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Jiri Novak
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Feb 21, 2018
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| [Desktop Entry] | ||
| Comment=A tool for de novo sequencing of nonribosomal peptides from accurate product ion mass spectra. | ||
| Exec=CycloBranch | ||
| Icon=/usr/share/cyclobranch/images/cb.png | ||
| Name=CycloBranch | ||
| NoDisplay=false | ||
| StartupNotify=false | ||
| Terminal=false | ||
| Type=Application |
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| ###################################################################### | ||
| # Automatically generated by qmake (3.0) Fri Dec 5 03:02:26 2014 | ||
| ###################################################################### | ||
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| TEMPLATE = app | ||
| TARGET = CycloBranch | ||
| QT += core gui widgets printsupport svg | ||
| INCLUDEPATH += . core gui parallel | ||
| QMAKE_CXXFLAGS += -std=c++0x -DUNIX -m64 | ||
| QMAKE_LIBS += -lboost_regex | ||
| OBJECTS_DIR = build/ | ||
| MOC_DIR = moc/ | ||
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| # Input | ||
| RESOURCES = images.qrc | ||
| HEADERS += core/cAllocator.h \ | ||
| core/cBrick.h \ | ||
| core/cBricksDatabase.h \ | ||
| core/cCandidate.h \ | ||
| core/cCandidateSet.h \ | ||
| core/cDeNovoGraph.h \ | ||
| core/cDeNovoGraphNode.h \ | ||
| core/cFragmentIons.h \ | ||
| core/cParameters.h \ | ||
| core/cPeak.h \ | ||
| core/cPeaksList.h \ | ||
| core/cSequence.h \ | ||
| core/cSequenceDatabase.h \ | ||
| core/cSummaryFormula.h \ | ||
| core/cTheoreticalSpectrum.h \ | ||
| core/cTheoreticalSpectrumList.h \ | ||
| core/utilities.h \ | ||
| gui/cAboutWidget.h \ | ||
| gui/cBranchedWidget.h \ | ||
| gui/cBricksDatabaseWidget.h \ | ||
| gui/cCyclicWidget.h \ | ||
| gui/cDrawPeptideWidget.h \ | ||
| gui/cEventFilter.h \ | ||
| gui/cFragmentIonsListWidget.h \ | ||
| gui/cGraphWidget.h \ | ||
| gui/cLassoWidget.h \ | ||
| gui/cLinearWidget.h \ | ||
| gui/cMainThread.h \ | ||
| gui/cMainWindow.h \ | ||
| gui/cModificationsWidget.h \ | ||
| gui/cParametersWidget.h \ | ||
| gui/cSequenceDatabaseWidget.h \ | ||
| gui/cSpectrumDetailWidget.h \ | ||
| gui/cSpectrumSceneWidget.h \ | ||
| parallel/cGraphReaderThread.h \ | ||
| parallel/cSpectrumComparatorThread.h | ||
| SOURCES += core/cBrick.cpp \ | ||
| core/cBricksDatabase.cpp \ | ||
| core/cCandidate.cpp \ | ||
| core/cCandidateSet.cpp \ | ||
| core/cDeNovoGraph.cpp \ | ||
| core/cDeNovoGraphNode.cpp \ | ||
| core/cFragmentIons.cpp \ | ||
| core/cParameters.cpp \ | ||
| core/cPeak.cpp \ | ||
| core/cPeaksList.cpp \ | ||
| core/cSequence.cpp \ | ||
| core/cSequenceDatabase.cpp \ | ||
| core/cSummaryFormula.cpp \ | ||
| core/cTheoreticalSpectrum.cpp \ | ||
| core/cTheoreticalSpectrumList.cpp \ | ||
| core/utilities.cpp \ | ||
| gui/cAboutWidget.cpp \ | ||
| gui/cBranchedWidget.cpp \ | ||
| gui/cBricksDatabaseWidget.cpp \ | ||
| gui/cCyclicWidget.cpp \ | ||
| gui/cDrawPeptideWidget.cpp \ | ||
| gui/cEventFilter.cpp \ | ||
| gui/cFragmentIonsListWidget.cpp \ | ||
| gui/cGraphWidget.cpp \ | ||
| gui/cLassoWidget.cpp \ | ||
| gui/cLinearWidget.cpp \ | ||
| gui/cMainThread.cpp \ | ||
| gui/cMainWindow.cpp \ | ||
| gui/cModificationsWidget.cpp \ | ||
| gui/cParametersWidget.cpp \ | ||
| gui/cSequenceDatabaseWidget.cpp \ | ||
| gui/cSpectrumDetailWidget.cpp \ | ||
| gui/cSpectrumSceneWidget.cpp \ | ||
| parallel/cGraphReaderThread.cpp \ | ||
| parallel/cSpectrumComparatorThread.cpp \ | ||
| main.cpp |
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| /** | ||
| \file cAllocator.h | ||
| \brief An allocator of objects. | ||
| */ | ||
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| #ifndef _CALLOCATOR_H | ||
| #define _CALLOCATOR_H | ||
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| #include <vector> | ||
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| using namespace std; | ||
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| /** | ||
| \brief An allocator of objects. | ||
| */ | ||
| template <class T> | ||
| class cAllocator | ||
| { | ||
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| vector<T*> strips; | ||
| int itemsperstrip; | ||
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| int currentfreestrip; | ||
| int currentfreeitem; | ||
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| public: | ||
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| /** | ||
| \brief The constructor. | ||
| */ | ||
| cAllocator(); | ||
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| /** | ||
| \brief The destructor. | ||
| */ | ||
| ~cAllocator(); | ||
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| /** | ||
| \brief Remove all allocated items. | ||
| */ | ||
| void reset(); | ||
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| /** | ||
| \brief Get a reference to a new item. | ||
| \retval reference to a new item | ||
| */ | ||
| T* getNewItem(); | ||
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| }; | ||
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| template <class T> | ||
| cAllocator<T>::cAllocator() { | ||
| strips.clear(); | ||
| itemsperstrip = 500; | ||
| currentfreestrip = 0; | ||
| currentfreeitem = 0; | ||
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| T* newstrip = new T[itemsperstrip]; | ||
| strips.push_back(newstrip); | ||
| } | ||
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| template <class T> | ||
| cAllocator<T>::~cAllocator() { | ||
| for (int i = 0; i < (int)strips.size(); i++) { | ||
| delete [] strips[i]; | ||
| } | ||
| } | ||
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| template <class T> | ||
| void cAllocator<T>::reset() { | ||
| for (int i = 0; i < (int)strips.size(); i++) { | ||
| delete [] strips[i]; | ||
| } | ||
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| strips.clear(); | ||
| itemsperstrip = 500; | ||
| currentfreestrip = 0; | ||
| currentfreeitem = 0; | ||
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| T* newstrip = new T[itemsperstrip]; | ||
| strips.push_back(newstrip); | ||
| } | ||
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| template <class T> | ||
| T* cAllocator<T>::getNewItem() { | ||
| T* freeitem = &strips[currentfreestrip][currentfreeitem]; | ||
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| currentfreeitem++; | ||
| if (currentfreeitem == itemsperstrip) { | ||
| currentfreestrip++; | ||
| currentfreeitem = 0; | ||
| T* newstrip = new T[itemsperstrip]; | ||
| strips.push_back(newstrip); | ||
| } | ||
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| return freeitem; | ||
| } | ||
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| #endif | ||
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