  
    iniMatch, finMatch: CARDINAL;
    reversed: BOOLEAN;
  ): TEXT =
  VAR mIni, mFin: CARDINAL;
  BEGIN
    WITH wr = NEW(TextWr.T).init() DO
      IF reversed THEN
        mIni := m - 1 - finMatch + seg.ini;
        mFin := m - 1 - iniMatch + seg.ini;
      ELSE
        mIni := iniMatch + seg.ini;
        mFin := finMatch + seg.ini
      END;
      Wr.PutText(wr, " [" & Fmt.Int(mIni));
      Wr.PutText(wr, ".." & Fmt.Int(mFin) & "]");
      RETURN TextWr.ToText(wr)
    END
  END FmtMatchedRange;






  
      ,
      ma = NUMBER(cha.c^),
      mb = NUMBER(chb.c^),
      na = (cNew.seg[0].fin - cNew.seg[0].ini) MOD ma, 
      nb = (cNew.seg[1].fin - cNew.seg[1].ini) MOD mb 
      
      <* ASSERT NUMBER(ca)>0 *>
      <* ASSERT NUMBER(cb)>0 *>
      IF reverse THEN PZLR3Chain.Reverse(cb) END;
      
      aOldSeg = cOld.seg[0],
      cha = ch[aOldSeg.cvx],
      ma = NUMBER(cha.c^),
      aStep =  chLength[aOldSeg.cvx] / FLOAT(nSamples, LONGREAL),
      aNewSeg := ExpandSegment(aOldSeg, ma, aStep, o.extraLength),
      
      bOldSeg = cOld.seg[1],
      chb = ch[bOldSeg.cvx],
      mb = NUMBER(chb.c^),
      bStep = chLength[bOldSeg.cvx] / FLOAT(mb, LONGREAL),
      bExtra = CEILING(o.extraLength / bStep),
      rnb = (bOldSeg.fin - bOldSeg.ini) MOD mb + 1,
      nb = MIN(rnb + 2*bExtra, mb),
      bStretch = (nb - rnb) DIV 2,
      ib = (bOldSeg.ini - bStretch) MOD mb,
      fb = (ib + nb) MOD mb,
      

      





PROCEDURE ReadAllFLCFiles(
    chainPrefix : TEXT;
    nChains, band: CARDINAL; 
  ): REF ARRAY OF ChainData =
  BEGIN 
   WITH 
     ch = NEW(REF ARRAY OF ChainData, nChains)
   DO 
     FOR i := 0 TO nChains-1 DO  
       WITH 
         chainTag  = Fmt.Pad(Fmt.Int(i), 4, '0'),
         bandTag = Fmt.Pad(Fmt.Int(band), 3, '0'),
         fileName = 
            chainTag & "/" & chainPrefix & "-" & chainTag & "-f" & bandTag & "-c-u.flc",
         rd = FileRd.Open(fileName)
       DO
         Wr.PutText(stderr, fileName & "\n");
         WITH d = PZLR3Chain.Read(rd) DO
           ch[i] := ChainData{
             cmt := d.cmt,
             length := PZLR3Chain.Length(d.c^, 0, LAST(d.c^)),
             c := d.c
           }
         END;
         Rd.Close(rd);
       END;
     END;
     RETURN ch;
    END;  
  END ReadAllFLCFiles;



PROCEDURE DisplaceChain(
    READONLY c: PZLR3Chain.T;
    displace: LONGREAL
  ): REF PZLR3Chain.T =
  BEGIN 
    IF displace > 0.0d0 THEN 
      WITH 
        u = PZGeo.CalculateDir(c[0], c[LAST(c)]), 
        mt = PZGeo.BuildMatrixT(-u[1]*displace, u[0]*displace)
      DO   
        RETURN PZLR3Chain.Map(c, mt);
      END;
    ELSE  
      RETURN  PZLR3Chain.Map(c, Identity());
    END;
  END DisplaceChain;



      d := 0.0d0; i:= 0;
      REPEAT  
        INC(i);
        d := Dist(q[(i+s) MOD n] , q[(i+s-1) MOD n]) + d;
      UNTIL d > length OR i = n;





  PROCEDURE   ComputeRandomSubFloatChain (
    READONLY c: FloatChain; 
    length: LONGREAL; 
    VAR reg : Reg): 
    REF FloatChain =
    VAR sc : REF FloatChain;
  BEGIN  
    WITH 
      n = NUMBER(c),  
      r = NEW(Random.Default).init(),
      i = r.integer(0,n-1)
    DO   
      sc := GetSubChain(c,length,i,reg);
      
      RETURN sc;
    END;  
  END ComputeRandomSubFloatChain;