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kome::objects::Peak2DElement Class Reference

2-dimentional peak element More...

#include <Peak2DElement.h>

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Classes

struct  DataInfo
 data information More...
 
struct  ParamInfo
 parameter information More...
 

Public Member Functions

 Peak2DElement (Peaks2D *peaks)
 constructor More...
 
virtual ~Peak2DElement ()
 destructor
 
void setRt (const double rt, const double startRt, const double endRt)
 sets RT More...
 
double getRt ()
 gets RT More...
 
double getStartRt ()
 gets start RT More...
 
double getEndRt ()
 gets end RT More...
 
void setMz (const double mz, const double startMz, const double endMz)
 sets m/z More...
 
double getMz ()
 gets m/z More...
 
double getStartMz ()
 gets start m/z More...
 
double getEndMz ()
 gets end m/z More...
 
void setIntensity (const double intensity)
 sets intensity More...
 
double getIntensity ()
 gets intensity More...
 
void setCluster (PeaksCluster2D *cluster)
 sets peaks cluster More...
 
PeaksCluster2D * getCluster ()
 gets cluster More...
 
void setPrecursorMass (const double precursor)
 sets the precursor mass More...
 
double getPrecursorMass ()
 gets the precursor mass More...
 
void setCharge (const int charge)
 sets the charge state More...
 
int getCharge ()
 gets the charge state More...
 
void setFwhm (const double fwhm)
 sets FWHM More...
 
double getFwhm ()
 gets FWHM More...
 
void setArea (const double area)
 sets area More...
 
double getArea ()
 gets area More...
 
void setId (int id)
 sets peak2d id More...
 
int getId ()
 gets peak2d id More...
 
void clearData ()
 clears data
 
unsigned int getDataListSize ()
 gets the data list size More...
 
void addData (const int sampleId, const int profileId, const double peakVal, PeakElement *peak)
 adds data More...
 
void setData (const int sampleId, const int profileId, const double peakVal, PeakElement *peak)
 sets data More...
 
PeakElement * getDataPeak (const unsigned int idx=0)
 gets data peak More...
 
int getDataProfileId (const unsigned int idx=0)
 gets data profile ID More...
 
int getDataSampleId (const unsigned int idx=0)
 gets data sample ID More...
 
double getDataPeakValue (const unsigned int idx=0)
 gets the data peak value More...
 
void clearParameters ()
 clears parameters
 
void setParameter (const char *name, const char *value, const int type=0)
 sets parameters More...
 
unsigned int getNumberOfParameters ()
 gets the number of parameters More...
 
const char * getParameterName (const int idx)
 gets parameter name More...
 
const char * getParameterValue (const char *name)
 gets parameter value More...
 
const char * getParameterValue (const int idx)
 gets parameter value More...
 
int getParameterType (const char *name)
 gets parameter type More...
 
int getParameterType (const int idx)
 gets parameter type More...
 

Protected Member Functions

int searchParameterIndex (const char *name)
 searches parameter index More...
 

Protected Attributes

double m_rt
 
double m_startRt
 
double m_endRt
 
double m_mz
 
double m_startMz
 
double m_endMz
 
double m_intensity
 
int m_charge
 
double m_fwhm
 
double m_area
 
Peaks2D * m_peaks
 
PeaksCluster2D * m_cluster
 
int m_elmId
 
int m_peak2dId
 
double m_precursor
 
std::vector< DataInfo > m_dataList
 
std::vector< ParamInfo > m_params
 

Detailed Description

2-dimentional peak element

Definition at line 33 of file Peak2DElement.h.

Constructor & Destructor Documentation

kome::objects::Peak2DElement::Peak2DElement ( Peaks2D *  peaks)

constructor

Parameters
[in]peakspeaks object

Definition at line 34 of file Peak2DElement.cpp.

34  {
35  // initialize
36  m_peaks = peaks;
37 
38  m_rt = double();
39  m_startRt = double();
40  m_endRt = double();
41 
42  m_mz = double();
43  m_startMz = double();
44  m_endMz = double();
45 
46  m_intensity = -1.0;
47 
48  m_cluster = NULL;
49  m_precursor = -1.0;
50  m_charge = -1;
51  m_fwhm = -1.0;
52  m_area = -1.0;
53 
54  m_elmId = -1;
55 
56  // issue peak2d id
57  if( m_peaks != NULL ){
58  m_peak2dId = m_peaks->issueId( this );
59  }
60 }
kome::objects::Peak2DElement::m_cluster
PeaksCluster2D * m_cluster
Definition: Peak2DElement.h:83
NULL
#define NULL
Definition: CoreMacros.h:18
kome::objects::Peaks2DArray::issueId
int issueId(Peak2DElement *peak2dElement)
to issue the peak2d id
Definition: Peaks2DArray.cpp:117

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Member Function Documentation

void kome::objects::Peak2DElement::addData ( const int  sampleId,
const int  profileId,
const double  peakVal,
PeakElement *  peak 
)

adds data

Parameters
[in]sampleIdsample ID
[in]profileIdprofile ID
[in]peakValpeak value
[in]peakpeak peak information

Definition at line 207 of file Peak2DElement.cpp.

207  {
208  m_dataList.resize( m_dataList.size() + 1 );
209  m_dataList.back().peakVal = peakVal;
210  if( peak != NULL ) {
211  m_dataList.back().peak = *peak;
212  }
213  m_dataList.back().sampleId = sampleId;
214  m_dataList.back().profile = profileId;
215 }
NULL
#define NULL
Definition: CoreMacros.h:18
kome::objects::Peak2DElement::m_dataList
std::vector< DataInfo > m_dataList
Definition: Peak2DElement.h:117
double kome::objects::Peak2DElement::getArea ( )

gets area

Returns
area

Definition at line 182 of file Peak2DElement.cpp.

182  {
183  return m_area;
184 }
int kome::objects::Peak2DElement::getCharge ( )

gets the charge state

Returns
charge state

Definition at line 162 of file Peak2DElement.cpp.

162  {
163  return m_charge;
164 }
PeaksCluster2D * kome::objects::Peak2DElement::getCluster ( )

gets cluster

Returns
cluster

Definition at line 142 of file Peak2DElement.cpp.

142  {
143  return m_cluster;
144 }
kome::objects::Peak2DElement::m_cluster
PeaksCluster2D * m_cluster
Definition: Peak2DElement.h:83
unsigned int kome::objects::Peak2DElement::getDataListSize ( )

gets the data list size

Returns
data list size

Definition at line 202 of file Peak2DElement.cpp.

202  {
203  return m_dataList.size();
204 }
kome::objects::Peak2DElement::m_dataList
std::vector< DataInfo > m_dataList
Definition: Peak2DElement.h:117
PeakElement * kome::objects::Peak2DElement::getDataPeak ( const unsigned int  idx = 0)

gets data peak

Parameters
[in]idxdata index
Returns
data peak

Definition at line 229 of file Peak2DElement.cpp.

229  {
230  if( idx >= m_dataList.size() ) {
231  return NULL;
232  }
233 
234  return &( m_dataList[ idx ].peak );
235 }
NULL
#define NULL
Definition: CoreMacros.h:18
kome::objects::Peak2DElement::m_dataList
std::vector< DataInfo > m_dataList
Definition: Peak2DElement.h:117
double kome::objects::Peak2DElement::getDataPeakValue ( const unsigned int  idx = 0)

gets the data peak value

Parameters
[in]idxdata index
Returns
peak value

Definition at line 256 of file Peak2DElement.cpp.

256  {
257  if( idx >= m_dataList.size() ) {
258  return -1.0;
259  }
260 
261  return m_dataList[ idx ].peakVal;
262 }
kome::objects::Peak2DElement::m_dataList
std::vector< DataInfo > m_dataList
Definition: Peak2DElement.h:117
int kome::objects::Peak2DElement::getDataProfileId ( const unsigned int  idx = 0)

gets data profile ID

Parameters
[in]idxdata index
Returns
profile ID

Definition at line 238 of file Peak2DElement.cpp.

238  {
239  if( idx >= m_dataList.size() ) {
240  return -1;
241  }
242 
243  return m_dataList[ idx ].profile;
244 }
kome::objects::Peak2DElement::m_dataList
std::vector< DataInfo > m_dataList
Definition: Peak2DElement.h:117
int kome::objects::Peak2DElement::getDataSampleId ( const unsigned int  idx = 0)

gets data sample ID

Parameters
[in]idxdata index
Returns
sample ID

Definition at line 247 of file Peak2DElement.cpp.

247  {
248  if( idx >= m_dataList.size() ) {
249  return -1;
250  }
251 
252  return m_dataList[ idx ].sampleId;
253 }
kome::objects::Peak2DElement::m_dataList
std::vector< DataInfo > m_dataList
Definition: Peak2DElement.h:117
double kome::objects::Peak2DElement::getEndMz ( )

gets end m/z

Returns
end m/z

Definition at line 106 of file Peak2DElement.cpp.

106  {
107  return m_endMz;
108 }
double kome::objects::Peak2DElement::getEndRt ( )

gets end RT

Returns
end RT

Definition at line 84 of file Peak2DElement.cpp.

84  {
85  return m_endRt;
86 }
double kome::objects::Peak2DElement::getFwhm ( )

gets FWHM

Returns
FWHM

Definition at line 172 of file Peak2DElement.cpp.

172  {
173  return m_fwhm;
174 }
int kome::objects::Peak2DElement::getId ( )

gets peak2d id

Returns
peak2d id

Definition at line 187 of file Peak2DElement.cpp.

187  {
188  return m_peak2dId;
189 }
double kome::objects::Peak2DElement::getIntensity ( )

gets intensity

Returns
intensity

Definition at line 116 of file Peak2DElement.cpp.

116  {
117  return m_intensity;
118 }
double kome::objects::Peak2DElement::getMz ( )

gets m/z

Returns
m/z

Definition at line 96 of file Peak2DElement.cpp.

96  {
97  return m_mz;
98 }
unsigned int kome::objects::Peak2DElement::getNumberOfParameters ( )

gets the number of parameters

Returns
the number of paramters

Definition at line 290 of file Peak2DElement.cpp.

290  {
291  return m_params.size();
292 }
kome::objects::Peak2DElement::m_params
std::vector< ParamInfo > m_params
Definition: Peak2DElement.h:120
const char * kome::objects::Peak2DElement::getParameterName ( const int  idx)

gets parameter name

Parameters
[in]idxparameter index (If NULL, the index is illegal.)

Definition at line 295 of file Peak2DElement.cpp.

295  {
296  if( idx < 0 || idx >= (int)m_params.size() ) {
297  return NULL;
298  }
299 
300  return m_params[ idx ].name.c_str();
301 }
kome::objects::Peak2DElement::m_params
std::vector< ParamInfo > m_params
Definition: Peak2DElement.h:120
NULL
#define NULL
Definition: CoreMacros.h:18
int kome::objects::Peak2DElement::getParameterType ( const char *  name)

gets parameter type

Parameters
[in]nameparameter name
Returns
parameter type

Definition at line 322 of file Peak2DElement.cpp.

322  {
323  // search index
324  int idx = searchParameterIndex( name );
325 
326  return getParameterType( idx );
327 }
kome::objects::Peak2DElement::getParameterType
int getParameterType(const char *name)
gets parameter type
Definition: Peak2DElement.cpp:322
kome::objects::Peak2DElement::searchParameterIndex
int searchParameterIndex(const char *name)
searches parameter index
Definition: Peak2DElement.cpp:339

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int kome::objects::Peak2DElement::getParameterType ( const int  idx)

gets parameter type

Parameters
[in]idxparameter index
Returns
parameter type

Definition at line 330 of file Peak2DElement.cpp.

330  {
331  if( idx < 0 || idx >= (int)m_params.size() ) {
332  return NULL;
333  }
334 
335  return m_params[ idx ].type;
336 }
kome::objects::Peak2DElement::m_params
std::vector< ParamInfo > m_params
Definition: Peak2DElement.h:120
NULL
#define NULL
Definition: CoreMacros.h:18
const char * kome::objects::Peak2DElement::getParameterValue ( const char *  name)

gets parameter value

Parameters
[in]nameparameter name
Returns
parameter value

Definition at line 304 of file Peak2DElement.cpp.

304  {
305  // search index
306  int idx = searchParameterIndex( name );
307 
308  // value
309  return getParameterValue( idx );
310 }
kome::objects::Peak2DElement::getParameterValue
const char * getParameterValue(const char *name)
gets parameter value
Definition: Peak2DElement.cpp:304
kome::objects::Peak2DElement::searchParameterIndex
int searchParameterIndex(const char *name)
searches parameter index
Definition: Peak2DElement.cpp:339

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const char * kome::objects::Peak2DElement::getParameterValue ( const int  idx)

gets parameter value

Parameters
[in]idxparameter index
Returns
parameter value

Definition at line 313 of file Peak2DElement.cpp.

313  {
314  if( idx < 0 || idx >= (int)m_params.size() ) {
315  return NULL;
316  }
317 
318  return m_params[ idx ].value.c_str();
319 }
kome::objects::Peak2DElement::m_params
std::vector< ParamInfo > m_params
Definition: Peak2DElement.h:120
NULL
#define NULL
Definition: CoreMacros.h:18
double kome::objects::Peak2DElement::getPrecursorMass ( )

gets the precursor mass

Returns
precursor mass

Definition at line 152 of file Peak2DElement.cpp.

152  {
153  return m_precursor;
154 }
double kome::objects::Peak2DElement::getRt ( )

gets RT

Returns
RT

Definition at line 74 of file Peak2DElement.cpp.

74  {
75  return m_rt;
76 }
double kome::objects::Peak2DElement::getStartMz ( )

gets start m/z

Returns
start m/z

Definition at line 101 of file Peak2DElement.cpp.

101  {
102  return m_startMz;
103 }
double kome::objects::Peak2DElement::getStartRt ( )

gets start RT

Returns
start RT

Definition at line 79 of file Peak2DElement.cpp.

79  {
80  return m_startRt;
81 }
int kome::objects::Peak2DElement::searchParameterIndex ( const char *  name)
protected

searches parameter index

Parameters
[in]nameparameter name
Returns
parameter index

Definition at line 339 of file Peak2DElement.cpp.

339  {
340  std::string n = NVL( name, "" );
341 
342  int idx = -1;
343  for( int i = 0; i < (int)m_params.size() && idx < 0; i++ ) {
344  if( n.compare( m_params[ i ].name ) == 0 ) {
345  idx = i;
346  }
347  }
348 
349  return idx;
350 }
kome::objects::Peak2DElement::m_params
std::vector< ParamInfo > m_params
Definition: Peak2DElement.h:120
NVL
#define NVL(checkVal, replaceVal)
Definition: CoreMacros.h:99
void kome::objects::Peak2DElement::setArea ( const double  area)

sets area

Parameters
[in]area

Definition at line 177 of file Peak2DElement.cpp.

177  {
178  m_area = area;
179 }
void kome::objects::Peak2DElement::setCharge ( const int  charge)

sets the charge state

Parameters
[in]chargecharge state

Definition at line 157 of file Peak2DElement.cpp.

157  {
158  m_charge = charge;
159 }
void kome::objects::Peak2DElement::setCluster ( PeaksCluster2D *  cluster)

sets peaks cluster

Parameters
[in]clusterpeaks cluster

Definition at line 121 of file Peak2DElement.cpp.

121  {
122  // check
123  if( m_cluster == cluster ) {
124  return;
125  }
126 
127  // remove
128  if( m_cluster != NULL ) {
129  m_cluster->removePeak( this );
130  }
131 
132  // set
133  m_cluster = cluster;
134 
135  // add
136  if( m_cluster != NULL ) {
137  m_cluster->addPeak( this );
138  }
139 }
kome::objects::Peak2DElement::m_cluster
PeaksCluster2D * m_cluster
Definition: Peak2DElement.h:83
kome::objects::PeaksCluster2D::addPeak
void addPeak(Peak2DElement *peak)
adds peak
Definition: PeaksCluster2D.cpp:136
kome::objects::PeaksCluster2D::removePeak
void removePeak(Peak2DElement *peak)
removes peak
Definition: PeaksCluster2D.cpp:152
NULL
#define NULL
Definition: CoreMacros.h:18

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void kome::objects::Peak2DElement::setData ( const int  sampleId,
const int  profileId,
const double  peakVal,
PeakElement *  peak 
)

sets data

Parameters
[in]sampleIdsample ID
[in]profileIdprofile ID
[in]peakValpeak value
[in]peakpeak peak information

Definition at line 218 of file Peak2DElement.cpp.

218  {
219  clearData();
220  addData( sampleId, profileId, peakVal, peak );
221 
222  // set values
223  setIntensity( peakVal );
224  setArea( peak == NULL ? -1.0 : peak->getArea() );
225  setFwhm( peak == NULL ? -1.0 : peak->getFwhm() );
226 }
kome::objects::PeakElement::getArea
double getArea()
gets peak area
Definition: PeakElement.cpp:241
kome::objects::Peak2DElement::setFwhm
void setFwhm(const double fwhm)
sets FWHM
Definition: Peak2DElement.cpp:167
kome::objects::Peak2DElement::setIntensity
void setIntensity(const double intensity)
sets intensity
Definition: Peak2DElement.cpp:111
kome::objects::Peak2DElement::clearData
void clearData()
clears data
Definition: Peak2DElement.cpp:197
kome::objects::Peak2DElement::setArea
void setArea(const double area)
sets area
Definition: Peak2DElement.cpp:177
NULL
#define NULL
Definition: CoreMacros.h:18
kome::objects::Peak2DElement::addData
void addData(const int sampleId, const int profileId, const double peakVal, PeakElement *peak)
adds data
Definition: Peak2DElement.cpp:207
kome::objects::PeakElement::getFwhm
double getFwhm()
gets the FWHM
Definition: PeakElement.cpp:307

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void kome::objects::Peak2DElement::setFwhm ( const double  fwhm)

sets FWHM

Parameters
[in]fwhm

Definition at line 167 of file Peak2DElement.cpp.

167  {
168  m_fwhm = fwhm;
169 }
void kome::objects::Peak2DElement::setId ( int  id)

sets peak2d id

Parameters
[in]idpeak2d id

Definition at line 192 of file Peak2DElement.cpp.

192  {
193  m_peak2dId = id;
194 }
void kome::objects::Peak2DElement::setIntensity ( const double  intensity)

sets intensity

Parameters
[in]intensityintensity

Definition at line 111 of file Peak2DElement.cpp.

111  {
112  m_intensity = intensity;
113 }
void kome::objects::Peak2DElement::setMz ( const double  mz,
const double  startMz,
const double  endMz 
)

sets m/z

Parameters
[in]mzm/z
[in]startMzstart m/z
[in]endMzendMz

Definition at line 89 of file Peak2DElement.cpp.

89  {
90  m_mz = mz;
91  m_startMz = startMz;
92  m_endMz = endMz;
93 }
void kome::objects::Peak2DElement::setParameter ( const char *  name,
const char *  value,
const int  type = 0 
)

sets parameters

Parameters
[in]nameparameter name
[in]valueparameter value
[in]typetype

Definition at line 270 of file Peak2DElement.cpp.

270  {
271  // search index
272  int idx = searchParameterIndex( name );
273 
274  // set parametr
275  if( idx < 0 ) { // add
276  m_params.resize( m_params.size() + 1 );
277  m_params.back().name = NVL( name, "" );
278  m_params.back().value = NVL( value, "" );
279  m_params.back().type = type;
280  }
281  else { // update
282  m_params[ idx ].value = NVL( value, "" );
283  if( type > 0 ) {
284  m_params[ idx ].type = type;
285  }
286  }
287 }
kome::objects::Peak2DElement::m_params
std::vector< ParamInfo > m_params
Definition: Peak2DElement.h:120
NVL
#define NVL(checkVal, replaceVal)
Definition: CoreMacros.h:99
kome::objects::Peak2DElement::searchParameterIndex
int searchParameterIndex(const char *name)
searches parameter index
Definition: Peak2DElement.cpp:339

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void kome::objects::Peak2DElement::setPrecursorMass ( const double  precursor)

sets the precursor mass

Parameters
[in]precursorprecursor mass

Definition at line 147 of file Peak2DElement.cpp.

147  {
148  m_precursor = precursor;
149 }
void kome::objects::Peak2DElement::setRt ( const double  rt,
const double  startRt,
const double  endRt 
)

sets RT

Parameters
[in]rtRT
[in]startRtstart RT
[in]endRtend RT

Definition at line 67 of file Peak2DElement.cpp.

67  {
68  m_rt = rt;
69  m_startRt = startRt;
70  m_endRt = endRt;
71 }

Member Data Documentation

double kome::objects::Peak2DElement::m_area
protected

area

Definition at line 77 of file Peak2DElement.h.

int kome::objects::Peak2DElement::m_charge
protected

charge

Definition at line 71 of file Peak2DElement.h.

PeaksCluster2D* kome::objects::Peak2DElement::m_cluster
protected

cluster

Definition at line 83 of file Peak2DElement.h.

std::vector< DataInfo > kome::objects::Peak2DElement::m_dataList
protected

data

Definition at line 117 of file Peak2DElement.h.

int kome::objects::Peak2DElement::m_elmId
protected

element data ID

Definition at line 86 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_endMz
protected

end m/z

Definition at line 65 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_endRt
protected

end RT

Definition at line 56 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_fwhm
protected

fwhm

Definition at line 74 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_intensity
protected

intensity

Definition at line 68 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_mz
protected

m/z

Definition at line 59 of file Peak2DElement.h.

std::vector< ParamInfo > kome::objects::Peak2DElement::m_params
protected

parameters

Definition at line 120 of file Peak2DElement.h.

int kome::objects::Peak2DElement::m_peak2dId
protected

peak2d id

Definition at line 89 of file Peak2DElement.h.

Peaks2D* kome::objects::Peak2DElement::m_peaks
protected

peaks

Definition at line 80 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_precursor
protected

precursor mass

Definition at line 92 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_rt
protected

RT

Definition at line 50 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_startMz
protected

start m/z

Definition at line 62 of file Peak2DElement.h.

double kome::objects::Peak2DElement::m_startRt
protected

start RT

Definition at line 53 of file Peak2DElement.h.

The documentation for this class was generated from the following files:
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