------------------------------------------------------------------------------- The Dendrogrammer v 1.0.1 Readme.txt ------------------------------------------------------------------------------- In this file - Installation - System requirements - Browser compatibility and Compatibility list - The application files - Data file format - Licence and copyright notices ------------------------------------------------------------------------------- Installation: ------------------------------------------------------------------------------- - Extract or copy the "dendrogrammer" directory into PHP enabled web space. Running the application: - Assuming you have installed the "dendrogrammer" directory in web space that can be addressed with the following URL www.mywebspace.com then you can run the application by asking your browser to request this URL www.mywebspace.com/dendrogrammer/version1_0_1/dendrogrammer.php Loading data using the calling URL: - If the name of the desired data file selection is known in advance, and that data file is present in the data directory, then the data to load can be specified as a querie string in the calling URL. e.g. www.mywebspace.com/dendrogrammer/version1_0_1/dendrogrammer.php?mydatafile.dat ------------------------------------------------------------------------------- System Requirements: ------------------------------------------------------------------------------- The application files need to be placed in PHP enabled web space. The application is run from a web browser requesting the PHP file (dendrogrammer.php). ------------------------------------------------------------------------------- Browser compatibility: ------------------------------------------------------------------------------- In theory the application can run on any modern JavaScript enabled browser (see compatibility list below). In practice with larger data sets, The 'JScript' engine in Internet Explorer 7 and 8 will struggle to cope with the processing demand unless run on high end PCs. All the other browsers should perform well even on modest equipment including tablet computers. ------------------------------------------------------------------------------- Compatibility list: ------------------------------------------------------------------------------- Firefox 3.6+, Safari 5.0+ (including iPad), Chrome 5.0+, Opera 11.5+ and Internet Explorer 7+. Performance is slow on IE 7 and 8. Performance is good on IE 9+. These are the compatible browsers proved in tests. It is a conservative list. The Raphael documentation claims that the graphics should render properly in Firefox 3.0+, Safari 3.0+, Chrome 5.0+, Opera 9.5+ and Internet Explorer 6.0+. JQuery UI claims to render properly in “IE 6.0+, Firefox 3+, Safari 3.1+, Opera 9.6+ and Google Chrome”. ------------------------------------------------------------------------------- The Files: ------------------------------------------------------------------------------- The application directory should contain this file and 2 directories: Readme.txt /version1_0_0 and /libraries The version1_0_0 directory should contain 3 files and a data directory dendrogrammer.js dendrogrammer.php dendrogrammer_styles.css and /data The data directory should contain 3 files (See Data file format section below) 1default.dat 1default.node.csv 1default.leaf.csv The libraries directory should contain 2 files and the ui directory: jquery-latest.min.js raphael.js and /ui The ui directory should contain the following files and an image directory: The jQuery UI js files required in the JQuery UI folder are: jquery.effects.core.js jquery.effects.pulsate.js jquery.ui.button.js jquery.ui.core.js jquery.ui.dialog.js jquery.ui.draggable.js jquery.ui.mouse.js jquery.ui.position.js jquery.ui.tabs.js jquery.ui.widget.js Associated css style sheet files are: jquery.ui.all.css jquery.ui.base.css jquery.ui.button.css jquery.ui.core.css jquery.ui.dialog.css jquery.ui.resizable.css jquery.ui.selectable.css jquery.ui.tabs.css jquery.ui.theme.css There is a directory of images in the ui directory /images The imges directory should contain the following files: ui-bg_flat_0_aaaaaa_40x100.png ui-bg_flat_75_ffffff_40x100.png ui-bg_glass_55_fbf9ee_1x400.png ui-bg_glass_65_ffffff_1x400.png ui-bg_glass_75_dadada_1x400.png ui-bg_glass_75_dadada_1x400.png ui-bg_glass_75_e6e6e6_1x400.png ui-bg_glass_95_fef1ec_1x400.png ui-bg_highlight-soft_75_cccccc_1x100.png ui-icons_2e83ff_256x240.png ui-icons_222222_256x240.png ui-icons_454545_256x240.png ui-icons_888888_256x240.png ui-icons_cd0a0a_256x240.png ------------------------------------------------------------------------------- Data File Format: ------------------------------------------------------------------------------- Data File Format The application requires that 3 files be present in the Data directory. 1default.dat, 1default.node.csv, and 1default.leaf.csv. (In fact it will run with no data directory at all. However it will only load demo data.) Further sets of data files should be added to the data directory. The format of these files is specified below 1) The .dat file holds meta-data: Line 1: the name of the node file to be loaded. Line 2: the name of the leaf file to be loaded. Line 3: a short text description of the origin of the data. Line 4: a search URL to which any leaf data gets appended to call a search engine. – Examine the supplied file, “1default.dat”, as an example 2) The other 2 files should be CSV files. 3) The node file holds the 3 column MATLAB clustering output. The column headings would be Item-A, Item-B, and Merge Ht. (However, any column headings should be removed from the file). - Examine the supplied file, “1default.node.csv”, as an example 4) The leaf file holds the leaf descriptions (short and long descriptions) keyed to their MATLAB leaf cluster ID number. The three column headings would be Leaf ID No, Short Description, and Long Description. (However, any column headings should be removed from the file). - Examine the supplied file, “1default.leaf.csv”, as an example. ------------------------------------------------------------------------------- Licence and copyright notices: ------------------------------------------------------------------------------- Copyright 2011 David Robb. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ------------------------------------------------------------------------------- jQuery and Raphael ------------------------------------------------------------------------------- The application makes use of the the jQuery and Raphael JavaScript libraries The following notices apply to those: ------------------------------------------------------------------------------- jQuery ------------------------------------------------------------------------------- Copyright (c) 2011 John Resig, http://jquery.com/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ------------------------------------------------------------------------------- Raphael ------------------------------------------------------------------------------- Copyright © 2008 Dmitry Baranovskiy Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. The software is provided “as is”, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.