The class representing lists of theoretical spectra.
More...
#include <cTheoreticalSpectrumList.h>
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| cTheoreticalSpectrumList () |
| | The constructor.
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void | clear () |
| | Clear the class.
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| void | clear (int fileid) |
| | Clear a specified file id. More...
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| void | initialize (cMainThread &os, cParameters ¶meters, cDeNovoGraph *graph) |
| | Initialize the list. More...
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| void | add (int fileid, cTheoreticalSpectrum &theoreticalspectrum) |
| | Add a spectrum to the list. More...
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| cTheoreticalSpectrum & | get (int fileid, int order) |
| | Get a reference to a spectrum. More...
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| int | size () |
| | Get the number of files. More...
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| int | size (int fileid) |
| | Get the number of spectra in a file. More...
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| void | resize (int size) |
| | Resize the vector of files. More...
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| void | resize (int fileid, int size) |
| | Resize a file id vector. More...
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| int | parallelCompareAndStore (int fileid, cCandidateSet &candidates, bool &terminatecomputation) |
| | Parallel comparison of theoretical spectra with an experimental spectrum. More...
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| double | updatekNNList (cTheoreticalSpectrum &theoreticalspectrum, int theoreticalpeaksrealsize, double score, regex *rxsearchedsequence) |
| | Update the kNN list of peptide sequence candidates (thread-safe). More...
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| void | sortAndFitSize (int fileid) |
| | Sort the list according to a score defined by cParameters::scoretype and crop the list according cParameters::hitsreported. More...
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The class representing lists of theoretical spectra.
◆ add()
Add a spectrum to the list.
- Parameters
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| fileid | file id |
| theoreticalspectrum | reference to a spectrum |
◆ clear()
| void cTheoreticalSpectrumList::clear |
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int |
fileid | ) |
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Clear a specified file id.
- Parameters
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◆ get()
Get a reference to a spectrum.
- Parameters
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| fileid | file id |
| order | id of a spectrum |
- Return values
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◆ initialize()
Initialize the list.
- Parameters
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| os | reference to the main thread of the application |
| parameters | reference to the parameters of the application |
| graph | pointer to the de novo graph |
◆ parallelCompareAndStore()
| int cTheoreticalSpectrumList::parallelCompareAndStore |
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int |
fileid, |
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cCandidateSet & |
candidates, |
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bool & |
terminatecomputation |
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Parallel comparison of theoretical spectra with an experimental spectrum.
- Parameters
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| fileid | file id |
| candidates | reference to a set of peptide sequence candidates |
| terminatecomputation | reference to a variable determining that the computation must be stopped |
- Return values
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| int | 0 when successfully finished; -1 when an error occurred |
◆ resize() [1/2]
| void cTheoreticalSpectrumList::resize |
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int |
fileid, |
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int |
size |
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Resize a file id vector.
- Parameters
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◆ resize() [2/2]
| void cTheoreticalSpectrumList::resize |
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int |
size | ) |
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Resize the vector of files.
- Parameters
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◆ size() [1/2]
| int cTheoreticalSpectrumList::size |
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Get the number of files.
- Return values
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◆ size() [2/2]
| int cTheoreticalSpectrumList::size |
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int |
fileid | ) |
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Get the number of spectra in a file.
- Parameters
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- Return values
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◆ sortAndFitSize()
| void cTheoreticalSpectrumList::sortAndFitSize |
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int |
fileid | ) |
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◆ updatekNNList()
| double cTheoreticalSpectrumList::updatekNNList |
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cTheoreticalSpectrum & |
theoreticalspectrum, |
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int |
theoreticalpeaksrealsize, |
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double |
score, |
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regex * |
rxsearchedsequence |
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Update the kNN list of peptide sequence candidates (thread-safe).
- Parameters
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| theoreticalspectrum | reference to the newly added spectrum |
| theoreticalpeaksrealsize | the number of peaks in the newly added spectrum (required because of a performance improvement) |
| score | score of the candidate to be inserted |
| rxsearchedsequence | regular expression corresponding to searched sequence |
- Return values
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| double | current value of the worst score in the list of candidates |
The documentation for this class was generated from the following files: