textarea-sequence

A custom element that creates a formatted text area to capture sequences. It uses QuillJS to format the textarea.

Usage

<textarea-sequence
  id="textareaID"
  height="10em"
  min-sequence-length="10"
  single="true"
/>

This readme is been use as a road map. A 🚧 emoji indicates that this feature is under construction.

Features

Formats the sequence interactively following the FastA format.
- ✅ Highlights headers
- ✅ Highlights bases/residues that are not part of it's alphabet.
- ✅ Highlights if the file includes multiple sequences, when the option single is included.
- ✅ Greys out comment lines (i.e. starts with ;)
✅ CleanUp funtionality.
✅ Error reporting.
✅ Highlights the textarea border if there are errors or is valid.
✅ Creates a hidden input that mirrors the value in quill, so it is included when a form is submitted.

API reference

Parameters

`alphabet`

Either a string explicitly listing the valid characters in the sequence or one of the predefined alphabets:

"protein": "ACDEFGHIKLMNPQRSTVWY "
"dna": "AGTCN "

type: enum('dna'|'protein') | string defaultValue: "protein"

`case-sensitive`

Indicates if the checks against the alphabet should consider the sequence casing

type: boolean defaultValue: false

`single`

Indicates if the textarea should only allow a single sequence

type: boolean defaultValue: false

`disable-header-check`

Indicates if the checks against the alphabet should consider the absence of the header. This will only makes sense if the attribute single is also true, if it's not, the value of the error headerCheckRequiredForMultipleSequences will be true.

type: boolean defaultValue: false

`min-sequence-length`

Defines the minimum number of bases required in the textarea

type: number defaultValue: 0

`height`

Height of the textarea element.

type: auto|<length>|<percentage> defaultValue: "auto"

`width`

Width of the textarea element:

type: auto|<length>|<percentage> defaultValue: "auto"

`inner-style`

Inline CSS style for the main container. The attributes width and height would have higher priority of any value for height and width created in the inline style.

type: <CSSStyleDeclaration> defaultValue:

        border: 1px solid #ccc;
        font-family: 'Courier New', Courier, monospace; font-size: 1em;
        letter-spacing: .1rem;
        height: auto;
        margin: 0 auto;
        width: auto;

Properties

`sequence` [Read Only]

The current value of the text-area.

type: string

`errors` [Read Only]

The current value of the error report. In the shape of an object, where the keys are the type of error, and their values are booleans indicating if the current text has that error.

type: object

Example:

{
  hasInvalidCharacters: false,
  missingFirstHeader: false,
  multipleSequences: false,
  tooShort: true, // The current sequence is too short
  headerCheckRequiredForMultipleSequences: false,
}

`quill`

We use quill to apply the formatting of the textarea. The object related to it, is exposed in this parameter. See the Quill API documentation for more details of what can you do with this object.

type: object

`formatSequence`

A formatting function to use in the cleanUp method. It should add desired spaces a line splits.

The signature of the function should be:

<string> formatSequence(<string> sequence)

type: function defaultValue: Splits the sequence in lines of 50, adding a space every 10 characters

parameters:

sequence: type: string

Returns

string

Note: This parameter can be overwritten, so you can define such format. For example, to avoid any formatting you can pass the identity function:

document.getElementByID("textareaID").formatSequence = (x) => x;

Methods

`cleanUp()`

This method tries to clean up the current sequence in the textarea, in the following way:

Adds a generated header to the sequence in case is missing
Removes any character that is not included in the current alphabet
Trims lines and get rid of spaces
If the attribute single is true, it will keep the first sequence and remove the rest.
Executes the formatSequence function to include spaces and line lengths.

Events

`error-change`

Is dispatched when there is a change in the reported errors. Includes the errors object in the details.

Usage example:

element.addEventListener("error-change", (e) => {
  console.log(e.detail.errors);
});

Quill Events

As mentioned before, we use quill, and its instance is exposed in the parameter quill. Quill implement some events, that you could also use. See the Quill API documentation for more details.

Usage Example:

element.quill.on("text-change", (e) => {
  console.log(element.sequence);
});

Exposed functions

We have exposed some functions tht can be use without having to load the web component:

`formatSequence(sequence, block = 10, line = 50)`

Splits a string into lines of length line with block of block length separated by white spaces.

parameters:

sequence: type: string
block: type: number default: 10
line: type: number default: 50

Returns:

string

Usage example:

import { formatSequence } from "textarea-sequence";
const seq = "XXXXXXXXXXXXXXX";
formatSequence(seq, 4, 8); // 'XXXX XXXX\nXXXX XXX'
formatSequence(seq, 2, 8); // 'XX XX XX XX\nXX XX XX X'
formatSequence(seq, 5, 10); // 'XXXXX XXXXX\nXXXXX'

`cleanUpText(text,alphabet = alphabets.protein, caseSensitive = false, removeComments = true, single = true, format = formatSequence)`

Takes a sequence and transform it, applying the following heuristics:

removes any character that's not in the alphabet.
Generates a header if the sequence doesn't have one
formats the sequence using the goven function. default: blocks of 10 chars separated with a white space and lines of 50 bases.
If case_sensitive is true cases mismatches are removed.
If removeComments is true, removes any line that starts with ;
If single is true, removes any sequence after the first one.

When all of those things are executed, the string is formatted with the function format().

parameters:

text: type: string
alphabet: type: string default: "ACDEFGHIKLMNPQRSTVWY "
caseSensitive: type: boolean default: false
removeComments: type: boolean default: true
single: type: boolean default: true
format: type: function default: formatSequence