-
Notifications
You must be signed in to change notification settings - Fork 11
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #124 from AliTVTeam/rc/version1.0.0
Rc/version1.0.0
- Loading branch information
Showing
8 changed files
with
52 additions
and
50 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -35,11 +35,11 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| /* global bootbox: false */ | ||
|
|
||
| // use const instead of var as soon as EcmaScript 6 (ES6 is widely used) | ||
| var AliTV_VERSION = "0.4.1"; | ||
| var AliTV_VERSION = "1.0.0"; | ||
|
|
||
| /** | ||
| * Creates an object of type AliTV for drawing whole genome alignment visualizations | ||
| * @author Markus Ankenbrand <[email protected]> | ||
| * @author Markus Ankenbrand <[email protected]> | ||
| * @constructor | ||
| * @param {Object} svg - jQuery object containing a svg DOM element. Visualizations will be drawn on this svg. Size may be changed by object methods. Previous content will be deleted. | ||
| * @example | ||
|
|
@@ -88,7 +88,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| * @property {Object} filters.karyo - the chromosome dependent displaying information | ||
| * @property {Boolean} filters.skipChromosomesWithoutVisibleLinks - If a chromosome has no visible links, because they are filtered, it is possible to skip this chromosome. | ||
| * @property {Boolean} filters.showAllChromosomes - Allows to show all chromosomes, even if when they are set not visible. | ||
| * @property {Boolean} filters.onlyShowAdjacentLinks - Allows to show only adjacent links or all links. | ||
| * @property {Boolean} filters.onlyShowAdjacentLinks - Allows to show only adjacent links or all links. | ||
| * @property {Array} filters.karyo.order - array of chromosome IDs in the desired order (circular layout) | ||
| * @property {Array} filters.karyo.genome_order - array of genome IDs in the desired order (linear layout) | ||
| * @property {Object} filters.karyo.chromosomes - the chromosome drawing details, karyo IDs as keys | ||
|
|
@@ -111,13 +111,13 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| * @property {String} linear.endLineColor - The end color of the color gradient. | ||
| * @property {String} linear.hideHalfVisibleLinks - If true - do not show links with only one end in a visible region. | ||
| * @property {Object} circular - The configuration options for the circular layout. | ||
| * @property {Number} circular.tickSize - The size of the ticks in pixels. | ||
| * @property {Number} circular.tickSize - The size of the ticks in pixels. | ||
| * @property {Number} minLinkIdentity - The minimum of the link identity the user wants to color. | ||
| * @property {Number} maxLinkIdentity - The maximum of the link identity the user wants to color. | ||
| * @property {Number} midLinkIdentity - The middle of the link identity the user wants to color. | ||
| * @property {String} minLinkIdentityColor - The color of the minimum link. | ||
| * @property {String} maxLinkIdentityColor - The color of the maximum link. | ||
| * @property {String} midLinkIdentityColor - The color of the middle link. | ||
| * @property {String} midLinkIdentityColor - The color of the middle link. | ||
| * @property {Number} minLinkLength - The minimum length of a link: | ||
| * @property {Number} maxLinkLength - The maximum length of a link. | ||
| * @property {Object} graphicalParameters - The configuration options for all graphical parameters. | ||
|
|
@@ -1629,7 +1629,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| }; | ||
|
|
||
| /** | ||
| * This function returns an array which contains the color of the first and the last genome. | ||
| * This function returns an array which contains the color of the first and the last genome. | ||
| * The colors are defined in the conf-object. | ||
| * @returns {Array} The color of the first and the last genome. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -1662,7 +1662,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| }; | ||
|
|
||
| /** | ||
| * This function returns an array which contains the color of the minLinkIdentity and the maxLinkIdentity. | ||
| * This function returns an array which contains the color of the minLinkIdentity and the maxLinkIdentity. | ||
| * The colors are defined in the conf-object. | ||
| * @returns {Array} The color of the links with the minimal and maximal identity. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -1719,7 +1719,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| *This method should filter all chromosome which are set visible in conf.filters.karyo.chromosomes[<chromosome>].visible | ||
| * @param visibleChromosomes: the method gets all current visible chromosomes. | ||
| * @returns filteredChromosomes: the method returns only chromosomes whose visibility is set true | ||
| * @author Sonja Hohlfeld | ||
| * @author Sonja Hohlfeld | ||
| */ | ||
| AliTV.prototype.filterVisibleChromosomes = function(visibleChromosomes) { | ||
| var that = this; | ||
|
|
@@ -1736,7 +1736,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| * This method should filter all chromosome which have no visible links with the current configurations | ||
| * @param visibleChromosomes: the method gets all current visible chromosomes. | ||
| * @returns filteredChromosomes: the method returns only chromosomes which have visible links | ||
| * @author Sonja Hohlfeld | ||
| * @author Sonja Hohlfeld | ||
| */ | ||
| AliTV.prototype.filterChromosomeWithoutVisibleLinks = function(visibleChromosomes) { | ||
| var that = this; | ||
|
|
@@ -2669,7 +2669,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the color of the genomeLabels. | ||
| * This function returns the color of the genomeLabels. | ||
| * The color is defined in the conf-object. | ||
| * @returns The color of the genome labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2696,7 +2696,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the size of the genomeLabels. | ||
| * This function returns the size of the genomeLabels. | ||
| * The size is defined in the conf-object. | ||
| * @returns The size of the genome labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2730,7 +2730,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the color of the tick Labels. | ||
| * This function returns the color of the tick Labels. | ||
| * The color is defined in the conf-object. | ||
| * @returns The color of the tick labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2756,7 +2756,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the size of the tick Labels. | ||
| * This function returns the size of the tick Labels. | ||
| * The size is defined in the conf-object. | ||
| * @returns The size of the tick labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2834,7 +2834,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| /** | ||
| * This function is supposed to return the value of the longest chromosome. | ||
| * @return maxLinkLength: the value of the longest chromosome in bp. | ||
| * @author Sonja Hohlfeld | ||
| * @author Sonja Hohlfeld | ||
| */ | ||
| AliTV.prototype.getMaxChromosomeLength = function() { | ||
| var length = []; | ||
|
|
@@ -3020,7 +3020,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| this.triggerChange(); | ||
| }; | ||
|
|
||
| /** | ||
| /** | ||
| * This function is supposed to change the visibility of a selected chromosome. | ||
| * The function gets the name of a chromosome and set his visibility in filters.karyo.chromosomes equal false or true. | ||
| * @param {String} chromosomeName: the name of the selected chromosome. | ||
|
|
@@ -3159,7 +3159,7 @@ <h1 class="page-title">Source: AliTV.js</h1> | |
| } | ||
| }; | ||
|
|
||
| /** | ||
| /** | ||
| * This function is supposed to return an array of supported features | ||
| * @returns {Array} supportedFeatures | ||
| * @author: Sonja Hohlfeld and Markus Ankenbrand | ||
|
|
@@ -3558,7 +3558,7 @@ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="AliTV.htm | |
| <br class="clear"> | ||
|
|
||
| <footer> | ||
| Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.4.0</a> on Fri Aug 05 2016 10:13:29 GMT+0200 (CEST) | ||
| Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.4.0</a> on Thu Apr 13 2017 17:44:50 GMT+0200 (CEST) | ||
| </footer> | ||
|
|
||
| <script> prettyPrint(); </script> | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -7,11 +7,11 @@ | |
| /* global bootbox: false */ | ||
|
|
||
| // use const instead of var as soon as EcmaScript 6 (ES6 is widely used) | ||
| var AliTV_VERSION = "0.4.1"; | ||
| var AliTV_VERSION = "1.0.0"; | ||
|
|
||
| /** | ||
| * Creates an object of type AliTV for drawing whole genome alignment visualizations | ||
| * @author Markus Ankenbrand <[email protected]> | ||
| * @author Markus Ankenbrand <[email protected]> | ||
| * @constructor | ||
| * @param {Object} svg - jQuery object containing a svg DOM element. Visualizations will be drawn on this svg. Size may be changed by object methods. Previous content will be deleted. | ||
| * @example | ||
|
|
@@ -60,7 +60,7 @@ function AliTV(svg) { | |
| * @property {Object} filters.karyo - the chromosome dependent displaying information | ||
| * @property {Boolean} filters.skipChromosomesWithoutVisibleLinks - If a chromosome has no visible links, because they are filtered, it is possible to skip this chromosome. | ||
| * @property {Boolean} filters.showAllChromosomes - Allows to show all chromosomes, even if when they are set not visible. | ||
| * @property {Boolean} filters.onlyShowAdjacentLinks - Allows to show only adjacent links or all links. | ||
| * @property {Boolean} filters.onlyShowAdjacentLinks - Allows to show only adjacent links or all links. | ||
| * @property {Array} filters.karyo.order - array of chromosome IDs in the desired order (circular layout) | ||
| * @property {Array} filters.karyo.genome_order - array of genome IDs in the desired order (linear layout) | ||
| * @property {Object} filters.karyo.chromosomes - the chromosome drawing details, karyo IDs as keys | ||
|
|
@@ -83,13 +83,13 @@ function AliTV(svg) { | |
| * @property {String} linear.endLineColor - The end color of the color gradient. | ||
| * @property {String} linear.hideHalfVisibleLinks - If true - do not show links with only one end in a visible region. | ||
| * @property {Object} circular - The configuration options for the circular layout. | ||
| * @property {Number} circular.tickSize - The size of the ticks in pixels. | ||
| * @property {Number} circular.tickSize - The size of the ticks in pixels. | ||
| * @property {Number} minLinkIdentity - The minimum of the link identity the user wants to color. | ||
| * @property {Number} maxLinkIdentity - The maximum of the link identity the user wants to color. | ||
| * @property {Number} midLinkIdentity - The middle of the link identity the user wants to color. | ||
| * @property {String} minLinkIdentityColor - The color of the minimum link. | ||
| * @property {String} maxLinkIdentityColor - The color of the maximum link. | ||
| * @property {String} midLinkIdentityColor - The color of the middle link. | ||
| * @property {String} midLinkIdentityColor - The color of the middle link. | ||
| * @property {Number} minLinkLength - The minimum length of a link: | ||
| * @property {Number} maxLinkLength - The maximum length of a link. | ||
| * @property {Object} graphicalParameters - The configuration options for all graphical parameters. | ||
|
|
@@ -1601,7 +1601,7 @@ AliTV.prototype.setFeatureProperty = function(groupId, property, val) { | |
| }; | ||
|
|
||
| /** | ||
| * This function returns an array which contains the color of the first and the last genome. | ||
| * This function returns an array which contains the color of the first and the last genome. | ||
| * The colors are defined in the conf-object. | ||
| * @returns {Array} The color of the first and the last genome. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -1634,7 +1634,7 @@ AliTV.prototype.setGenomeColor = function(color) { | |
| }; | ||
|
|
||
| /** | ||
| * This function returns an array which contains the color of the minLinkIdentity and the maxLinkIdentity. | ||
| * This function returns an array which contains the color of the minLinkIdentity and the maxLinkIdentity. | ||
| * The colors are defined in the conf-object. | ||
| * @returns {Array} The color of the links with the minimal and maximal identity. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -1691,7 +1691,7 @@ AliTV.prototype.filterChromosomes = function() { | |
| *This method should filter all chromosome which are set visible in conf.filters.karyo.chromosomes[<chromosome>].visible | ||
| * @param visibleChromosomes: the method gets all current visible chromosomes. | ||
| * @returns filteredChromosomes: the method returns only chromosomes whose visibility is set true | ||
| * @author Sonja Hohlfeld | ||
| * @author Sonja Hohlfeld | ||
| */ | ||
| AliTV.prototype.filterVisibleChromosomes = function(visibleChromosomes) { | ||
| var that = this; | ||
|
|
@@ -1708,7 +1708,7 @@ AliTV.prototype.filterVisibleChromosomes = function(visibleChromosomes) { | |
| * This method should filter all chromosome which have no visible links with the current configurations | ||
| * @param visibleChromosomes: the method gets all current visible chromosomes. | ||
| * @returns filteredChromosomes: the method returns only chromosomes which have visible links | ||
| * @author Sonja Hohlfeld | ||
| * @author Sonja Hohlfeld | ||
| */ | ||
| AliTV.prototype.filterChromosomeWithoutVisibleLinks = function(visibleChromosomes) { | ||
| var that = this; | ||
|
|
@@ -2641,7 +2641,7 @@ AliTV.prototype.setJSON = function(json) { | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the color of the genomeLabels. | ||
| * This function returns the color of the genomeLabels. | ||
| * The color is defined in the conf-object. | ||
| * @returns The color of the genome labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2668,7 +2668,7 @@ AliTV.prototype.setGenomeLabelColor = function(color) { | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the size of the genomeLabels. | ||
| * This function returns the size of the genomeLabels. | ||
| * The size is defined in the conf-object. | ||
| * @returns The size of the genome labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2702,7 +2702,7 @@ AliTV.prototype.setGenomeLabelSize = function(size) { | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the color of the tick Labels. | ||
| * This function returns the color of the tick Labels. | ||
| * The color is defined in the conf-object. | ||
| * @returns The color of the tick labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2728,7 +2728,7 @@ AliTV.prototype.setTickLabelColor = function(color) { | |
| }; | ||
|
|
||
| /** | ||
| * This function returns the size of the tick Labels. | ||
| * This function returns the size of the tick Labels. | ||
| * The size is defined in the conf-object. | ||
| * @returns The size of the tick labels. | ||
| * @author Sonja Hohlfeld | ||
|
|
@@ -2806,7 +2806,7 @@ AliTV.prototype.showInvisibleLink = function(selectedLinkID) { | |
| /** | ||
| * This function is supposed to return the value of the longest chromosome. | ||
| * @return maxLinkLength: the value of the longest chromosome in bp. | ||
| * @author Sonja Hohlfeld | ||
| * @author Sonja Hohlfeld | ||
| */ | ||
| AliTV.prototype.getMaxChromosomeLength = function() { | ||
| var length = []; | ||
|
|
@@ -2992,7 +2992,7 @@ AliTV.prototype.resetGenomeRegion = function(genome_id) { | |
| this.triggerChange(); | ||
| }; | ||
|
|
||
| /** | ||
| /** | ||
| * This function is supposed to change the visibility of a selected chromosome. | ||
| * The function gets the name of a chromosome and set his visibility in filters.karyo.chromosomes equal false or true. | ||
| * @param {String} chromosomeName: the name of the selected chromosome. | ||
|
|
@@ -3131,7 +3131,7 @@ AliTV.prototype.setOffset = function(offset, karyoId) { | |
| } | ||
| }; | ||
|
|
||
| /** | ||
| /** | ||
| * This function is supposed to return an array of supported features | ||
| * @returns {Array} supportedFeatures | ||
| * @author: Sonja Hohlfeld and Markus Ankenbrand | ||
|
|
||
Oops, something went wrong.