### Configure JBrowse-REST Source

Source: https://www.biodalliance.org/config-source.html

Example configuration for a JBrowse-REST source, including the base URI and query parameters.

```javascript
{
name: 'JBTest',
jbURI: 'http://my.server.com/jbrowse/rest',
jbQuery: 'type=IntergenicRegion'
}
```

--------------------------------

### Configure Tabix Source

Source: https://www.biodalliance.org/config-source.html

Example configuration for a Tabix-indexed source, specifying the URI, tier type, and payload format.

```javascript
{
name: "Variants",
uri: "http://server/myfile.vcf.gz",
tier_type: 'tabix',
payload: 'vcf'
}
```

--------------------------------

### JSON-encoded Stylesheet Example

Source: https://www.biodalliance.org/stylesheets.html

Define stylesheets using JSON format as an alternative to XML. This example shows how to specify glyph types, colors, and dimensions for 'PLIMSOLL' and 'CROSS' glyphs.

```json
[
   {type: 'default',
    style: {
       glyph: 'PLIMSOLL',
       HEIGHT: '12',
       STROKECOLOR: 'black',
       FGCOLOR: 'red'}},
   {type: 'nasty',
    style: {
        glyph: 'CROSS',
        FGCOLOR: 'green'}}
]
```

--------------------------------

### Configure Feature Info Plugin

Source: https://www.biodalliance.org/config-source.html

Example of configuring a feature-info plugin for a specific tier. This allows custom information to be displayed for features within that tier.

```javascript
{
name:                'BBD test',
bwgURI:              'http://www.biodalliance.org/datasets/ensGene.bb',
collapseSuperGroups: true,
featureInfoPlugin:   function(f, info) {
                          info.add('Testing', 'This is a test');
                      }
}
```

--------------------------------

### Protocol-Relative URL Example

Source: https://www.biodalliance.org/https.html

Use protocol-relative URLs for resources available over both HTTP and HTTPS. The browser will automatically select the appropriate protocol.

```html
//www.biodalliance.org/datasets/ensgene.bb
```

--------------------------------

### Ensembl REST Source Configuration

Source: https://www.biodalliance.org/config-source.html

Example configuration object for an Ensembl REST source. Specifies the base URI, species, and desired feature types.

```javascript
{name:                 'e! transcripts',
 uri:                  'http://beta.rest.ensembl.org',
 tier_type:            'ensembl',
 species:              'human',
 type:                 ['transcript', 'exon', 'cds']}
```

--------------------------------

### Set Default Viewport in Dalliance

Source: https://www.biodalliance.org/config.html

Configure the initial genomic region displayed when the browser loads. Specify the chromosome and the start and end coordinates.

```javascript
chr:          '22',
viewStart:    30000000,
viewEnd:      30030000
```

--------------------------------

### setLocation([chr], start, end)

Source: https://www.biodalliance.org/interacting.html

Navigates the browser to a specific genomic location. If the new location is similar to the current one and the width is the same, it scrolls; otherwise, it reloads data. If 'chr' is null or undefined, the current chromosome is used.

```APIDOC
## setLocation

### Description
Navigates the browser to a specific genomic location.

### Parameters
#### Path Parameters
- **chr** (string) - Optional - The chromosome name. If null or undefined, the current chromosome is used.
- **start** (integer) - Required - The starting position of the genomic region.
- **end** (integer) - Required - The ending position of the genomic region.

### Request Example
```javascript
browser.setLocation("chr1", 100000, 200000);
```

### Response
This method does not return a value.
```

--------------------------------

### addInitListener(callback)

Source: https://www.biodalliance.org/interacting.html

Registers a callback function to be executed on a newly constructed `Browser` instance once its initialization is complete.

```APIDOC
## addInitListener

### Description
Registers a callback function to be invoked when the `Browser` instance initialization is complete.

### Parameters
#### Request Body
- **callback** (function) - Required - The function to execute after initialization.

### Request Example
```javascript
browser.addInitListener(function() {
    console.log('Dalliance browser initialized.');
});
```

### Response
This method does not return a value.
```

--------------------------------

### Configure Memstore Source

Source: https://www.biodalliance.org/config-source.html

Configuration for a Memstore source, similar to Tabix, for loading entire small textual files into memory.

```javascript
{
name: "Variants",
uri: "http://server/myfile.vcf",
tier_type: 'memstore',
payload: 'vcf'
}
```

--------------------------------

### Configure BAM Source

Source: https://www.biodalliance.org/config-source.html

Configuration for a BAM source, including the URI for the BAM file. An index file URI can also be explicitly provided.

```javascript
{
name: "MyBAMTrack",
bamURI: "http://server/myfile.sort.bam"
}
```

--------------------------------

### Configure DAS Source

Source: https://www.biodalliance.org/config-source.html

Basic configuration for a DAS source, specifying the base URI for the DAS server.

```javascript
{
name:                 'MeDIP raw',
uri:                  'http://www.derkholm.net:8080/das/medipseq_reads'
}
```

--------------------------------

### Add a New Browser Tier

Source: https://www.biodalliance.org/interacting.html

Use `addTier` to create a new browser tier with the provided configuration object, including its name, description, data source URI, and stylesheet URI.

```javascript
browser.addTier({
    name: 'Repeats',
    desc: 'Repeat annotation from Ensembl 59',
    bwgURI: 'http://www.biodalliance.org/datasets/repeats.bb',
    stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats.xml'
});
```

--------------------------------

### addTier(config)

Source: https://www.biodalliance.org/interacting.html

Creates a new browser tier (track) using the provided configuration object. This allows adding custom data visualizations to the browser.

```APIDOC
## addTier

### Description
Creates a new browser tier using the specified configuration object.

### Parameters
#### Request Body
- **config** (object) - Required - Configuration object for the new tier.
  - **name** (string) - Required - The name of the tier.
  - **desc** (string) - Optional - A description for the tier.
  - **bwgURI** (string) - Required - The URI for the bigWig or bigBed data file.
  - **stylesheet_uri** (string) - Optional - The URI for the stylesheet to render the tier.

### Request Example
```javascript
browser.addTier({
    name: 'Repeats',
    desc: 'Repeat annotation from Ensembl 59',
    bwgURI: 'http://www.biodalliance.org/datasets/repeats.bb',
    stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats.xml'
});
```

### Response
This method does not return a value.
```

--------------------------------

### addTierListener(callback)

Source: https://www.biodalliance.org/interacting.html

Registers a callback function to be executed when the set or order of browser tiers changes.

```APIDOC
## addTierListener

### Description
Registers a callback function that is invoked when the set or order of tiers changes.

### Parameters
#### Request Body
- **callback** (function) - Required - The function to execute when tiers change.

### Request Example
```javascript
browser.addTierListener(function() {
    console.log('Tier set or order changed.');
});
```

### Response
This method does not return a value.
```

--------------------------------

### Apache Configuration for Secure Resources

Source: https://www.biodalliance.org/cors.html

This Apache configuration enables CORS for secure resources requiring authentication. It echoes the origin dynamically, allows credentials, and permits the Range header. Note that a wildcard origin is not permitted when credentials are allowed.

```apache
<Directory /var/www/secure/>
    Options  FollowSymLinks MultiViews
    AllowOverride FileInfo
    Order allow,deny
    allow from all
    <LimitExcept OPTIONS>
        Require user dalliance
    </LimitExcept>
    AuthType Basic
    AuthName "Dalliance security test"
    AuthUserFile /var/data/dalliance-passwd


    SetEnvIf Origin "http(s)?://.*$" AccessControlAllowOrigin=$0
    Header add Access-Control-Allow-Origin %{AccessControlAllowOrigin}e env=AccessControlAllowOrigin
    Header set Access-Control-Allow-Headers "Range"
    Header set Access-Control-Allow-Credentials "true"       
</Directory>
```

--------------------------------

### Apache Configuration for Static Data Files

Source: https://www.biodalliance.org/cors.html

This Apache configuration sets the necessary CORS headers for serving static data files. It allows requests from any origin and permits the use of the Range header.

```apache
Header set Access-Control-Allow-Origin "*"
Header set Access-Control-Allow-Headers "Range"
Header set Access-Control-Max-Age "36000"
```

--------------------------------

### Configure Track Hubs in Dalliance

Source: https://www.biodalliance.org/config.html

Add UCSC-style track hubs to Dalliance for displaying additional data tracks. Ensure hubs are served over HTTP and support CORS.

```javascript
hubs: ['http://www.biodalliance.org/datasets/testhub/hub.txt',
       'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt']
```

--------------------------------

### Configure Apache for Cross-Origin Requests

Source: https://www.biodalliance.org/adding.html

These directives enable cross-origin requests and allow the use of the Range header for fetching specific portions of data. Place them in a .htaccess file or the global Apache configuration.

```apache
Header set Access-Control-Allow-Origin "*"
Header set Access-Control-Allow-Headers "Range"
```

--------------------------------

### addViewListener(callback)

Source: https://www.biodalliance.org/interacting.html

Registers a callback function to be executed whenever the viewed region in the browser changes. The callback receives the current chromosome, minimum, and maximum visible positions.

```APIDOC
## addViewListener

### Description
Registers a callback function that is invoked when the viewed region changes.

### Parameters
#### Request Body
- **callback** (function) - Required - The function to execute when the view changes. It receives `chr` (string), `min` (integer), and `max` (integer) as arguments.

### Request Example
```javascript
browser.addViewListener(function(chr, min, max) {
    console.log(`View changed to: ${chr}:${min}-${max}`);
});
```

### Response
This method does not return a value.
```

--------------------------------

### CORS Headers for Static Data Files

Source: https://www.biodalliance.org/cors.html

These headers are required when serving static data files to enable cross-origin requests. `Access-Control-Allow-Origin: *` allows requests from any origin. `Access-Control-Allow-Headers: Range` permits the use of the Range header for partial file fetching. `Access-Control-Max-Age` is optional and improves performance by caching CORS information.

```http
Access-Control-Allow-Origin: *
Access-Control-Allow-Headers: Range
Access-Control-Max-Age: 36000
```

--------------------------------

### Configure Coordinate System Mappings in Dalliance

Source: https://www.biodalliance.org/config.html

Define custom coordinate system mappings using the 'chains' property. Specify the URI, type, and coordinate details for each mapping.

```javascript
chains: {
      hg18ToHg19: {
                   uri: 'http://www.biodalliance.org/datasets/GRCh37/hg18ToHg19.bb',
                   type: 'bigbed',
                   coords: {
                        speciesName: 'Human',
                        taxon: 9606,
                        auth: 'NCBI',
                        version: 36
                   }
                  }
    }
```

--------------------------------

### Basic Dalliance Embedding

Source: https://www.biodalliance.org/embed.html

Include this script to load the Dalliance library. Then, instantiate a new Browser object with your desired configuration, specifying the genome, coordinate system, and data sources. A target div is required for the browser to render into.

```html
<script language="javascript" src="//www.biodalliance.org/release-0.13/dalliance-compiled.js"></script>
<script language="javascript">
  new Browser({
    chr:          '22',
    viewStart:    30700000,
    viewEnd:      30900000,

    coordSystem: {
      speciesName: 'Human',
      taxon: 9606,
      auth: 'GRCh',
      version: '37',
      ucscName: 'hg19'
    },

    sources:     [{name:                 'Genome',
                   twoBitURI:            '//www.biodalliance.org/datasets/hg19.2bit',
                   tier_type:            'sequence'},
                  {name:                 'Genes',
                   desc:                 'Gene structures from GENCODE 19',
                   bwgURI:               '//www.biodalliance.org/datasets/gencode.bb',
                   stylesheet_uri:       '//www.biodalliance.org/stylesheets/gencode.xml',
                   collapseSuperGroups:  true,
                   trixURI:              '//www.biodalliance.org/datasets/geneIndex.ix'},
                  {name:                 'Repeats',
                   desc:                 'Repeat annotation from Ensembl',
                   bwgURI:               '//www.biodalliance.org/datasets/repeats.bb',
                   stylesheet_uri:       '//www.biodalliance.org/stylesheets/bb-repeats.xml'},
                  {name:                 'Conservation',
                   desc:                 'Conservation', 
                   bwgURI:               '//www.biodalliance.org/datasets/phastCons46way.bw',
                   noDownsample:         true}],

  });
</script>

<div id="svgHolder"></div>
```

--------------------------------

### addFeatureHoverListener(callback)

Source: https://www.biodalliance.org/interacting.html

Registers a callback function to be executed when the mouse pointer hovers over a feature. This is typically not called on touch devices. The callback parameters are the same as for `addFeatureListener`.

```APIDOC
## addFeatureHoverListener

### Description
Registers a callback function that is invoked when the pointer hovers over a feature.

### Parameters
#### Request Body
- **callback** (function) - Required - The function to execute when hovering over a feature. It receives `event` (MouseEvent), `feature` (object), `hit` (array), and `tier` (object) as arguments.

### Request Example
```javascript
browser.addFeatureHoverListener(function(event, feature, hit, tier) {
    console.log('Hovering over feature:', feature.name);
});
```

### Response
This method does not return a value.
```

--------------------------------

### Listen for View Changes

Source: https://www.biodalliance.org/interacting.html

Use `addViewListener` to register a callback function that is invoked whenever the viewed genomic region changes. The callback receives the current chromosome, minimum, and maximum visible positions.

```javascript
browser.addViewListener(function(chr, min, max) {
    var link = document.getElementById('enslink');
    link.href = 'http://www.ensembl.org/Homo_sapiens/Location/View?r=' + 
        chr + ':' + min + '-' + max;
});
```

--------------------------------

### Add Feature Info Plugin

Source: https://www.biodalliance.org/plugins.html

Use this to add custom rows to the default feature-info box. It runs when the user clicks on a feature. You can add strings or DOM elements.

```javascript
browser.addFeatureInfoPlugin(function(f, info) {
    info.add('Testing', 'This is a test!');
});
```

--------------------------------

### addFeatureListener(callback)

Source: https://www.biodalliance.org/interacting.html

Registers a callback function to be executed when a user clicks on a feature in the browser. The callback receives event details, the feature object, hit information, and the tier it belongs to.

```APIDOC
## addFeatureListener

### Description
Registers a callback function that is invoked when the user clicks on a feature.

### Parameters
#### Request Body
- **callback** (function) - Required - The function to execute when a feature is clicked. It receives `event` (MouseEvent), `feature` (object), `hit` (array), and `tier` (object) as arguments.

### Request Example
```javascript
browser.addFeatureListener(function(event, feature, hit, tier) {
    console.log('Feature clicked:', feature);
});
```

### Response
This method does not return a value.
```

--------------------------------

### highlightRegion(chr, min, max)

Source: https://www.biodalliance.org/interacting.html

Creates a visual highlight over a specified genomic region.

```APIDOC
## highlightRegion

### Description
Creates a highlight over the specified genomic region.

### Parameters
#### Path Parameters
- **chr** (string) - Required - The chromosome name.
- **min** (integer) - Required - The minimum position of the region to highlight.
- **max** (integer) - Required - The maximum position of the region to highlight.

### Request Example
```javascript
browser.highlightRegion("chr1", 50000, 75000);
```

### Response
This method does not return a value.
```

--------------------------------

### Specify Mapping for a Data Track in Dalliance

Source: https://www.biodalliance.org/config.html

Assign a configured coordinate system mapping to a data track by setting the 'mapping' property in the 'sources' array.

```javascript
sources: [
  {
    name: "My track",
    bwgURI: "http://some/old.data.bb",
    mapping: 'hg18ToHg19'
  }
]
```

--------------------------------

### Configure Coordinate System in Dalliance

Source: https://www.biodalliance.org/config.html

Define the reference genome coordinate system for the browser. This is crucial for querying data sources and re-mapping data between systems. Ensure 'taxon' is an NCBI Taxonomy ID and 'auth'/'version' match DAS Registry strings.

```javascript
coordSystem: {
    speciesName: 'Danio rerio',
    taxon: 7955,
    auth: 'Zv',
    version: 9,
    ucscName: 'danRer7'
}
```

--------------------------------

### removeTier(config)

Source: https://www.biodalliance.org/interacting.html

Removes a browser tier that matches the provided configuration object. Note: future versions may handle multiple matching tiers more robustly.

```APIDOC
## removeTier

### Description
Removes a browser tier whose configuration matches the specified configuration object.

### Parameters
#### Request Body
- **config** (object) - Required - The configuration object of the tier to remove.
  - **name** (string) - Required - The name of the tier.
  - **desc** (string) - Optional - A description for the tier.
  - **bwgURI** (string) - Required - The URI for the bigWig or bigBed data file.
  - **stylesheet_uri** (string) - Optional - The URI for the stylesheet to render the tier.

### Request Example
```javascript
browser.removeTier({
    name: 'Repeats',
    desc: 'Repeat annotation from Ensembl 59',
    bwgURI: 'http://www.biodalliance.org/datasets/repeats.bb',
    stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats.xml'
});
```

### Response
This method does not return a value.
```

--------------------------------

### Navigate to a Genomic Location

Source: https://www.biodalliance.org/interacting.html

Call `setLocation` to navigate to a specific genomic location. If the new location is close to the current one and the width is similar, it scrolls; otherwise, it reloads data. `chr` can be null to use the current chromosome.

```javascript
function moveRight() {
    browser.setLocation(
        browser.chr,
        (browser.viewStart|0) + 1000,
        (browser.viewEnd|0) + 1000
    );
}
```

--------------------------------

### Regexp Matching in TYPE Elements

Source: https://www.biodalliance.org/stylesheets.html

Use regular expressions for 'id' and 'label' attributes in TYPE elements to filter features. This allows for more flexible matching than exact string comparisons.

```xml
<TYPE id="repeat" label="L1.+">
  <GLYPH>
    <BOX>
      <HEIGHT>10</HEIGHT>
      <BGCOLOR>red</BGCOLOR>
    </BOX>
  </GLYPH>
</TYPE>
<TYPE id="repeat">
  <GLYPH>
    <BOX>
      <HEIGHT>10</HEIGHT>
      <BGCOLOR>orange</BGCOLOR>
    </BOX>
  </GLYPH>
</TYPE>
```

--------------------------------

### clearHighlights()

Source: https://www.biodalliance.org/interacting.html

Removes all currently highlighted regions from the browser view.

```APIDOC
## clearHighlights

### Description
Removes all highlighted regions from the browser.

### Request Example
```javascript
browser.clearHighlights();
```

### Response
This method does not return a value.
```

--------------------------------

### Orientation Matching in TYPE Elements

Source: https://www.biodalliance.org/stylesheets.html

Filter features based on their orientation using the 'orientation' attribute in TYPE elements. '+' matches positive orientation, and '-' matches negative orientation.

```xml
<TYPE id="foo" orientation="+">
  <GLYPH>
    <BOX>
      <BGCOLOR>red</BGCOLOR>
    </BOX>
  </GLYPH>
</TYPE>
<TYPE id="foo" orientation="-">
  <GLYPH>
    <BOX>
      <BGCOLOR>blue</BGCOLOR>
    </BOX>
  </GLYPH>
</TYPE>
```

--------------------------------

### SCATTER Attribute with STAR Glyph

Source: https://www.biodalliance.org/stylesheets.html

Configure a STAR glyph to display as a scatter plot. The 'SCATTER' attribute set to 'yes' adjusts the y-position based on feature score. 'POINTS', 'SIZE', 'MIN', 'MAX', and 'HEIGHT' control the appearance and range of the scatter points.

```xml
<TYPE id='default'>
  <GLYPH>
    <STAR>
      <SCATTER>yes</SCATTER>
      <POINTS>8</POINTS>
      <SIZE>6</SIZE>
      <FGCOLOR>blue</FGCOLOR>
      <MIN>0</MIN>
      <MAX>100</MAX>
      <HEIGHT>50</HEIGHT>
    </STAR>
  </GLYPH>
</TYPE>
```

--------------------------------

### Remove a Browser Tier

Source: https://www.biodalliance.org/interacting.html

Call `removeTier` to remove a browser tier that matches the specified configuration object. Note: This API may change to better handle multiple matching tiers.

```javascript
browser.removeTier({
    name: 'Repeats',
    desc: 'Repeat annotation from Ensembl 59',
    bwgURI: 'http://www.biodalliance.org/datasets/repeats.bb',
    stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats.xml'
});
```

=== COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.