// Generated by CoffeeScript 1.8.0
var abs, calc_crosstab, chrscales, colSums, displayError, expand2vector, forceAsArray, formatAxis, getLeftRight, log10, log2, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, missing2null, pullVarAsArray, reorgLodData, rowSums, selectGroupColors, sumArray, transpose, unique;

formatAxis = function(d, extra_digits) {
  var ndig;
  if (extra_digits == null) {
    extra_digits = 0;
  }
  d = d[1] - d[0];
  ndig = Math.floor(Math.log(d % 10) / Math.log(10));
  if (ndig > 0) {
    ndig = 0;
  }
  ndig = Math.abs(ndig) + extra_digits;
  return d3.format("." + ndig + "f");
};

unique = function(x) {
  var output, v, _i, _len, _results;
  output = {};
  for (_i = 0, _len = x.length; _i < _len; _i++) {
    v = x[_i];
    if (v) {
      output[v] = v;
    }
  }
  _results = [];
  for (v in output) {
    _results.push(output[v]);
  }
  return _results;
};

pullVarAsArray = function(data, variable) {
  var i, v;
  v = [];
  for (i in data) {
    v = v.concat(data[i][variable]);
  }
  return v;
};

reorgLodData = function(data, lodvarname) {
  var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
  if (lodvarname == null) {
    lodvarname = null;
  }
  data.posByChr = {};
  data.lodByChr = {};
  if ('additive' in data){
    data.additiveByChr = {};
  }
  _ref = data.chrnames;
  for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
    chr = _ref[i];
    data.posByChr[chr[0]] = [];
    data.lodByChr[chr[0]] = [];
    if ('additive' in data){
      data.additiveByChr[chr[0]] = [];
    }
    _ref1 = data.pos;

    for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
      pos = _ref1[j];
      if (data.chr[j].toString() === chr[0]) {
        data.posByChr[chr[0]].push(pos);
        if (!Array.isArray(data.lodnames)) {
          data.lodnames = [data.lodnames];
        }
        lodval = (function() {
          var _k, _len2, _ref2, _results;
          _ref2 = data.lodnames;
          _results = [];
          for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
            lodcolumn = _ref2[_k];
            _results.push(data[lodcolumn][j]);
          }
          return _results;
        })();
        data.lodByChr[chr[0]].push(lodval);

        if ('additive' in data){
          addval = data['additive'][j]
          data.additiveByChr[chr[0]].push(addval);
        }

      }
    }
  }
  if (lodvarname != null) {
    data.markers = [];
    _ref2 = data.markernames;
    for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
      marker = _ref2[i];
      if (marker !== "") {
        data.markers.push({
          name: marker,
          chr: data.chr[i],
          pos: data.pos[i],
          lod: data[lodvarname][i]
        });
      }
    }
  }
  return data;
};

chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) {
  var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
  chrStart = [];
  chrEnd = [];
  chrLength = [];
  totalChrLength = 0;
  maxd = 0;
  _ref = data.chrnames;
  for (_i = 0, _len = _ref.length; _i < _len; _i++) {
    chr = _ref[_i];
    d = maxdiff(data.posByChr[chr[0]]);
    if (d > maxd) {
      maxd = d;
    }
    //rng = d3.extent(data.posByChr[chr[0]]);
    //chrStart.push(rng[0]);
    //chrEnd.push(rng[1]);
    //L = rng[1] - rng[0];
    chrStart.push(0);
    chrEnd.push(chr[1]);
    L = chr[1]
    chrLength.push(L);
    totalChrLength += L;
  }
  if (pad4heatmap) {
    data.recwidth = maxd;
    chrStart = chrStart.map(function(x) {
      return x - maxd / 2;
    });
    chrEnd = chrEnd.map(function(x) {
      return x + maxd / 2;
    });
    chrLength = chrLength.map(function(x) {
      return x + maxd;
    });
    totalChrLength += chrLength.length * maxd;
  }
  data.chrStart = [];
  data.chrEnd = [];
  cur = leftMargin;
  if (!pad4heatmap) {
    cur += chrGap / 2;
  }
  data.xscale = {};
  _ref1 = data.chrnames;
  for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
    chr = _ref1[i];
    data.chrStart.push(cur);
    w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]);
    data.chrEnd.push(cur + w);
    cur = data.chrEnd[i] + chrGap;

    if (mappingScale == "morgan") {
        max_pos = d3.max(data.posByChr[chr[0]])
        data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]);
    }
    else {
        data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
    }
  }
  return data;
};

selectGroupColors = function(ngroup, palette) {
  if (ngroup === 0) {
    return [];
  }
  if (palette === "dark") {
    if (ngroup === 1) {
      return ["slateblue"];
    }
    if (ngroup === 2) {
      return ["MediumVioletRed", "slateblue"];
    }
    if (ngroup <= 9) {
      return colorbrewer.Set1[ngroup];
    }
    return d3.scale.category20().range().slice(0, ngroup);
  } else {
    if (ngroup === 1) {
      return ["#bebebe"];
    }
    if (ngroup === 2) {
      return ["lightpink", "lightblue"];
    }
    if (ngroup <= 9) {
      return colorbrewer.Pastel1[ngroup];
    }
    return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup);
  }
};

expand2vector = function(input, n) {
  var i;
  if (input == null) {
    return input;
  }
  if (Array.isArray(input) && input.length >= n) {
    return input;
  }
  if (!Array.isArray(input)) {
    input = [input];
  }
  if (input.length === 1 && n > 1) {
    input = (function() {
      var _results;
      _results = [];
      for (i in d3.range(n)) {
        _results.push(input[0]);
      }
      return _results;
    })();
  }
  return input;
};

median = function(x) {
  var n;
  if (x == null) {
    return null;
  }
  n = x.length;
  x.sort(function(a, b) {
    return a - b;
  });
  if (n % 2 === 1) {
    return x[(n - 1) / 2];
  }
  return (x[n / 2] + x[(n / 2) - 1]) / 2;
};

getLeftRight = function(x) {
  var i, n, result, v, xdif, _i, _j, _k, _len, _ref;
  n = x.length;
  x.sort(function(a, b) {
    return a - b;
  });
  xdif = [];
  result = {};
  for (_i = 0, _len = x.length; _i < _len; _i++) {
    v = x[_i];
    result[v] = {};
  }
  for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) {
    xdif.push(x[i] - x[i - 1]);
    result[x[i]].left = x[i - 1];
  }
  for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) {
    result[x[i]].right = x[i + 1];
  }
  xdif = median(xdif);
  result.mediandiff = xdif;
  result[x[0]].left = x[0] - xdif;
  result[x[n - 1]].right = x[n - 1] + xdif;
  result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2];
  return result;
};

maxdiff = function(x) {
  var d, i, result, _i, _ref;
  if (x.length < 2) {
    return null;
  }
  result = x[1] - x[0];
  if (x.length < 3) {
    return result;
  }
  for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
    d = x[i] - x[i - 1];
    if (d > result) {
      result = d;
    }
  }
  return result;
};

matrixMin = function(mat) {
  var i, j, result;
  result = mat[0][0];
  for (i in mat) {
    for (j in mat[i]) {
      if (result > mat[i][j]) {
        result = mat[i][j];
      }
    }
  }
  return result;
};

matrixMax = function(mat) {
  var i, j, result;
  result = mat[0][0];
  for (i in mat) {
    for (j in mat[i]) {
      if (result < mat[i][j]) {
        result = mat[i][j];
      }
    }
  }
  return result;
};

matrixMaxAbs = function(mat) {
  var i, j, result;
  result = Math.abs(mat[0][0]);
  for (i in mat) {
    for (j in mat[i]) {
      if (result < mat[i][j]) {
        result = Math.abs(mat[i][j]);
      }
    }
  }
  return result;
};

matrixExtent = function(mat) {
  return [matrixMin(mat), matrixMax(mat)];
};

d3.selection.prototype.moveToFront = function() {
  return this.each(function() {
    return this.parentNode.appendChild(this);
  });
};

d3.selection.prototype.moveToBack = function() {
  return this.each(function() {
    var firstChild;
    firstChild = this.parentNode.firstchild;
    if (firstChild) {
      return this.parentNode.insertBefore(this, firstChild);
    }
  });
};

forceAsArray = function(x) {
  if (x == null) {
    return x;
  }
  if (Array.isArray(x)) {
    return x;
  }
  return [x];
};

missing2null = function(vec, missingvalues) {
  if (missingvalues == null) {
    missingvalues = ['NA', ''];
  }
  return vec.map(function(value) {
    if (missingvalues.indexOf(value) > -1) {
      return null;
    } else {
      return value;
    }
  });
};

displayError = function(message) {
  if (d3.select("div.error").empty()) {
    d3.select("body").insert("div", ":first-child").attr("class", "error");
  }
  return d3.select("div.error").append("p").text(message);
};

sumArray = function(vec) {
  return vec.reduce(function(a, b) {
    return a + b;
  });
};

calc_crosstab = function(data) {
  var col, cs, i, ncol, nrow, result, row, rs, _i, _j;
  nrow = data.ycat.length;
  ncol = data.xcat.length;
  result = (function() {
    var _i, _results;
    _results = [];
    for (row = _i = 0; 0 <= nrow ? _i <= nrow : _i >= nrow; row = 0 <= nrow ? ++_i : --_i) {
      _results.push((function() {
        var _j, _results1;
        _results1 = [];
        for (col = _j = 0; 0 <= ncol ? _j <= ncol : _j >= ncol; col = 0 <= ncol ? ++_j : --_j) {
          _results1.push(0);
        }
        return _results1;
      })());
    }
    return _results;
  })();
  for (i in data.x) {
    result[data.y[i]][data.x[i]] += 1;
  }
  rs = rowSums(result);
  cs = colSums(result);
  for (i = _i = 0; 0 <= ncol ? _i < ncol : _i > ncol; i = 0 <= ncol ? ++_i : --_i) {
    result[nrow][i] = cs[i];
  }
  for (i = _j = 0; 0 <= nrow ? _j < nrow : _j > nrow; i = 0 <= nrow ? ++_j : --_j) {
    result[i][ncol] = rs[i];
  }
  result[nrow][ncol] = sumArray(rs);
  return result;
};

rowSums = function(mat) {
  var x, _i, _len, _results;
  _results = [];
  for (_i = 0, _len = mat.length; _i < _len; _i++) {
    x = mat[_i];
    _results.push(sumArray(x));
  }
  return _results;
};

transpose = function(mat) {
  var i, j, _i, _ref, _results;
  _results = [];
  for (j = _i = 0, _ref = mat[0].length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) {
    _results.push((function() {
      var _j, _ref1, _results1;
      _results1 = [];
      for (i = _j = 0, _ref1 = mat.length; 0 <= _ref1 ? _j < _ref1 : _j > _ref1; i = 0 <= _ref1 ? ++_j : --_j) {
        _results1.push(mat[i][j]);
      }
      return _results1;
    })());
  }
  return _results;
};

colSums = function(mat) {
  return rowSums(transpose(mat));
};

log2 = function(x) {
  if (x == null) {
    return x;
  }
  return Math.log(x) / Math.log(2.0);
};

log10 = function(x) {
  if (x == null) {
    return x;
  }
  return Math.log(x) / Math.log(10.0);
};

abs = function(x) {
  if (x == null) {
    return x;
  }
  return Math.abs(x);
};