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Iris_PCA.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="author" content="Raphael Balzer, Felix Blum" />
<meta name="date" content="2023-04-26" />
<title>Principal Component Analysis</title>
<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});
</script>
<style type="text/css">.pagedtable {
overflow: auto;
padding-left: 8px;
padding-right: 8px;
}
.pagedtable-wrapper {
border: 1px solid #ccc;
border-radius: 4px;
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width: 100%;
max-width: 100%;
margin: 0;
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border-bottom: 2px solid #dddddd;
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padding: 0 4px 0 4px;
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background-color: rgba(140, 140, 140, 0.1);
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display: none;
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.pagedtable a {
-webkit-touch-callout: none;
-webkit-user-select: none;
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-moz-user-select: none;
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user-select: none;
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.pagedtable-index-nav {
cursor: pointer;
padding: 0 5px 0 5px;
float: right;
border: 0;
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text-decoration: none;
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float: right;
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cursor: default;
text-decoration: none;
font-weight: bold;
color: #333;
border: 0;
}
a.pagedtable-index-current:hover {
text-decoration: none;
font-weight: bold;
color: #333;
}
.pagedtable-index {
width: 30px;
display: inline-block;
text-align: center;
border: 0;
}
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display: inline-block;
color: #333;
font-size: 9px;
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.pagedtable-not-empty .pagedtable-footer {
border-top: 2px solid #dddddd;
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.pagedtable-info {
overflow: hidden;
color: #999;
white-space: nowrap;
text-overflow: ellipsis;
}
.pagedtable-header-name {
overflow: hidden;
text-overflow: ellipsis;
}
.pagedtable-header-type {
color: #999;
font-weight: 400;
}
.pagedtable-na-cell {
font-style: italic;
opacity: 0.3;
}
</style>
<script>// Production steps of ECMA-262, Edition 5, 15.4.4.18
// Reference: http://es5.github.io/#x15.4.4.18
if (!Array.prototype.forEach) {
Array.prototype.forEach = function(callback, thisArg) {
var T, k;
if (this === null) {
throw new TypeError(' this is null or not defined');
}
// 1. Let O be the result of calling toObject() passing the
// |this| value as the argument.
var O = Object(this);
// 2. Let lenValue be the result of calling the Get() internal
// method of O with the argument "length".
// 3. Let len be toUint32(lenValue).
var len = O.length >>> 0;
// 4. If isCallable(callback) is false, throw a TypeError exception.
// See: http://es5.github.com/#x9.11
if (typeof callback !== "function") {
throw new TypeError(callback + ' is not a function');
}
// 5. If thisArg was supplied, let T be thisArg; else let
// T be undefined.
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// 6. Let k be 0
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var kValue;
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// This is implicit for LHS operands of the in operator
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// internal method of O with argument Pk.
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// c. If kPresent is true, then
if (k in O) {
// i. Let kValue be the result of calling the Get internal
// method of O with argument Pk.
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// ii. Call the Call internal method of callback with T as
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callback.call(T, kValue, k, O);
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// d. Increase k by 1.
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}
// 8. return undefined
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}
// Production steps of ECMA-262, Edition 5, 15.4.4.19
// Reference: http://es5.github.io/#x15.4.4.19
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Array.prototype.map = function(callback, thisArg) {
var T, A, k;
if (this == null) {
throw new TypeError(' this is null or not defined');
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// 1. Let O be the result of calling ToObject passing the |this|
// value as the argument.
var O = Object(this);
// 2. Let lenValue be the result of calling the Get internal
// method of O with the argument "length".
// 3. Let len be ToUint32(lenValue).
var len = O.length >>> 0;
// 4. If IsCallable(callback) is false, throw a TypeError exception.
// See: http://es5.github.com/#x9.11
if (typeof callback !== 'function') {
throw new TypeError(callback + ' is not a function');
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// 5. If thisArg was supplied, let T be thisArg; else let T be undefined.
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// 7. Let k be 0
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// 8. Repeat, while k < len
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// a. Let Pk be ToString(k).
// This is implicit for LHS operands of the in operator
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// This step can be combined with c
// c. If kPresent is true, then
if (k in O) {
// i. Let kValue be the result of calling the Get internal
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// ii. Let mappedValue be the result of calling the Call internal
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// list containing kValue, k, and O.
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// iii. Call the DefineOwnProperty internal method of A with arguments
// Pk, Property Descriptor
// { Value: mappedValue,
// Writable: true,
// Enumerable: true,
// Configurable: true },
// and false.
// In browsers that support Object.defineProperty, use the following:
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// value: mappedValue,
// writable: true,
// enumerable: true,
// configurable: true
// });
// For best browser support, use the following:
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}
// d. Increase k by 1.
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// 9. return A
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};
}
var PagedTable = function (pagedTable) {
var me = this;
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var sourceElems = [].slice.call(pagedTable.children).filter(function(e) {
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});
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throw("A single data-pagedtable-source was not found");
}
return JSON.parse(sourceElems[0].innerHTML);
}(pagedTable);
var options = function(source) {
var options = typeof(source.options) !== "undefined" &&
source.options !== null ? source.options : {};
var columns = typeof(options.columns) !== "undefined" ? options.columns : {};
var rows = typeof(options.rows) !== "undefined" ? options.rows : {};
var positiveIntOrNull = function(value) {
return parseInt(value) >= 0 ? parseInt(value) : null;
};
return {
pages: positiveIntOrNull(options.pages),
rows: {
min: positiveIntOrNull(rows.min),
max: positiveIntOrNull(rows.max),
total: positiveIntOrNull(rows.total)
},
columns: {
min: positiveIntOrNull(columns.min),
max: positiveIntOrNull(columns.max),
total: positiveIntOrNull(columns.total)
}
};
}(source);
var Measurer = function() {
// set some default initial values that will get adjusted in runtime
me.measures = {
padding: 12,
character: 8,
height: 15,
defaults: true
};
me.calculate = function(measuresCell) {
if (!me.measures.defaults)
return;
var measuresCellStyle = window.getComputedStyle(measuresCell, null);
var newPadding = parsePadding(measuresCellStyle.paddingLeft) +
parsePadding(measuresCellStyle.paddingRight);
var sampleString = "ABCDEFGHIJ0123456789";
var newCharacter = Math.ceil(measuresCell.clientWidth / sampleString.length);
if (newPadding <= 0 || newCharacter <= 0)
return;
me.measures.padding = newPadding;
me.measures.character = newCharacter;
me.measures.height = measuresCell.clientHeight;
me.measures.defaults = false;
};
return me;
};
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var me = this;
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max: 7,
rows: 10
};
var totalPages = function() {
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};
me.number = 0;
me.max = options.pages !== null ? options.pages : defaults.max;
me.visible = me.max;
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me.setRows = function(newRows) {
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me.total = totalPages();
};
me.setPageNumber = function(newPageNumber) {
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me.number = newPageNumber;
};
me.setVisiblePages = function(visiblePages) {
me.visible = Math.min(me.max, visiblePages);
me.setPageNumber(me.number);
};
me.getVisiblePageRange = function() {
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var end = me.number + Math.floor(me.visible / 2) + 1;
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var diffToStart = 0 - start;
start += diffToStart;
end += diffToStart;
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if (end > pageCount) {
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start -= diffToEnd;
end -= diffToEnd;
}
start = start < 0 ? 0 : start;
end = end >= pageCount ? pageCount : end;
var first = false;
var last = false;
if (start > 0 && me.visible > 1) {
start = start + 1;
first = true;
}
if (end < pageCount && me.visible > 2) {
end = end - 1;
last = true;
}
return {
first: first,
start: start,
end: end,
last: last
};
};
me.getRowStart = function() {
var rowStart = page.number * page.rows;
if (rowStart < 0)
rowStart = 0;
return rowStart;
};
me.getRowEnd = function() {
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return Math.min(rowStart + me.rows, data.length);
};
me.getPaddingRows = function() {
var rowStart = me.getRowStart();
var rowEnd = me.getRowEnd();
return data.length > me.rows ? me.rows - (rowEnd - rowStart) : 0;
};
};
var Columns = function(data, columns, options) {
var me = this;
me.defaults = {
min: 5
};
me.number = 0;
me.visible = 0;
me.total = columns.length;
me.subset = [];
me.padding = 0;
me.min = options.columns.min !== null ? options.columns.min : me.defaults.min;
me.max = options.columns.max !== null ? options.columns.max : null;
me.widths = {};
var widthsLookAhead = Math.max(100, options.rows.min);
var paddingColChars = 10;
me.emptyNames = function() {
columns.forEach(function(column) {
if (columns.label !== null && columns.label !== "")
return false;
});
return true;
};
var parsePadding = function(value) {
return parseInt(value) >= 0 ? parseInt(value) : 0;
};
me.calculateWidths = function(measures) {
columns.forEach(function(column) {
var maxChars = Math.max(
column.label.toString().length,
column.type.toString().length
);
for (var idxRow = 0; idxRow < Math.min(widthsLookAhead, data.length); idxRow++) {
maxChars = Math.max(maxChars, data[idxRow][column.name.toString()].length);
}
me.widths[column.name] = {
// width in characters
chars: maxChars,
// width for the inner html columns
inner: maxChars * measures.character,
// width adding outer styles like padding
outer: maxChars * measures.character + measures.padding
};
});
};
me.getWidth = function() {
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for (var idxCol = 0; idxCol < me.subset.length; idxCol++) {
var columnName = me.subset[idxCol].name;
widthOuter = widthOuter + me.widths[columnName].outer;
}
widthOuter = widthOuter + me.padding * paddingColChars * measurer.measures.character;
if (me.hasMoreLeftColumns()) {
widthOuter = widthOuter + columnNavigationWidthPX + measurer.measures.padding;
}
if (me.hasMoreRightColumns()) {
widthOuter = widthOuter + columnNavigationWidthPX + measurer.measures.padding;
}
return widthOuter;
};
me.updateSlice = function() {
if (me.number + me.visible >= me.total)
me.number = me.total - me.visible;
if (me.number < 0) me.number = 0;
me.subset = columns.slice(me.number, Math.min(me.number + me.visible, me.total));
me.subset = me.subset.map(function(column) {
Object.keys(column).forEach(function(colKey) {
column[colKey] = column[colKey] === null ? "" : column[colKey].toString();
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column.width = null;
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});
};
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me.visible = newVisibleColumns;
me.padding = paddingCount;
me.updateSlice();
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me.setColumnNumber = function(newNumber) {
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me.getPaddingCount = function() {
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me.hasMoreLeftColumns = function() {
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};
me.hasMoreRightColumns = function() {
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};
me.updateSlice(0);
return me;
};
var data = source.data;
var page = new Page(data, options);
var measurer = new Measurer(data, options);
var columns = new Columns(data, source.columns, options);
var table = null;
var tableDiv = null;
var header = null;
var footer = null;
var tbody = null;
// Caches pagedTable.clientWidth, specially for webkit
var cachedPagedTableClientWidth = null;
var onChangeCallbacks = [];
var clearSelection = function() {
if(document.selection && document.selection.empty) {
document.selection.empty();
} else if(window.getSelection) {
var sel = window.getSelection();
sel.removeAllRanges();
}
};
var columnNavigationWidthPX = 5;
var renderColumnNavigation = function(increment, backwards) {
var arrow = document.createElement("div");
arrow.setAttribute("style",
"border-top: " + columnNavigationWidthPX + "px solid transparent;" +
"border-bottom: " + columnNavigationWidthPX + "px solid transparent;" +
"border-" + (backwards ? "right" : "left") + ": " + columnNavigationWidthPX + "px solid;");
var header = document.createElement("th");
header.appendChild(arrow);
header.setAttribute("style",
"cursor: pointer;" +
"vertical-align: middle;" +
"min-width: " + columnNavigationWidthPX + "px;" +
"width: " + columnNavigationWidthPX + "px;");
header.onclick = function() {
columns.incColumnNumber(backwards ? -1 : increment);
me.animateColumns(backwards);
renderFooter();
clearSelection();
triggerOnChange();
};
return header;
};
var maxColumnWidth = function(width) {
var padding = 80;
var columnMax = Math.max(cachedPagedTableClientWidth - padding, 0);
return parseInt(width) > 0 ?
Math.min(columnMax, parseInt(width)) + "px" :
columnMax + "px";
};
var clearHeader = function() {
var thead = pagedTable.querySelectorAll("thead")[0];
thead.innerHTML = "";
};
var renderHeader = function(clear) {
cachedPagedTableClientWidth = pagedTable.clientWidth;
var fragment = document.createDocumentFragment();
header = document.createElement("tr");
fragment.appendChild(header);
if (columns.number > 0)
header.appendChild(renderColumnNavigation(-columns.visible, true));
columns.subset = columns.subset.map(function(columnData) {
var column = document.createElement("th");
column.setAttribute("align", columnData.align);
column.style.textAlign = columnData.align;
column.style.maxWidth = maxColumnWidth(null);
if (columnData.width) {
column.style.minWidth =
column.style.maxWidth = maxColumnWidth(columnData.width);
}
var columnName = document.createElement("div");
columnName.setAttribute("class", "pagedtable-header-name");
if (columnData.label === "") {
columnName.innerHTML = " ";
}
else {
columnName.appendChild(document.createTextNode(columnData.label));
}
column.appendChild(columnName);
var columnType = document.createElement("div");
columnType.setAttribute("class", "pagedtable-header-type");
if (columnData.type === "") {
columnType.innerHTML = " ";
}
else {
columnType.appendChild(document.createTextNode("<" + columnData.type + ">"));
}
column.appendChild(columnType);
header.appendChild(column);
columnData.element = column;
return columnData;
});
for (var idx = 0; idx < columns.getPaddingCount(); idx++) {
var paddingCol = document.createElement("th");
paddingCol.setAttribute("class", "pagedtable-padding-col");
header.appendChild(paddingCol);
}
if (columns.number + columns.visible < columns.total)
header.appendChild(renderColumnNavigation(columns.visible, false));
if (typeof(clear) == "undefined" || clear) clearHeader();
var thead = pagedTable.querySelectorAll("thead")[0];
thead.appendChild(fragment);
};
me.animateColumns = function(backwards) {
var thead = pagedTable.querySelectorAll("thead")[0];
var headerOld = thead.querySelectorAll("tr")[0];
var tbodyOld = table.querySelectorAll("tbody")[0];
me.fitColumns(backwards);
renderHeader(false);
header.style.opacity = "0";
header.style.transform = backwards ? "translateX(-30px)" : "translateX(30px)";
header.style.transition = "transform 200ms linear, opacity 200ms";
header.style.transitionDelay = "0";
renderBody(false);
if (headerOld) {
headerOld.style.position = "absolute";
headerOld.style.transform = "translateX(0px)";
headerOld.style.opacity = "1";
headerOld.style.transition = "transform 100ms linear, opacity 100ms";
headerOld.setAttribute("class", "pagedtable-remove-head");
if (headerOld.style.transitionEnd) {
headerOld.addEventListener("transitionend", function() {
var headerOldByClass = thead.querySelector(".pagedtable-remove-head");
if (headerOldByClass) thead.removeChild(headerOldByClass);
});
}
else {
thead.removeChild(headerOld);
}
}
if (tbodyOld) table.removeChild(tbodyOld);
tbody.style.opacity = "0";
tbody.style.transition = "transform 200ms linear, opacity 200ms";
tbody.style.transitionDelay = "0ms";
// force relayout
window.getComputedStyle(header).opacity;
window.getComputedStyle(tbody).opacity;
if (headerOld) {
headerOld.style.transform = backwards ? "translateX(20px)" : "translateX(-30px)";
headerOld.style.opacity = "0";
}
header.style.transform = "translateX(0px)";
header.style.opacity = "1";
tbody.style.opacity = "1";
}
me.onChange = function(callback) {
onChangeCallbacks.push(callback);
};
var triggerOnChange = function() {
onChangeCallbacks.forEach(function(onChange) {
onChange();
});
};
var clearBody = function() {
if (tbody) {
table.removeChild(tbody);
tbody = null;
}
};
var renderBody = function(clear) {
cachedPagedTableClientWidth = pagedTable.clientWidth
var fragment = document.createDocumentFragment();
var pageData = data.slice(page.getRowStart(), page.getRowEnd());
pageData.forEach(function(dataRow, idxRow) {
var htmlRow = document.createElement("tr");
htmlRow.setAttribute("class", (idxRow % 2 !==0) ? "even" : "odd");
if (columns.hasMoreLeftColumns())
htmlRow.appendChild(document.createElement("td"));
columns.subset.forEach(function(columnData) {
var cellName = columnData.name;
var dataCell = dataRow[cellName];
var htmlCell = document.createElement("td");
if (dataCell === "NA") htmlCell.setAttribute("class", "pagedtable-na-cell");
if (dataCell === "__NA__") dataCell = "NA";
var cellText = document.createTextNode(dataCell);
htmlCell.appendChild(cellText);
if (dataCell.length > 50) {
htmlCell.setAttribute("title", dataCell);
}
htmlCell.setAttribute("align", columnData.align);
htmlCell.style.textAlign = columnData.align;
htmlCell.style.maxWidth = maxColumnWidth(null);
if (columnData.width) {
htmlCell.style.minWidth = htmlCell.style.maxWidth = maxColumnWidth(columnData.width);
}
htmlRow.appendChild(htmlCell);
});
for (var idx = 0; idx < columns.getPaddingCount(); idx++) {
var paddingCol = document.createElement("td");
paddingCol.setAttribute("class", "pagedtable-padding-col");
htmlRow.appendChild(paddingCol);
}
if (columns.hasMoreRightColumns())
htmlRow.appendChild(document.createElement("td"));
fragment.appendChild(htmlRow);
});
for (var idxPadding = 0; idxPadding < page.getPaddingRows(); idxPadding++) {
var paddingRow = document.createElement("tr");
var paddingCellRow = document.createElement("td");
paddingCellRow.innerHTML = " ";
paddingCellRow.setAttribute("colspan", "100%");
paddingRow.appendChild(paddingCellRow);
fragment.appendChild(paddingRow);
}
if (typeof(clear) == "undefined" || clear) clearBody();
tbody = document.createElement("tbody");
tbody.appendChild(fragment);
table.appendChild(tbody);
};
var getLabelInfo = function() {
var pageStart = page.getRowStart();
var pageEnd = page.getRowEnd();
var totalRows = data.length;
var totalRowsLabel = options.rows.total ? options.rows.total : totalRows;
var totalRowsLabelFormat = totalRowsLabel.toString().replace(/(\d)(?=(\d\d\d)+(?!\d))/g, '$1,');
var infoText = (pageStart + 1) + "-" + pageEnd + " of " + totalRowsLabelFormat + " rows";
if (totalRows < page.rows) {
infoText = totalRowsLabel + " row" + (totalRows != 1 ? "s" : "");
}
if (columns.total > columns.visible) {
var totalColumnsLabel = options.columns.total ? options.columns.total : columns.total;
infoText = infoText + " | " + (columns.number + 1) + "-" +
(Math.min(columns.number + columns.visible, columns.total)) +
" of " + totalColumnsLabel + " columns";
}
return infoText;
};
var clearFooter = function() {
footer = pagedTable.querySelectorAll("div.pagedtable-footer")[0];
footer.innerHTML = "";
return footer;
};
var createPageLink = function(idxPage) {
var pageLink = document.createElement("a");
pageLinkClass = idxPage === page.number ? "pagedtable-index pagedtable-index-current" : "pagedtable-index";
pageLink.setAttribute("class", pageLinkClass);
pageLink.setAttribute("data-page-index", idxPage);
pageLink.onclick = function() {
page.setPageNumber(parseInt(this.getAttribute("data-page-index")));
renderBody();
renderFooter();
triggerOnChange();
};
pageLink.appendChild(document.createTextNode(idxPage + 1));
return pageLink;
}
var renderFooter = function() {
footer = clearFooter();
var next = document.createElement("a");
next.appendChild(document.createTextNode("Next"));
next.onclick = function() {
page.setPageNumber(page.number + 1);
renderBody();
renderFooter();
triggerOnChange();
};
if (data.length > page.rows) footer.appendChild(next);
var pageNumbers = document.createElement("div");
pageNumbers.setAttribute("class", "pagedtable-indexes");
var pageRange = page.getVisiblePageRange();
if (pageRange.first) {
var pageLink = createPageLink(0);
pageNumbers.appendChild(pageLink);
var pageSeparator = document.createElement("div");
pageSeparator.setAttribute("class", "pagedtable-index-separator-left");
pageSeparator.appendChild(document.createTextNode("..."))
pageNumbers.appendChild(pageSeparator);
}
for (var idxPage = pageRange.start; idxPage < pageRange.end; idxPage++) {
var pageLink = createPageLink(idxPage);
pageNumbers.appendChild(pageLink);
}
if (pageRange.last) {
var pageSeparator = document.createElement("div");
pageSeparator.setAttribute("class", "pagedtable-index-separator-right");
pageSeparator.appendChild(document.createTextNode("..."))
pageNumbers.appendChild(pageSeparator);
var pageLink = createPageLink(page.total - 1);
pageNumbers.appendChild(pageLink);
}
if (data.length > page.rows) footer.appendChild(pageNumbers);
var previous = document.createElement("a");
previous.appendChild(document.createTextNode("Previous"));
previous.onclick = function() {
page.setPageNumber(page.number - 1);
renderBody();
renderFooter();
triggerOnChange();
};
if (data.length > page.rows) footer.appendChild(previous);
var infoLabel = document.createElement("div");
infoLabel.setAttribute("class", "pagedtable-info");
infoLabel.setAttribute("title", getLabelInfo());
infoLabel.appendChild(document.createTextNode(getLabelInfo()));
footer.appendChild(infoLabel);
var enabledClass = "pagedtable-index-nav";
var disabledClass = "pagedtable-index-nav pagedtable-index-nav-disabled";
previous.setAttribute("class", page.number <= 0 ? disabledClass : enabledClass);
next.setAttribute("class", (page.number + 1) * page.rows >= data.length ? disabledClass : enabledClass);
};
var measuresCell = null;
var renderMeasures = function() {
var measuresTable = document.createElement("table");
measuresTable.style.visibility = "hidden";
measuresTable.style.position = "absolute";
measuresTable.style.whiteSpace = "nowrap";
measuresTable.style.height = "auto";
measuresTable.style.width = "auto";