ahda 0.1.0

// ahda: Pseudoalignment compression and conversion between formats.
//
// Copyright 2025 Tommi Mäklin [tommi@maklin.fi].
//
// Copyrights in this project are retained by contributors. No copyright assignment
// is required to contribute to this project.
//
// Except as otherwise noted (below and/or in individual files), this
// project is licensed under the Apache License, Version 2.0
// <LICENSE-APACHE> or <http://www.apache.org/licenses/LICENSE-2.0> or
// the MIT license, <LICENSE-MIT> or <http://opensource.org/licenses/MIT>,
// at your option.
//

//! Error types from the ahda library.

use crate::Format;

/// Not a valid [ahda library version](crate::AhdaVersion).
#[derive(Debug, Clone)]
pub struct AhdaVersionError;
impl std::fmt::Display for AhdaVersionError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Not a valid AhdaVersion")
    }
}
impl std::error::Error for AhdaVersionError {}

/// Not a valid [ahda file format version](crate::AhdaFormatVersion).
#[derive(Debug, Clone)]
pub struct AhdaFormatVersionErr;
impl std::fmt::Display for AhdaFormatVersionErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Not a valid AhdaFormatVersion")
    }
}
impl std::error::Error for AhdaFormatVersionErr {}

/// Binary data given to [check_ahda_header](crate::headers::file::check_ahda_header) does not start with the ahda header bytes.
///
/// ## Returned by
///
/// - [check_ahda_header](crate::headers::file::check_ahda_header).
///
#[derive(Debug, Clone)]
pub struct AhdaHeaderError;
impl std::fmt::Display for AhdaHeaderError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "bytes do not start with a valid ahda file header")
    }
}
impl std::error::Error for AhdaHeaderError {}

/// Set bits iterator given to [BitmapEncoder](crate::encoder::bitmap_encoder::BitmapEncoder) is not sorted.
///
/// ## Returned by
///
/// - [BitmapEncoder::next](crate::encoder::bitmap_encoder::BitmapEncoder::next).
///
#[derive(Debug, Clone)]
pub struct SetBitsIteratorNotSorted;
impl std::fmt::Display for SetBitsIteratorNotSorted {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "`set_bits` iterator given to BitmapEncoder::new() (argument #1) must be sorted.")
    }
}
impl std::error::Error for SetBitsIteratorNotSorted {}

/// Could not format [PseudoAln](crate::PseudoAln)(crate::PseudoAln) as a Themisto plain text line.
#[derive(Debug, Clone)]
pub struct ThemistoPrinterError;
impl std::fmt::Display for ThemistoPrinterError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for ThemistoPrinterError {}

/// Could not format [PseudoAln](crate::PseudoAln)(crate::PseudoAln) as a SAM plain text line.
#[derive(Debug, Clone)]
pub struct SamPrinterError;
impl std::fmt::Display for SamPrinterError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for SamPrinterError {}

/// Could not format [PseudoAln](crate::PseudoAln)(crate::PseudoAln) as a Fulgor plain text line.
#[derive(Debug, Clone)]
pub struct FulgorPrinterError;
impl std::fmt::Display for FulgorPrinterError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for FulgorPrinterError {}

/// Could not format [PseudoAln](crate::PseudoAln)(crate::PseudoAln) as a ahda .tsv plain text line.
#[derive(Debug, Clone)]
pub struct AhdaTSVPrinterError;
impl std::fmt::Display for AhdaTSVPrinterError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for AhdaTSVPrinterError {}

/// Could not format [PseudoAln](crate::PseudoAln)(crate::PseudoAln) as a Bifrost plain text line.
#[derive(Debug, Clone)]
pub struct BifrostPrinterError;
impl std::fmt::Display for BifrostPrinterError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for BifrostPrinterError {}

/// Could not format [PseudoAln](crate::PseudoAln)(crate::PseudoAln) as a Metagraph plain text line.
#[derive(Debug, Clone)]
pub struct MetagraphPrinterError;
impl std::fmt::Display for MetagraphPrinterError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for MetagraphPrinterError {}

/// [Format::from_bytes] did not recognize the input format given to [Parser](crate::parser::Parser).
#[derive(Debug, Clone)]
pub struct UnrecognizedInputFormatErr;
impl std::fmt::Display for UnrecognizedInputFormatErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Unrecognized input format.")
    }
}
impl std::error::Error for UnrecognizedInputFormatErr {}

/// [Format::from_bytes] found a valid input format to [Parser](crate::parser::Parser) but could not confirm it with certainty.
#[derive(Debug, Clone)]
pub struct AmbiguousInputFormatErr;
impl std::fmt::Display for AmbiguousInputFormatErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Ambiguous input format.")
    }
}
impl std::error::Error for AmbiguousInputFormatErr {}

/// Plaintext data given to [Parser](crate::parser::Parser) is not in the expected format.
///
/// ## Returned by
///
/// - [Parser::read_header](crate::parser::Parser::read_header) (private method).
///
#[derive(Debug, Clone)]
pub struct CorruptedInputErr;
impl std::fmt::Display for CorruptedInputErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Corrupted input alignment data.")
    }
}
impl std::error::Error for CorruptedInputErr {}

/// Input format given to [Parser](crate::parser::Parser) requires supplying the target sequence names.
///
/// ## Returned by
///
/// - [Parser::new](crate::parser::Parser::new).
/// - [Parser::new_with_format](crate::parser::Parser::new_with_format).
///
#[derive(Debug, Clone)]
pub struct NeedTargetSequences {
    pub format: Format,
}
impl std::fmt::Display for NeedTargetSequences {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Detected input format `{}` requires supplying the target sequence names.", self.format)
    }
}
impl std::error::Error for NeedTargetSequences {}

/// Input format given to [Parser](crate::parser::Parser) requires supplying the query sequence names.
#[derive(Debug, Clone)]
pub struct NeedQueryNamesErr {
    pub format: Format,
}

impl std::fmt::Display for NeedQueryNamesErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Detected input format `{}` requires supplying the query sequence names.", self.format)
    }
}

impl std::error::Error for NeedQueryNamesErr {}

/// A [PseudoAln](crate::PseudoAln)(crate::PseudoAln) record given to encoder does not contain `query_id` and/or `ones`.
#[derive(Debug, Clone)]
pub struct EncodeError;
impl std::fmt::Display for EncodeError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "invalid input to encode")
    }
}
impl std::error::Error for EncodeError {}

/// Bifrost header line was not consumed before calling [read_bifrost](crate::parser::bifrost::read_bifrost).
#[derive(Debug, Clone)]
pub struct BifrostHeaderNotConsumedError;
impl std::fmt::Display for BifrostHeaderNotConsumedError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Bifrost header not consumed from input `Read`.")
    }
}
impl std::error::Error for BifrostHeaderNotConsumedError {}

/// Duplicated queries in files being concatenated.
#[derive(Debug, Clone)]
pub struct DuplicatedQueriesErr;
impl std::fmt::Display for DuplicatedQueriesErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Inputs contain duplicated query records, use a set operation to merge instead.")
    }
}
impl std::error::Error for DuplicatedQueriesErr {}

/// [BlockFlags](crate::headers::block::BlockFlags).query_ids is not filled.
///
/// ## Returned by
///
/// - [alns_from_set_bits](crate::decoder::Decoder::alns_from_set_bits). (private method)
///
#[derive(Debug, Clone)]
pub struct QueryIdsNotFilled;
impl std::fmt::Display for QueryIdsNotFilled {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `query_ids` in BlockFlags is not filled.")
    }
}
impl std::error::Error for QueryIdsNotFilled {}

/// [BlockFlags](crate::headers::block::BlockFlags).queries is not filled.
#[derive(Debug, Clone)]
pub struct QueryNamesNotFilled;
impl std::fmt::Display for QueryNamesNotFilled {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `queries` in BlockFlags is not filled.")
    }
}
impl std::error::Error for QueryNamesNotFilled {}

/// Duplicated queries in files being concatenated.
#[derive(Debug, Clone)]
pub struct IncompatibleFileHeadersErr;
impl std::fmt::Display for IncompatibleFileHeadersErr {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Incompatible file headers.")
    }
}
impl std::error::Error for IncompatibleFileHeadersErr {}

/// Ahda .tsv header line was not consumed before calling [read_ahda_tsv](crate::parser::ahda_tsv::read_ahda_tsv).
#[derive(Debug, Clone)]
pub struct AhdaTSVHeaderNotConsumedError;
impl std::fmt::Display for AhdaTSVHeaderNotConsumedError {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "AhdaTSV header not consumed from input `Read`.")
    }
}
impl std::error::Error for AhdaTSVHeaderNotConsumedError {}

/// Expected [PseudoAln](crate::PseudoAln).ones to be filled but it was empty
#[derive(Debug, Clone)]
pub struct PseudoAlnOnesIsEmpty;
impl std::fmt::Display for PseudoAlnOnesIsEmpty {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `ones` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnOnesIsEmpty {}

/// Expected [PseudoAln](crate::PseudoAln).ones to be filled but it was None.
///
/// ## Returned by
///
/// - [convert_to_roaring](crate::compression::roaringwrapper::convert_to_roaring).
/// - [Decoder::fill_record][crate::decoder::Decoder::fill_record] (private method).
/// - [Parser::fill_record][crate::parser::Parser::fill_record] (private method).
///
#[derive(Debug, Clone)]
pub struct PseudoAlnOnesIsNone;
impl std::fmt::Display for PseudoAlnOnesIsNone {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `ones` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnOnesIsNone {}

/// Expected [PseudoAln](crate::PseudoAln).ones_names to be filled but it was None
///
/// ## Returned by
///
/// - [Decoder::fill_record][crate::decoder::Decoder::fill_record] (private method).
/// - [Parser::fill_record][crate::parser::Parser::fill_record] (private method).
///
#[derive(Debug, Clone)]
pub struct PseudoAlnOnesNamesIsNone;
impl std::fmt::Display for PseudoAlnOnesNamesIsNone {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `ones_names` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnOnesNamesIsNone {}

/// Expected [PseudoAln](crate::PseudoAln).ones_names to be filled but it was empty
#[derive(Debug, Clone)]
pub struct PseudoAlnOnesNamesIsEmpty;
impl std::fmt::Display for PseudoAlnOnesNamesIsEmpty {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `ones_names` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnOnesNamesIsEmpty {}

/// Expected [PseudoAln](crate::PseudoAln).query_name to be filled but it was empty
#[derive(Debug, Clone)]
pub struct PseudoAlnQueryNameIsEmpty;
impl std::fmt::Display for PseudoAlnQueryNameIsEmpty {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `query_name` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnQueryNameIsEmpty {}

/// Expected [PseudoAln](crate::PseudoAln).query_name to be filled but it was None
///
/// ## Returned by
///
/// - [Parser::fill_record][crate::parser::Parser::fill_record] (private method).
///
#[derive(Debug, Clone)]
pub struct PseudoAlnQueryNameIsNone;
impl std::fmt::Display for PseudoAlnQueryNameIsNone {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `query_name` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnQueryNameIsNone {}

/// Expected [PseudoAln](crate::PseudoAln).query_id to be filled but it was empty
#[derive(Debug, Clone)]
pub struct PseudoAlnQueryIdIsEmpty;
impl std::fmt::Display for PseudoAlnQueryIdIsEmpty {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `query_id` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnQueryIdIsEmpty {}

/// Expected [PseudoAln](crate::PseudoAln).query_id to be filled but it was None.
///
/// ## Returned by
///
/// - [convert_to_roaring](crate::compression::roaringwrapper::convert_to_roaring).
/// - [alns_from_set_bits](crate::decoder::Decoder::alns_from_set_bits) (private method).
/// - [Decoder::fill_record][crate::decoder::Decoder::fill_record] (private method).
/// - [Parser::fill_record][crate::parser::Parser::fill_record] (private method).
///
#[derive(Debug, Clone)]
pub struct PseudoAlnQueryIdIsNone;
impl std::fmt::Display for PseudoAlnQueryIdIsNone {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Field `query_id` of PseudoAln is set but empty.")
    }
}
impl std::error::Error for PseudoAlnQueryIdIsNone {}

/// Key was not found in a map
///
/// ## Returned by
///
/// - [Decoder::fill_record][crate::decoder::Decoder::fill_record] (private method).
/// - [Parser::fill_record][crate::parser::Parser::fill_record] (private method).
///
#[derive(Debug, Clone)]
pub struct KeyNotFound {
    pub key: Vec<u8>,
    pub map_name: String,
}

impl std::fmt::Display for KeyNotFound {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Key {} was not found in map {}.", String::from_utf8(self.key.clone()).unwrap(), self.map_name)
    }
}
impl std::error::Error for KeyNotFound {}

/// Map contains less records than the requested index
///
/// ## Returned by
///
/// - [Decoder::fill_record][crate::decoder::Decoder::fill_record] (private method).
/// - [Parser::fill_record][crate::parser::Parser::fill_record] (private method).
///
#[derive(Debug, Clone)]
pub struct MapDoesNotContainIndex {
    pub index: usize,
    pub map_name: String,
}

impl std::fmt::Display for MapDoesNotContainIndex {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Map {} does not contain index {}.", self.map_name, self.index)
    }
}
impl std::error::Error for MapDoesNotContainIndex {}

/// A [FileHeader](crate::headers::file::FileHeader) or [BlockHeader](crate::headers::block::BlockHeader) promised a field is filled but it was not.
///
/// ## Returned by
///
/// - [pack_records](crate::compression::pack_records).
/// - [pack_block_roaring](crate::compression::roaringwrapper::pack_block_roaring).
/// - [alns_from_set_bits](crate::decoder::Decoder::alns_from_set_bits). (private method)
///
#[derive(Debug, Clone)]
pub struct HeaderPromiseNotHonoured {
    pub promise: String,
}
impl std::fmt::Display for HeaderPromiseNotHonoured {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "File or block header promised field {} in flags but it was None.", self.promise)
    }
}
impl std::error::Error for HeaderPromiseNotHonoured {}

/// Cannot convert between two values.
///
/// ## Returned by
///
/// - [BitmapType::from_u16](crate::compression::BitmapType::from_u16).
/// - [MetadataCompression::from_u16](crate::compression::MetadataCompression::from_u8).
///
#[derive(Debug, Clone)]
pub struct InvalidConversion {
    pub from: String,
    pub to: String,
}
impl std::fmt::Display for InvalidConversion {
    fn fmt(&self, f: &mut std::fmt::Formatter) -> std::fmt::Result {
        write!(f, "Invalid conversion of {} to {}.", self.from, self.to)
    }
}
impl std::error::Error for InvalidConversion {}