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psmcbor2json.h
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/**
* \file pappsomspp/processing/cbor/psm/psmcbor2json.h
* \date 19/07/2025
* \author Olivier Langella
* \brief convert CBOR PSM to JSON
*/
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of PAPPSOms-tools.
*
* PAPPSOms-tools is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms-tools is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include "psmfilereaderbase.h"
#include "pappsomspp/core/processing/cbor/jsonstreamwriter.h"
#include "pappsomspp/export-import-config.h"
namespace pappso::cbor::psm
{
/**
* @todo write docs
*/
class PMSPP_LIB_DECL PsmCbor2Json : public PsmFileReaderBase
{
public:
/**
* Default constructor
*/
PsmCbor2Json(pappso::cbor::JsonStreamWriter *json_output_p);
/**
* Destructor
*/
virtual ~PsmCbor2Json();
void close() override;
protected:
void informationsReady(pappso::UiMonitorInterface &monitor) override;
void logReady(pappso::UiMonitorInterface &monitor) override;
void parameterMapReady(pappso::UiMonitorInterface &monitor) override;
void fastaFilesReady(pappso::UiMonitorInterface &monitor) override;
// void readSample(pappso::UiMonitorInterface &monitor) override;
void sampleStarted(pappso::UiMonitorInterface &monitor) override;
void sampleFinished(pappso::UiMonitorInterface &monitor) override;
void sampleListStarted(pappso::UiMonitorInterface &monitor) override;
void sampleListFinished(pappso::UiMonitorInterface &monitor) override;
void scanStarted(pappso::UiMonitorInterface &monitor) override;
void scanFinished(pappso::UiMonitorInterface &monitor) override;
void psmReady(pappso::UiMonitorInterface &monitor) override;
// void readScan(pappso::UiMonitorInterface &monitor) override;
// void readPsm(pappso::UiMonitorInterface &monitor) override;
void readProteinMap(pappso::UiMonitorInterface &monitor) override;
protected:
pappso::cbor::JsonStreamWriter *mp_jsonOutput;
};
} // namespace pappso::cbor::psm
pappso::UiMonitorInterface
Definition uimonitorinterface.h:50
pappso::cbor::JsonStreamWriter
helper class to write json text using CBOR data structures
Definition jsonstreamwriter.h:43
pappso::cbor::psm::PsmCbor2Json::informationsReady
void informationsReady(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:71
pappso::cbor::psm::PsmCbor2Json::scanFinished
void scanFinished(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:158
pappso::cbor::psm::PsmCbor2Json::sampleStarted
void sampleStarted(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:166
pappso::cbor::psm::PsmCbor2Json::sampleFinished
void sampleFinished(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:198
pappso::cbor::psm::PsmCbor2Json::psmReady
void psmReady(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:206
pappso::cbor::psm::PsmCbor2Json::mp_jsonOutput
pappso::cbor::JsonStreamWriter * mp_jsonOutput
Definition psmcbor2json.h:78
pappso::cbor::psm::PsmCbor2Json::readProteinMap
void readProteinMap(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:113
pappso::cbor::psm::PsmCbor2Json::fastaFilesReady
void fastaFilesReady(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:55
pappso::cbor::psm::PsmCbor2Json::logReady
void logReady(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:80
pappso::cbor::psm::PsmCbor2Json::sampleListStarted
void sampleListStarted(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:96
pappso::cbor::psm::PsmCbor2Json::parameterMapReady
void parameterMapReady(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:88
pappso::cbor::psm::PsmCbor2Json::close
void close() override
convenient function to clean pointer before leaving
Definition psmcbor2json.cpp:48
pappso::cbor::psm::PsmCbor2Json::sampleListFinished
void sampleListFinished(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:105
pappso::cbor::psm::PsmCbor2Json::scanStarted
void scanStarted(pappso::UiMonitorInterface &monitor) override
Definition psmcbor2json.cpp:138
pappso::cbor::psm::PsmCbor2Json::PsmCbor2Json
PsmCbor2Json(pappso::cbor::JsonStreamWriter *json_output_p)
Definition psmcbor2json.cpp:35
pappso::cbor::psm::PsmFileReaderBase::PsmFileReaderBase
PsmFileReaderBase()
Definition psmfilereaderbase.cpp:44
export-import-config.h
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
jsonstreamwriter.h
pappso::cbor::psm
Definition cborscanmapbase.h:40
psmfilereaderbase.h