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ChangeLog
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150605 *src/GlobalParameter.h,
*src/MyState.h,
*src/PairHashTable.h,
*src/ParKin_Explore.cpp,
*src/parKin.cpp,
*src/StructureUtils.h,
*src/TypeID.h: docu extended.
150408 *src/ParKin_Explore.cpp: Print overall partitionsum.
150404 *src/Makefile.am: SC_DotPlot added
*src/ParKin_Explore.cpp: new dotplot parameter: generate overall dotplot output if requested
*src/ParKin_Explore.cpp: instantiation of ScBasin now parameter dependent (Martin)
*src/SC_DotPlot.cpp: BUGFIX : missing index shift when preparing vienna plist data structure (Martin)
150402 *src/SC_PartitionFunction.*: docu extended, Boltzmann weight computation as function, constructor takes temperature (Martin)
+src/SC_DotPlot.*: computes base pair probabilities as subclass of SC_PartitionFunction, supports read and write of vienna PS dot plots (Martin)
*src/MyState.*: typedef for structure data type (Martin)
150326 *src/RNAkinetics/RateMatrixUtil.cpp,
src/ParKin_Explore.cpp: rate normalization corrected.
150310 *src/Flooder.cpp,
src/GlobalParamerter.h,
src/MyState.cpp/.h,
src/ParKin_Explore.cpp,
src/SC_PartitionFunction.h/.cpp: changed initialization -> more ISO conform.
150310 *src/Flooder.cpp,
src/GlobalParamerter.cpp,
src/MyState.h,
src/PairHashTable.h,
src/ParKin_Explore.cpp,
src/parKin.cpp,
src/PriorityQueue.cpp,
src/StateCollector.cpp,
src/WalkGradientHashed.cpp: sorted variables, cleaned imports, fixed memory leak in flooder.
150306 *src/ParKin_Explore.cpp,
*src/RNAkinetics/RateMatrixUtil.cpp: new parameter "partitionFunctions" to write partitionFunctions to a file (which enables further clustering strategies).
150224 *src/ParKin_Explore.cpp: dont read parameterfile with turner2004 because its wrong in ViennaRNA2.1.9
150214 *src/ParKin_Explore.cpp: set dangling ends parameter.
150212 *src/ParKin_Explore.cpp: set BoltzmanTemperatur B with general EnergyTemperatur T.
150210 *src/ParKin_Explore.cpp: final structure as parameter. (the exploration stops if this basin is done).
150209 *src/ParKin_Explore.cpp: boltzmann-temperature is a separate parameter.
150206 *src/ParKin_Explore.cpp: new dynamicMaxToHash estimated value, to prevent the system from swapping if large sequences are computed.
150205 *src/ParKin_Explore.cpp: EnergyParameter read corrected. Output start basin.
150203 *src/ParKin_Explore.cpp: description corrected. EnergyParameter read corrected.
150131 *src/ParKin_Explore.cpp: mfe array corrected.
150129 *src/ParKin_Explore.cpp: store energies only if a file is given.
150129 *src/ParKin_Explore.cpp: delete neighborCombinator before update.
150127 *src/ParKin_Explore.cpp: dynamic K filter corrected (selection of the k-th neighbor in each loop)
150126 *unused regions removed.
150125 *BIU and ELL dependency removed.
150123 *src/ParKin_Explore.cpp: scbasin temperature korrekted.
*src/RNAkinetics/RateMatrixUtil.cpp: equilibrium vector corrected (indices of minima corrected).
150122 *src/ParKin_Explore.cpp: korrected dynamic best k filterupdate.
150121 +misc: energy model parameter files (from viennaRNA)
+misc/Makefile.am,
*Makefile.am, configure.ac: to install the parameter files in the share folder.
*src/Flooder.cpp,
src/GlobalParameter.cpp,
src/ParKin_Explore.cpp,
src/SC_PartitionFunction.cpp,
src/StatePairCollector.cpp,
src/WalkGradientHashed.cpp: Changes with energy parameter. Global parameter with new temperature value.
*src/ParKin_Explore.cpp: new temperature value, new energy model options.
Output equilibrium probability vector for all states.
141223 *src/ParKin_Explore.cpp: dynamic best k filter improved.
*src/RNAkinetics/RNA_NeighMinFilter.cpp: moved GreaterByZMatrix class definition in header.
141215 *src/PairHashTable.h,
src/SpookyHash/SpookyHashMap.h: 64bit hash keys.
*src/ParKin_Explore.cpp: new parameter "dynamicBestK" that automatically adjusts the K-Value if the mfe is not in the final minima.
141207 *src/ParKin_Explore.cpp: filterBestK corrected.
141207 *src/RNAkinetics/RNA_NeighMinFilter.cpp: copy of indices adjusted.
*src/Flooder.cpp, Flooder.h: changed maxToQueue from int to size_t
*src/ParKin_Explore.cpp: adjusted default values, filter initialization corrected.
141202 *src/ParKin_Explore.cpp: rate calculation corrected.
141129 *src/ParKin_Explore.cpp: rate calculation corrected.
141128 *src/ParKin_Explore.cpp: bug with exportEnergies corrected (print energies only once per basin).
141128 *src/ParKin_Explore.cpp: rate calculation corrected.
141126 +src/SC_StoreEnergies.h,
src/SC_StoreEnergies.cpp,
src/Makefile.am: new statecollector for storing the energies of all states.
*src/SC_PartitionFunction.cpp: adjusted for new statecollector.
*MyState.h: comment.
*src/ParKin_Explore.cpp: Energycalculation corrected. New Parameter for energyFile (only for tests!).
141122 *src/Flooder.cpp: maxEnergy deletion of last element changed.
*ParKin_Explore.cpp: new parameter deltaE -> maxEnergy = localMin.Energy+deltaE.
*parKin.cpp: changed because flooder has been changed.
141109 *src/RNAkinetics/RateMatrixUtil.cpp: print rate matrix with sorted states (by energy).
+src/SpookyHash/SpookyV2.cpp,
+src/SpookyHash/SpookyV2.h,
+src/SpookyHash/SpookyHashMap.h: New HashMap which calculates hashes for arrays. (Function by Bob Jenkins).
*src/WalkGradientHashed: uses the new HashMap.
*src/StructureUtils.cpp: parameters are const.
*src/ParKin_Explore.cpp: Processed States are counted for comparison.
*src/Flooder.cpp: Energythreshold is determined.
*src/Makefile.am: new HashMap included.
141106 *src/WalkGradientHashed.cpp: stored state instead of string.
141105 *src/Flooder.cpp: maxToStore is renamed to maxToQueue.
*src/ParKin_Explore.cpp: new maxEnergy parameter to set a max. flood level.
*src/StateCollector.cpp: getMaxEnergy in basin.
*src/RNAkinetics/RateMatrixUtil.cpp: new printRateMatrix sorted by energy for better comparison.
141104 *src/ParKin_Explore.cpp,
src/parKin.cpp: initial maxToStore and maxToHash changed.
141007 *src/ParKin_Explore.cpp: indicesOfNeighbors and reverse minima list removed. --> redundant.
Filter is initialized in main (not in parallel loop).
*src/parKin.cpp,
src/StatePairCollector.cpp,
src/RNAkinetics/RNA_NeighMinFilter.cpp: indicesOfNeighbors removed.
*src/WalkGradientHashed: less allocation, only copy. -->speedup.
140930 *src/ParKin_Explore.cpp: filtering(indice adjustment) corrected.
140929 *src/StructureUtils.cpp: faster comparison.
*src/Flooder.cpp,
src/WalkGradientHashed.cpp: adjusted to new ParKin_ViennaRNA version.
*src/MyState.cpp: removed useless output.
*src/ParKin_Explore: output of basin sizes and times. Filtering is done in each thread.
*src/StatePairCollector: stores number of outer states.
140923 *src/Flooder.cpp,
*src/ParKin_Explore.cpp,
*src/parKin.cpp,
*src/WalkGradientHashed.cpp: maxNeighbors added, to allocate the space for all neighbors only once.
*src/MyState.cpp: toString method optimized.
*src/StructureUtils.cpp: getStructure method optimized.
*StatePairCollector.cpp: faster neighbor id look up.
140921 *src/Flooder.cpp,
src/WalkGradientHashed.cpp: adjusted for new ParkinViennaRNA version which allocates the neighborlist only once.
*src/WalkGradientHashed.cpp: allocation for S0,S1 and EnergyParameters only once.
*src/TypeID.cpp,
src/StructureUtils,
src/PriorityQueue: format changed.
*src/StatePairCollector.cpp,
src/parKin.cpp,
src/ParKin_Explore.cpp: adjusted according to WalkGradient.
*src/PairHashTable.h,
*src/MyState: modifier, format.
*src/RateMatrixUtil: toString method from MyState.
140918 *src/ParKin_Explore.cpp: critical section added.
140916 *src/Flooder.cpp,
*src/WalkGradientHashed.cpp: has a new dedicated "neighborList" as replacement for the mapping
from threadID to List, because the ViennaRNA-Lib was changed to
return the list at once.
*src/Makefile.am: new class TypeID was added.
*src/PairHashTable.h: unused includes removed.
*src/ParKin_Explore.cpp: new method for flooding with input and output parameters, to make clear
what variables are used in the omp parallel for loop. This makes the
merge process with the indices easier to understand.
*src/StatePairCollector.h: unused includes removed.
*src/StructureUtils.cpp: inline removed.
+src/TypeID.cpp: new class which is used to assign unique ids to the minima.
*README: Issue with heap contention among threads added.
140909 *src/Flooder.cpp,
src/WalkGradientHashed.cpp: cleaned up parameters.
src/StatePairCollector: comment removed.
src/ParKin_Explore: StopWatch added.
140908 -src/Flooder.cpp: test removed.
*src/ParKin_Explore.cpp: cleaned up.
filter enabled.
merged indices from threads correctly.
*src/StructureUtils.cpp: comparison corrected.
*src/RNAkinetics/RNA_NeighMinFilter: adjusted for multithreaded filtering.
140907 +src/MyState.cpp: new wrapper for ViennaRNA struct_en with destructor.
*src/Flooder.cpp,
src/GlobalParameter.cpp,
src/PairHashTable.cpp,
src/parKin.cpp,
src/ParKin_Explore.cpp,
src/PriorityQueue.cpp,
src/StateCollector.cpp,
src/WalkGradientHashed: multithreading optimizations + MyState updates.
*src/StructureUtils: faster equals comparison.
140818 +src/WalkGradientHashed.cpp: finally added.
*src/ParKin_Explore.cpp: parallelization test.
maxThreads parameter.
*configure.ac: openMP (default enabled)
140816 +src/Flooder.cpp,
*src/ParKin.cpp,
*src/ParKin_Explore.cpp : maxToStore parameter, handle deletion from PriorityQueue!
+src/MakeFile.am,
*src/StatePairCollector: now with hashed gradientwalk.
*src/PriorityQueue.cpp: deletion corrected.
*src/StructureUtils.cpp: handle NULL values.
140813 + src/GlobalParameter.cpp: new global energy parameter -> is faster.
!works only with adjusted move_set.c in ViennaRNA package!
* src/Flooder.cpp: now with global parameters.
* src/MakeFile.am: with global parameters and with filters.
* src/ParKin_Explore: with filters.
* src/SC_PartitionFunction.cpp: calculates with floats to be consistent with RNA_Explore.
* src/StatePairCollector.cpp: now with global parameters.
140809 * configure.ac: from now on we need also the BIU- and the ELL-library, because we have ParKin_explore.
* Flooder.cpp: @author corrected.
* src/MakeFile.am: ParKin_explore added.
* src/StructureUtils.cpp: equal comparison handles NULL.
+ src/ParKin_Explore.cpp: new tool which calculates the rate matrix,
with a flooder that is only based on the viennaRNA-lib.
+ src/RNAkinetics/RateMatrixUtil.cc: function to print the rate matrix.
+ src/RNAkinetics/RateMatrixUtil.hh: header for that.
140808 * StatePairCollector.cpp: added own gradient walk. Like this one in ELL.
* Flooder.cpp: cleaned up.
* parKin.cpp: added initial gradient walk;
140807 * parKin.cpp: cleaned up.
* StatePairCollector.cpp: gradient walk calculate correct energies.
* Flooder.cpp: improved energy calculation.
140806 * StatePairCollector.cpp: energy recalculation.
* StateCollector.cpp, SC_PartitionFunction.cpp: corrected inheritance.
* parKin.cpp: cleaned up.
* Flooder.cpp: cleaned up. Set Neighborlistlength to 0 after each iteration.
140805 * Flooder.cpp: Comparison improved.
* configure.ac: c++11 std. m4 included.
140804 * Flooder.cpp: tests with energy calculation. TODO: find correct parameters.
140802 * rename SC_PartitionFunction, add to makefile.
140801 + new flooder class and other classes.
140728 + vienna libraray experiments with neighbor generation.
140721 project start