ContigStoreElement - SeqAn API Documentation

# Class ContigStoreElement
Represents a single contig.

Defined in | <seqan/store.h>
Signature | `template <typename TContigSeq, typename TGapAnchor[, typename TSpec]> class ContigStoreElement;`

## Template Parameters

`TContigSeq` | Type to store the contig sequence.
`TGapAnchor` | Type of the GapAnchor.
`TSpec` | Specializing type. Default: `void`.

## Member Function Overview

- `ContigStoreElement::ContigStoreElement();`
  Constructor.

## Member Typedef Overview

- `typedef (...) ContigStoreElement::TContigSeq;`
  Type fo the seq member.
- `typedef (...) ContigStoreElement::TGapAnchors;`
  Type of the gaps member.
- `typedef (...) ContigStoreElement::TPos;`
  Type of the fileBeginPos and fileEndPos emmbers.
- `typedef (...) ContigStoreElement::TSpec;`
  The specializing type.

## Member Variable Overview

- `TPos ContigStoreElement::fileBeginPos`
  Begin position of the contig sequence fragment in the file.
- `TPos ContigStoreElement::fileEndPos`
  End position of the contig sequence fragment in the file.
- `TId ContigStoreElement::fileId`
  Refers to a file in the contigFileStore or is INVALID_ID if the contig has no file association.
- `TGaps ContigStoreElement::gaps`
  String of contig GapAnchor objects. CAn be used to create a AnchorGaps alignment row.
- `TId ContigStoreElement::INVALID_ID`
  Constant to represent an invalid.
- `TContigSeq ContigStoreElement::seq`
  Contig sequence.
- `unsigned ContigStoreElement::usage`
  Count the number of locks.

## Detailed Description

Value type of the contigStore string.

## Member Functions Detail

### `ContigStoreElement::ContigStoreElement();`

Constructor.

Set fileId to INVALID_ID and usage, fileBeginPos, fileEndPos to 0.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

## Member Typedef Detail

### `typedef (...) ContigStoreElement::TContigSeq;`

Type fo the seq member.

### `typedef (...) ContigStoreElement::TGapAnchors;`

Type of the gaps member.

### `typedef (...) ContigStoreElement::TPos;`

Type of the fileBeginPos and fileEndPos emmbers.

### `typedef (...) ContigStoreElement::TSpec;`

The specializing type.

## Member Variables Detail

### `TPos ContigStoreElement::fileBeginPos`

Begin position of the contig sequence fragment in the file.

### `TPos ContigStoreElement::fileEndPos`

End position of the contig sequence fragment in the file.

### `TId ContigStoreElement::fileId`

Refers to a file in the contigFileStore or is INVALID_ID if the contig has no file association.

### `TGaps ContigStoreElement::gaps`

String of contig GapAnchor objects. CAn be used to create a AnchorGaps alignment row.

### `TId ContigStoreElement::INVALID_ID`

Constant to represent an invalid.

### `TContigSeq ContigStoreElement::seq`

Contig sequence.

### `unsigned ContigStoreElement::usage`

Count the number of locks.

#### Dox Sources

    /*!
     * @class ContigStoreElement
     *
     * @headerfile <seqan/store.h>
     *
     * @brief Represents a single contig.
     *
     * @signature template <typename TContigSeq, typename TGapAnchor[, typename
     *            TSpec]> class ContigStoreElement;
     *
     * @tparam TContigSeq Type to store the contig sequence.
     * @tparam TGapAnchor Type of the @link GapAnchor @endlink.
     * @tparam TSpec Specializing type. Default: <tt>void</tt>.
     *
     * Value type of the @link FragmentStore::contigStore @endlink string.
     *
     * @fn ContigStoreElement::ContigStoreElement
     *
     * @brief Constructor.
     *
     * @signature ContigStoreElement::ContigStoreElement();
     *
     * Set fileId to INVALID_ID and usage, fileBeginPos, fileEndPos to 0.
     *
     * @typedef ContigStoreElement::TContigSeq
     *
     * @brief Type fo the seq member.
     *
     * @signature typedef (...) ContigStoreElement::TContigSeq;
     *
     * @typedef ContigStoreElement::TGapAnchors
     *
     * @brief Type of the gaps member.
     *
     * @signature typedef (...) ContigStoreElement::TGapAnchors;
     *
     * @typedef ContigStoreElement::TPos
     *
     * @brief Type of the fileBeginPos and fileEndPos emmbers.
     *
     * @signature typedef (...) ContigStoreElement::TPos;
     *
     * @typedef ContigStoreElement::TSpec
     *
     * @brief The specializing type.
     *
     * @signature typedef (...) ContigStoreElement::TSpec;
     *
     * @var TContigSeq ContigStoreElement::seq;
     *
     * @brief Contig sequence.
     *
     * @var TGaps ContigStoreElement::gaps;
     *
     * @brief String of contig @link GapAnchor @endlink objects. CAn be used to
     *        create a @link AnchorGaps @endlink alignment row.
     *
     * @var unsigned ContigStoreElement::usage;
     *
     * @brief Count the number of locks.
     *
     * @see FragmentStore#lockContig
     *
     * @var TId ContigStoreElement::fileId;
     *
     * @brief Refers to a file in the @link FragmentStore::contigFileStore @endlink
     *        or is INVALID_ID if the contig has no file association.
     *
     * @var TPos ContigStoreElement::fileBeginPos;
     *
     * @brief Begin position of the contig sequence fragment in the file.
     *
     * @var TPos ContigStoreElement::fileEndPos;
     *
     * @brief End position of the contig sequence fragment in the file.
     *
     * @var TId ContigStoreElement::INVALID_ID;
     *
     * @brief Constant to represent an invalid.
     */