ProteoWizard
PeakelPicker.hpp
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1//
2// $Id$
3//
4//
5// Original author: Darren Kessner <darren@proteowizard.org>
6//
7// Copyright 2009 Center for Applied Molecular Medicine
8// University of Southern California, Los Angeles, CA
9//
10// Licensed under the Apache License, Version 2.0 (the "License");
11// you may not use this file except in compliance with the License.
12// You may obtain a copy of the License at
13//
14// http://www.apache.org/licenses/LICENSE-2.0
15//
16// Unless required by applicable law or agreed to in writing, software
17// distributed under the License is distributed on an "AS IS" BASIS,
18// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19// See the License for the specific language governing permissions and
20// limitations under the License.
21//
22
23#ifndef _PEAKELPICKER_HPP_
24#define _PEAKELPICKER_HPP_
25
26
27#include "PeakelPicker.hpp"
28#include "MZRTField.hpp"
30
31
32namespace pwiz {
33namespace analysis {
34
35
36///
37/// interface for picking Peakels and arranging into Features;
38/// note: Peakels are actually removed from the PeakelField
39///
41{
42 public:
43
44 virtual void pick(PeakelField& peakels, FeatureField& features) const = 0;
45
46 virtual ~PeakelPicker(){}
47};
48
49
50///
51/// basic implementation
52///
54{
55 public:
56
57 struct Config
58 {
59 std::ostream* log;
60 size_t minCharge;
61 size_t maxCharge;
66
67 //double intensityThreshold; // ? // some kind of tolerance to match isotope envelope
68 //double relativeIntensityTolerance;
69
71 : log(0),
72 minCharge(2),
73 maxCharge(5),
74 minMonoisotopicPeakelSize(3),
75 mzTolerance(10, MZTolerance::PPM),
76 rtTolerance(5), // seconds
77 minPeakelCount(3)
78 {}
79 };
80
81 PeakelPicker_Basic(const Config& config = Config()) : config_(config) {}
82
83 virtual void pick(PeakelField& peakels, FeatureField& features) const;
84
85 private:
87};
88
89
90} // namespace analysis
91} // namespace pwiz
92
93
94#endif // _PEAKELPICKER_HPP_
95
#define PWIZ_API_DECL
Definition Export.hpp:32
virtual void pick(PeakelField &peakels, FeatureField &features) const
PeakelPicker_Basic(const Config &config=Config())
interface for picking Peakels and arranging into Features; note: Peakels are actually removed from th...
virtual void pick(PeakelField &peakels, FeatureField &features) const =0
MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT.
Definition MZRTField.hpp:95
struct for expressing m/z tolerance in either amu or ppm