Changelog.txt

	
version 2.0.3

180927 MR :
	* R/mica-functions.R :
	  * interpolateCurve() :
	    * bugfix interval length formula

180927 MR :
	* controller/MicaR :
	  * getAlignedX() :
	  * getAlignedSlope() :
	  * getConsensusX() :
	  * getConsensusY() :
	    + dedicated exception handling
	* view/ViewCsvExpSettings : 
	  * initForm() :
	    * default height increased to 190 (was 150) to avoid layouting issues
	      (thanks to Alexander Mattheis, solves PR #21)
	
version 2.0.2

180212 MR :
	* view/View* : 
	  * delimiter fixed to ";" to avoid confusion on different systems

171027 MR :
	* R/mica-functions.R :
	  * converting all na.omit() calls to vector via as.vector()
	  * smoothData() :
	    + handle errors/warnings produced by loess function (eg. not enough data)
	  + getNormData() : provides normalized data, i.e. (data-mean)/sd
	
version 2.0.1

170919 MR :
	* minimal GUI resolution lowered to 800x600
	+ installation documentation added
	+ test data and documentation added
	
version 2.0.0

170529 MM :
	* manual split point alignment fixed
	* CLI tested and fixed

170524 MM :
	* CSV and PNG export revisited and corrected

170508 MM :
	* view/MicaMainFrame :
	  * refreshPlot() :
	    * bugfix: curve copy did not copy filters
	  * constructor() :
	    + profilePlotIn now observer for filterExtremaValue and filterInflectionValue
	      to fix strange filter update bug
	* model/FileFormatCsv :
	  + pruneQuotes : prunes quote signs from read CSV entries
	* view/ViewExportSelection :
	  * use MicaData in constructor
	* controller/GuiController :
	  * exportResult() :
	    * bugfix: use new ViewExportSelection constructor to avoid 
	      exception if no alignment consensus available
	* algorithm/AnnotatedCurve :
	  * addAnnotations() : 
	    * bugfix : was ignoring one position after plateau check
	* algorithm/CurveInflectionFilter :
	  * setMinRelHeight() :
	    * only change value and inform listener if value different from old one
	* view/ColoredAnnotatedCurvePlot :
	  + implements ChangeListener<Number> to fix strange filter update bug
	  + changed() : triggers repaint() on call

170508 MM :
	* model/FileFormatCsv :
	  * load() : 
	    * bugfix : special handling if index column present (header of first column empty)
	* algorithm/CurveExtremaFilter :
	  * setMinRelNeighDiff() :
	    * update only if new value differs from old value

170508 MM :
	* view/ColoredAnnotatedCurvePlot :
	  * paintAxisDashes() :
	    + pre-last dash is drawn (only label omitted)

161026 MM :
	* model/FileFormatCsv :
	  * load() : 
	    * bugfix : handling of empty parse result corrected

160912 MM :
	* algorithm/MICA :
		+ setOriginalSorting() : reorders an alignment given the input order of curves
		* align*() : 
			+ sort final alignment
	- obsolete/* : cleanup of old implementation classes
	* algorithm/PICA :
		* align() :
			* alignment computation now truely lazy at the end of all testing
	* controller/MicaController :
		+ version : central version information
	* controller/GuiController :
		- cleanup of old commented code
		- saveSetup() : obsolete
		- loadSetup() : obsolete
		- saveConfig() : obsolete
		- loadConfig() : obsolete
		- showView() : obsolete
	* controller/MicaMain :
		+ printVersionHeader() : header + version information
		+ "-v" argument for version information
	* model/Model :
		* receiveMultipleSplitAlignmentSolution() :
			* bugfix : has to call updateInterpolation() instead of resetFilteredAnnotations()
	* view/MicaMainFrame :
		- cleanup of old commented code
		* actionPerformed() :
			+ version information in "About" dialog
		* selected point info label : setup corrected to show text on selection
	- controller/CommandLineConfig : obsolete
	- controller/CommandLineController : obsolete
	- controller/ViewFilterAdjustment : obsolete
	* view/ColoredAnnotatedCurvePlot :
		* paintPoint() : bugfix : interface extended to enable correct coloring
	- bin/* : obsolete (moved to version)
	- data/* : obsolete (moved to data)
			
160909 MM :
	+ controller/MicaController : generic controller interface for MICA to be run
		by MicaMain
		+ Arguments : all command line arguments to be handled
	+ controller/CliController : command line interface controller to run MICA based
		on command line arguments only
	* controller/GuiController :
		* param* : adaption to DoubleParameter interface changes
	* view/DoubleParameter :
		+ setValue() : abstract function how to set the final value
		* set() : generic function that tests whether or not a value update
			is needed and informs all listeners in case the value was changed
	* view/DoubleParameterPanel :
		* construction : bugfix textfield tooltip setup
	* view/MicaMainFrame :
		+ setDistanceSlopeBased() : to set the distance base radio button via controller
	* view/ViewExportSelection :
		* constructor : 
			+ column delimiter now argument 
	* view/ViewParse :
		* constructor :
			+ parseHeader now argument 
	* model/Model :
		+ getMinIvalDecomp() : was missing
		* maxWarpFactorMax = 999
	* model/FileFormatCsv :
		+ writeX() : write x-coordinate table to file
	* controller/MicaR :
		+ default locale = english
	* controller/CommandLineConfig :
		- DistanceStrat : now MicaController.DistanceBase
		* adaption to other changes
	* controller/MicaMain :
		* command line argument setup via joptsimple
		+ setupArgumentParser() : generate arguments
		+ checkRanges() : checks if number arguments are within according ranges
		+ checkFiles() : checks existence of input files
		+ main() :
			+ negative exit status if exceptions raised
	* controller/GuiController :
		+ fileColumnSeparator + setter/getter : default column delimiter
		+ fileColumnHeader : default whether or not to parse CSV header
		* showView() : 
			+ repaint() triggered (needed eg. due to model changes etc.)
		+ start() : parses command line arguments, updates the model, and starts the GUI
	+ lib/Jopt-simple-5.0.2.* : command line argument library

160908 MM :
	* algorithm/AnnotatedCurve : 
		* resetFilteredAnnotations() : now public
	* algorithm/MICA :
		* align() :
			+ checks for currentThread.isInterrupted() to abort computation
		* ProgressiveAlignmentHandler :
		* ProgressiveReferenceAlignmentHandler :
			* addSubAlignment() :
				+ checks for currentThread.isInterrupted() to abort computation
	* algorithm/MicaRunner :
		* run() :
			+ checks for currentThread.isInterrupted() to abort computation
	* algorithm/MICA :
		* align() :
			+ checks for currentThread.isInterrupted() to abort computation
	* controller/CommandLineController :
		* adaption to IProgressIndicator changes
	* controller/GuiController :
		* paramDistanceSamples : max boundary now 100000
		- refreshMainViewPlot() : obsolete
		- clearMainOutput() : obsolete
		* distributeSolution() : 
			+ now also forwards consensus curve
	* model/Model :
		+ alignmentConsensus + getter : consensus of the alignment
		* calcAlignment() : 
			* thread generation now via IProgressIndicator to enable abortion
		* receiveMultipleSplitAlignmentSolution() :
			+ consensus extraction and storage
			* annotations of aligned curves are removed if not interval boundary
	* view/ColoredAnnotatedCurve :
		* addSplitPoint() :
			* bugfix : resetFilteredAnnotations() call missing
	* view/ColoredAnnotatedCurvePlot :
		* paintPlotLegend() :
			* bugfix : legend positioning corrected
		* paintCurve() :
			+ interval boundaries are always plotted
	* view/IProgressIndicator :
		+ Status enum for different states of progress
		* updateProgressIndication() : now with status argument
		+ startMica() : starts the Thread for a MicaRunner to have access for interrupt 
	- view/ViewReferenceMicaSelection : renamed to ReferenceSelectionDioalog
	+ view/ReferenceSelectionDioalog : former ViewReferenceMicaSelection
	* view/MicaMainFrame :
		- IProgressIndicator interface implementation now part of micaProgressDialog
		+ micaProgressDialog : modal dialog that locks frame during computation
		+ showConsensusInput/Output : switch to show/hide consensus in plot
		* refreshPlot() : 
			+ generates length corrected profiles and consensus if showConsensusInput is selected
		- repaintProfilePlot() : obsolete
		* displayResultPlot()
			+ adds consensus if showConsensusOutput is selected
		* actionPerformed() :
			+ new buttons registered
		+ MicaProgressDialog : dialog that handles mica running and abortion and blocks main view
		+ getProgressIndicator() : returns micaProgressDialog

160907 MM :
	* view/DoubleParameterPanel :
	  	* construction : 
	  		* tool tip generation now includes default value
	* view/MicaMainFrame :
		+ filterExtremaValuePanel : extrema filter value
		+ filterInflectionValuePanel : inflection filter value
		+ curve panels now listen on filter value changes
		* distance setup layout changed
		+ filter parameter panel
		+ distanceSamplesPanel : distance sample number parameter
		+ grouping of alignment parameters
		- menu items for config save/run
		- menu items for setup save/load
		+ implements Observer to listen for filter value changes to 
		  update curve information
		* changed profile->curve in most texts/tooltips
		- most main menu tooltips disabled
		* refreshPlot(): curve highlighting can be disabled now
		- getSelectedDistanceRadio() : obsolete
		- setSelectedDistanceRadio() : obsolete
	* controller/MicaR :
		* constructor : distWarpScaling was former warpScaling 
	* controller/CommandLineController :
		* adaptions to model changes
	* controller/GuiController : 
		+ paramFilterExtremaValue + getter
		+ paramFilterInflectionValue + getter
		+ paramDistanceSamples + getter
		+ get/setDistanceSamples() : model interface
		+ is/setDistanceSlopeBased() : model interface
		* startMica() : no need for distance function argument
		+ registerFilterChangeListener() : to enable notification on filter value changes
	* model/FileFormatCsv :
		* load() :
			+ check for missing entries/columns
	* model/Model :
		+ distanceFunction + getter/setter : was in controller or even gui
		* calcAlignment() : no distance function argument needed
		* discardAlignment() : 
			+ clears alignmentData
		* receiveMultipleSplitAlignmentSolution() 
			+ removes all automatic annotations from given curves
	* view/ColoredAnnotatedCurve :
		+ originalSplitAnnotation : to enable undo of split setting
	* view/ColoredAnnotatedCurvePlot :
		* selectCurveIndex default : no curve selected
		* setSelectedCurve() : repaint only if new selection different from old
		* updatePlotArea() :
			+ boundary updates check whether curve end already reached
		* paintCurve() :
			+ check for curve ends are within plot area for start/end segment plotting
		+ update() : Observer interface for CurveAnnotationFilter value changes : repaint
	* algorithm/MICA :
		* getConsensusCurve() :
			+ x-max boundary check for consensus y-coordinate computation
			+ split points are transferred into the consensus annotation
		

160812 MM :
	* algorithm/CurveInflectionFilter :
		* filter() : check now for <= min instead of > min
	* algorithm/CurveExtremaFilter :
		* filter() : check now for <= min instead of > min
	* R/mica-functions.R : 
		* getAnnotations() : bugfix : MicaR interface adaption
		* documentation extended
	* R/mica-example.R :
		+ getAnnotations called
	* algorithm/AnnotatedCurve : 
		+ AnnotatedCurve(AnnotatedCurve) : copy construction
	* algorithm/CurveAnnotation :
		* isIntervalBoundary() : check simplified 

160808 MM : 
	* view/ColoredAnnotatedCurvePlot :
		* paintCurve() : last segment painting corrected
	* view/MicaMainFrame :
		* displayResultPlot() :
			+ call clearPlot() to clear the plotting area

160803 MM : change summary
	* algorithm/Curve :
		+ getClosestPoint() : index of closest data point for a given x-coordinate
		+ getYequiX() : returns interpolated equidistant y-coordinates
	* algorithm/AnnotatedCurve : 
		+ AnnotatedCurve(Curve) : construction from Curve
	* algorithm/CurveAnnotation
		* Type :
			+ isIntervalBoundary() : check if end or split point
	* algorithm/PointType :
		+ toPointType() : conversion from CurveAnnotation 
	- algorithm/MultipleSplitAlignment : obsolete
	+ algorithm/IntRange : range of integer values
	+ algorithm/DoubleRange : range of double values
	+ algorithm/MicaRunner : thread for MICA computation
	* algorithm/IMsaSolutionReceiver : updated to MICA data
	- controller/Controller : renamed to GuiController
	+ controller/GuiController : former Controller
		+ parameter setup via DoubleParameter
		- local filter stuff removed
		+ maxRelXShift parameter
	* controller/Debug :
		* plotCurves() : 
			* now original curve data is plotted rather than interpolated data
	* controller/CommandLineConfig:
	* controller/CommandLineController:
	* controller/MicaMain:
		* adaption to new interface and data
	* model/* :
		* adaption to new interfaces and data
	+ view/DoubleParameter : represents a parameter with double values in given boundaries
		and enables automatic updates if its value is changed
	+ view/DoubleParameterPanel : button-label-combination to setup and show a DoubleParameter
	+ view/ColoredAnnotatedCurve : annotated curve with additional view information
	+ view/ColoredAnnotatedCurvePlot : plot panel for ColoredAnnotatedCurve objects
		+ point selection listening reenabled
		+ split point plotting reenabled
		+ zoom change anchors in plot area center
	* view/* : 
		* adaption to new interfaces and data
	* view/ISelectedPlotPointInfoListener :
		* selectedPlotPointChanged() : now double coordinates and CurveAnnotation.Type
	* view/ViewImportFilterExecute :
		* background color change now in Plot menu
		- point type combobox
		* curve foreground selection reenabled
	+ obsolete package : contains all old sources not needed anymore
	- view/ViewImportFilterExecute : rename MicaMainFrame
	+ view/MicaMainFrame : former ViewImportFilterExecute
		- generateTimeString() : now in Model
		+ paramMaxRelXShiftPanel : panel for maxRelXShift setup
	* model/Model :
		+ generateTimeString() : formerly in MicaMainFrame
		+ maxRelXShift getter and setter 

160711 MM
	* algorithm/PICA :
		* align() :
			+ x-coordinates shifted to mean x-min if necessary
	* algorithm/MICA :
		* fuseAlignments() :
			+ xShift computed and applied
		* updateX() :
			+ new param xShift : added to all x-coordinates

160706 MM
	* algorithm/Curve :
		* toString() : 
			* output format unified with Arrays.toString()
	* algorithm/AnnotatedCurve :
		* toString() : 
			* output format unified with Arrays.toString()
	* algorithm/CurveDistance :
	* algorithm/*Distance :
		+ getDescription() : string description of the distance measure
	* algorithm/SampledCurveDistance :
		* getDistance() :
			- BUGFIX : length check was useless and wrongly placed
	* algorithm/PICA :
		+ maxRelXShift : limitation of the x-warping by a relative x-shift boundary
		* construction() : 
			+ maxRelXShift parameter
		* align() :
			* only applies decomposition if the relative-x-shifts of the split-points <= maxRelXShift 
	* algorithm/MICA :
		+ maxRelXShift : limitation of the x-warping by a relative x-shift boundary
		* construction() : 
			+ maxRelXShift parameter
		* align*():
			+ maxRelXShift forwarding to PICA
		* MicaData :
			+ fuseGuide : PICA alignment used for fusing
		* fuseAlignments() :
			+ stores the used PICA alignment in MicaData.fuseGuide
	* controller/MicaR :
		+ final exception handling to push messages to Debug.out
		* construction :
			+ maxRelXShift parameter
		+ getOriginalPairwiseDistances() : pairwise distances before alignment with equal length
		+ getAlignedPairwiseDistances() : former getPairwiseDistances() : pairwise distances after alignment
		* getPairwiseDistances() : computation of pairwise distances for a given curve set
	* R/mica-functions.R :
		* alignCurves() :
			+ maxRelXShift parameter
			+ outSlope parameter : if TRUE, slope values are added to the return list
			* pairDist now a list of two tables (before and after alignment)
	* R/mica-example.R : updated

160705 MM
	* algorithm/SampledCurveDistance : 
		+ preFinalDistance() : reverse function for finalDistance() to combine 2 distances
		* getDistance() : bugfix : finalDistance() call was amiss
	* algorithm/*Distance :
		+ preFinalDistance() implementation
	* algorithm/PICA :
		* align() :
			+ local distance computation for the interval only 
				(should be more precise since warpingFactor only for relevant for curInterval) 
			+ distance computation based on non-warped curve data 
				(should be faster)
			+ lazy initialization of interval-specific data only if alignable points found 
				(should be faster)
			- curMinCurve* : obsolete due to distance computation without warping
	- controller/DebugController : renamed to Debug
	+ controller/Debug : former DebugController
		+ out : PrintStream to write debug messages to
	* controller/MicaR :
		+ implements AutoClosable to support close() function
		+ debugBuffer : buffer for debug output from MICA functions
		* construction : sets Debug.out to the debugBuffer
		+ close() : resets Debug.out to System.err
		+ finalize() : resets Debug.out to System.err
		+ getDebugOutput() : access to the accumulated debug output and debugBuffer reset
	* all temporary output etc. now goes to Debug.out
	* R/mica-functions.R :
		* alignCurves() :
		* getAnnotations() :
			+ check for debug output and print if present

160704 MM
	* R/mica-functions.R :
		+ getMeanCurve() : computes the mean consensus curve for a set of curves
		* getAnnotations() :
			* docu updated
			+ param minRelSlopeHeight : inflection point filter value
		* alignCurves() :
			+ param minRelSlopeHeight : inflection point filter value
			+ param minRelIntervalLength : minimal relative interval length to further decompose
	- algorithm/CurveManhattanDistance : now CurveMeanAbsoluteDistance
	- algorithm/SlopeManhattanDistance : now SlopeMeanAbsoluteDistance
	+ algorithm/SampledCurveDistance : super class for all sample-based distance functions
		+ getSamplePositions() : computes the sample points within an interval of the curve
		+ getStepSize() : x-step size for equidistant sampling
		+ getDistance() : generic distance computation
	+ algorithm/CurveMeanAbsoluteDistance : mean absolute error in y
	+ algorithm/SlopeMeanAbsoluteDistance : mean absolute error in slope
	* algorithm/CurveRmsdDistance : subclass of SampledCurveDistance
	* algorithm/SlopeRmsdDistance : subclass of SampledCurveDistance
	* algorithm/Curve :
		* fields now protected to enable access in subclass
		+ field slopeMin/Max
		- spline : renamed to interpolation
		+ interpolation : former spline but now more general
		- splineDerivative : renamed to derivative
		+ derivative : former splineDerivative
		- updateSpline() : renamed to updateInterpolation()
		+ updateInterpolation() : set new interpolator for x/y data
			* uses now a linear interpolator for the curve data
		+ initSlope() : general utility function for slope initialization
		* getSlope() :
			* slope intialization now done via initSlope()
		+ getSlopeMax/Min() : access to min/max value of slope
	* algorithm/AnnotatedCurve :
		* relabelInflectionPoints() : 
			* ascent/descent check now on slope data rather than y-data
			+ removes slope minima in ascents and slope maxima in descents
		+ updateInterpolation() : overwrites Curve method to ensure refiltering of annotations
		+ initSlope() : overwrites Curve method to ensure slope of curve min/max is set to 0
	* algorithm/CurveAnnotation :
		* Type :
			+ isExtremumY() : checks whether the annotation is a curve extremum
			+ isExtremumSlope() : checks whether the annotation is a slope extremum
			+ isInflection() : checks whether the annotation is an inflection point
			+ isManual() : checks whether the annotation is a manual one
	+ algorithm/CurveInflectionFilter : removes inflection points where the 
		absolute slope is below a given (relative) threshold
	* algorithm/IntervalDecomposition :
		* updated to Curve changes
	* algorithm/MICA :
		* distanceFunction : now SampledCurveDistance subclass
		+ minRelIntervalLength : minimal relative interval length to enable further decomposition
		- precisionDeltaLengthFactor : now part of MicaPrecision
		* updateX() : now takes curve length rather than precision delta
		* getPosToInsert() : now takes curve length rather than precision delta
	* algorithm/PICA :
		* distanceFunction : now SampledCurveDistance subclass
		+ minRelIntervalLength : minimal relative interval length to enable further decomposition
		* align() :
			+ checks for minimal interval length before trying to decompose
			+ computes distance BEFORE doing a decomposition by warping the set of
				sample points used for distance computation
	+ algorithm/MicaPrecision : utility function to scale precision of coordinate comparison
		+ precisionDeltaLengthFactor : factor to be multiplied to the curve length to get the 
			absolute precision delta for x-coordinate comparison
		+ sameX() : two position are considered as same if only differing in the length dependent 
			precision delta
		+ getPrecisionDelta() : computes the absolute precision delta for a given curve length
	* controller/MicaR :
		* distanceFunction : now SampledCurveDistance subclass
		+ curveInflectionFilter : CurveInflectionFilter registered for all curves

160701 MM
	* algorithm/IntervalDecomposition :
		* getIntervalAnnotations() :
			* BUGFIX : sublist was missing right most element
	+ algorithm/MicaPrecision : utility class to handle x-coordinate comparison
		with a given precision tolerance
		+ precisionDeltaLengthFactor : formerly member of MICA
		+ getPrecisionDelta() : generates the precision delta value for a curve length
		+ sameX() : tests two coordinates for equivalence given the precision delta value
		

160630 MM
	* algorithm/Curve :
		- spline : renamed to interpolation
		+ interpolation : former spline
		* splineDerivative : renamed to derivative
		+ derivative : former splineDerivative
		* construction: interpolation now a LinearInterpolation instead of SplineInterpolation
	* algorithm/LinearCurveDistanceWarpingCorrection :
		+ warpScaling : scaling factor for the warping factor
	* algorithm/PICA :
		* construction : setup of NoCurveDistanceWarpingCorrection or
			LinearCurveDistanceWarpingCorrection depending on parameters
	* algorithm/MICA :
		+ warpScaling : parameter to be forwarded to PICA
		* construction : setup of warpScaling
		* align*() : setup of PICA depending on warpScaling setup
	* controller/MicaR :
		+ warpScaling : parameter to be forwarded to MICA
		* construction : setup of warpScaling
		+ getAnnotations() : access to the filtered annotations of a curve
	* algorithm/AnnotatedCurve :
		* addAnnotations() :
			* BUGFIX : was checking at wrong indices before overwriting annotations
			* BUGFIX : overwrite check was using compare with IS_POINT instead of new annotation
	+ test/TestCurveAnnotation :
		+ testTypeCompare()

160629 MM
	* algorithm/AnnotatedCurve :
		* getFilteredAnnotations() : filter order preserved
	* algorithm/CurveAnnotation :
		* Type :
			* BUGFIX : IS_MINIMUM_AUTO had the same value than IS_DERIVATIVE_MAXIMUM_AUTO
			* isOpposite() : BUGFIX was not handling type1==minimum
			+ IS_INFLECTION_* : inflection point annotations
	* algorithm/AnnotatedCurve :
		+ relabelInflectionPoints() : replaces slope min/max annotations with 
			according inflection point annotations
	* algorithm/CurveExtremaFilter :
		* filter() :
			* BUGFIX : annotation comparison was not using coordinate index but annotation index
	* R/mica-functions.R :
		* alignCurves() : 
			* default minRelMinMaxDist = 0.01 (otherwise too much filtering)
	
160628 MM
	+ algorithm/SlopeManhattanDistance : Manhattan distance on slope
	* algorithm/MICA :
		+ alignToReference() : alignment with fixed reference curve
		+ ProgressiveReferenceAlignmentHandler : distance handler for fixed reference
	* algorithm/Curve :
		- Serializable interface : not needed for now
	* controller/MicaR  :
		* MicaR() : 
			+ handling of slope Manhattan distance function selection
		+ referenceIndex : index of the reference within originalCurves
		+ addReferenceCurve() : adds the reference (check if not already present)
		* align() : runs reference-based alignment if referenceIndex >= 0
	* R/mica-functions.R :
		* alignCurves() :
			+ handling of slope Manhattan distance function selection
			+ reference : index of the reference curve within the data (optional)
			  -> runs a reference-based alignment if > 0

160624 MM
	+ R/mica-functions.R : R interface utility functions
	+ R/mica-example.R : R mica example and how-to
	+ R/rJava.pdf : documentation of rJava R package
	+ controller/MicaR : controller for R-interface
		+ extremaFilter : filter used for all curves
		+ setExtremaFilterValue()
	+ controller/DebugController : controller to enable faster debugging of curve alignments
		+ plotCurves() : JDialog-based curve visualization
	* algorithm/PICA :
		+ distanceCorrectionFunction : CurveDistanceWarpCorrection for distance and warping factor
		* PICA() : 
			+ default distanceCorrectionFunction = LinearCurveDistanceWarpingCorrection
		* align() :
			* includes now distanceCorrectionFunction for final distance computation
	* algorithm/MICA :
		* getConsensusCurve() :
			* annotations are now not fused but newly computed for the consensus
			+ annotation filters common to all curves are added to the consensus
		* fuseAlignments() :
			* annotations are now not fused but newly computed for the consensus
		- updateAnnotations() : obsolete due to fuseAlignments() changes
		* MicaData :
			+ getGuideTree() : NEWICK string representation of the alignment guide tree
	* algorithm/AnnotatedCurve :
		* getAnnotationFilter() : return type updated
	* algorithm/Curve :
		* updateSpline() :
			* BUGFIX : was not updating splineDerivative
	* algorithm/IntervalDecomposition :
		+ getDecompositionString() : string representation of the decomposition (for debug)
	+ algorithm/CurveDistanceWarpCorrection : interface to combine warping and alignment distance
	+ algorithm/NoCurveDistanceWarpingCorrection : ignores the warping factor
	+ algorithm/LinearCurveDistanceWarpingCorrection : multiplies warping factor and distance

160616 MM
	* algorithm/Curve :
		+ hashCode() 
		+ equals()
	* algorithm/AnnotatedCurve :
		+ toString()
		+ toString(digits)
		+ equals()

160615 MM
	* algorithm/CurveAnnotation :
		- IS_* : now part of enum Type
		+ Type : enum that holds all possible annotation types
			+ manual annotations = negation of automatic annotations
			+ value : integer representation of this type
			+ ofValue() : returns Type for a given value
			+ isOpposite() : returns min/max opposite type
			+ compare() : defines an order on Types
			+ isAlignable() : checks whether or not two Types can be aligned
			+ toString() : according Type string representation
		- getTypeString() : part of Type
	* algorithm/AnnotatedCurve :
		* annotation : type changed from int to CurveAnnotation.Type
		* adaptions to CurveAnnotation.Type
	* algorithm/Curve :
		+ toString(int) : string representation with rounding to given number of digits
	* algorithm/CurveExtremaFilter :
		- isOppositeType() : directly using Type.isOpposite()
		* isExtremum() : + handling of manual annotations added
	* algorithm/IntervalDecomposition() :
		* curve name = orginal name + "'"
		* isCompatible() :
			* check using Type.isAlignable() rather than equivalence check
	* algorithm/PICA :
		* align() :
			* check using Type.isAlignable() rather than equivalence check
	* algorithm/MICA :
		* getConsensusName() 
			* bugfix : stream collection/joining fixed
		- guideTreeGenerator : obsolete, replaced by ProgressiveAlignmentHandler
		+ getRelativePositions() : computes relative positions for x-coordinates
		+ getPosToInsert() : extension of the binarySearch to allow for a given 
			precisionDelta for comparison
		+ getLengthRatio() : utility function to compute the x-coordinate correction factors
		* fuseAlignments() : implementation extended
		+ updateX() : utility function for x-coordinate update
		+ updateAnnotations() : utility function for annotation update
		* align() : 
			* bugfix : curve copy was using first curve only

160610 MM
	* algorithm/AnnotatedCurve :
		+ constructors that take (filtered) annotations as argument
	* algorithm/GuideTreeGenerator (and subclasses) :
		* PicaData now part of PICA
	* algorithm/PICA :
		+ PicaData : alignment result container
		* align*() : returns now PicaData and does not overwrite input arguments
	* algorithm/MICA :
		- PicaData : replaced by PICA.PicaData
		* precisionDeltaLengthFactor : compute minimal precision for x-coordinate comparisons 
		  based on length*factor
		* align() :
			* returns now MicaData, which represents the final alignment and all
			  progressive subalignments in a tree data structure
		+ MicaData : represents a multiple (sub)alignment
			+ curves : curves of the alignment
			+ consensus : the consensus of the alignment
			+ fusedAlignments : list of alignments that were fused to create this alignment
		+ ProgressiveAlignmentHandler : handler for pairwise distance computations
		+ getConsensusName() : generates a name for the consensus curve of an alignment
		+ getConsensusCurve() : computes the consensus curve for an alignment
		+ fuseAlignments() : fuses two alignments based on their consensus PicaData information

160609 MM
	- algorithm/AbstractCurveAnnotationFilter : renamed to ObservableCurveAnnotationFilter
	+ algorithm/ObservableCurveAnnotationFilter : former AbstractCurveAnnotationFilter 
		+ extends Observable
		- no specific listener interface necessary due to Observer superclass
	* algorithm/CurveAnnotationFilter :
		- listener interface (not needed in filter interface)
	* algorithm/CurveExtremumFilter :
		* now subclass of ObservableCurveAnnotationFilter
		* adaption to changed superclass
	* algorithm/AnnotatedCurve :
		* uses now list of ObservableCurveAnnotationFilter
		* implements now Observer interface
		* adaption to new Observer listener interface

160607 MM
	* algorithm/GuideTreeGenerator.GuideTreeNode
		+ implements Iterable interface
		+ PostOrderIterator
	+ test: tree iteration  

160606 MM
	+ algorithm/GuideTreeGenerator : general interface to compute a guide tree for a 
	  given distance matrix information
	+ algorithm/MinGuideTreeGenerator : computes a guide tree by using the minimal
	  pairwise distances between clusters
	+ algorithm/CurveManhattanDistance : former CurveAreaDistance
	- algorithm/CurveAreaDistance : renamed to CurveManhattanDistance
	* algorithm/*Distance : 
	  * using now FastMath instead of Math functions

160603 MM
	* algorithm/Curve :
		+ toString() : for debug output
		+ updateSpline() : has to be called whenever the data was changed
	* algorithm/IntervalDecomposition :
		* bugfix : updateSpline() calls added wherever x-coordinates changed
	* algorithm/PICA :
		* align() :
			* bugfix : updateSpline() calls added wherever x-coordinates changed
		+ alignRef() : reference-based alignment (calls align() with according weights) 
	+ algorithm/MICA :
		+ align() : general scheme sketched
	* test/PICA updated

160601 MM
	* algorithm/CurveAnnotationFilter :
		+ Listener interface to trigger updates in dependent classes when the filter was changed
			+ filterChanged()
		+ addListener() : adds a listener
		+ removeListener() : removes a listener
		+ filterChanged() : calls the Listener.filterChanged() for all registered listeners
	+ algorithm/AbstractCurveAnnotationFilter : implements the listener related classes
		+ addListener() : adds a listener
		+ removeListener() : removes a listener
		+ filterChanged() : calls the Listener.filterChanged() for all registered listeners
	* algorithm/AnnotatedCurve :
		+ implements CurveAnnotationFilter.Listener to updated filtered annotations on change
		+ registration/unregistration from added/removed filters
	* algorithm/CurveExtremaFilter :
		+ now subclass of AbstractCurveAnnotationFilter instead of direct interface implementation
		* setMinRelNeighDiff() :
			+ calls filterChanged()
	+ algorithm/CurveAreaDistance : implements a CurveDistance based on an estimator of the 
		enclosed area between both curves
	+ algorithm/CurveRmsdDistance : RMSD of y-coordinates on a given number of interpolation points 
	+ algorithm/SlopeRmsdDistance : RMSD of first derivative on a given number of interpolation points 
	* tests updated

160526 MM
	* algorithm/CurveExtremumFilter 
		* filter() :
			+ filters now also enclosed inflection points, since part of the noise
	+ algorithm/TestCurveExtremumFilter
	+ algorithm/TestIntervalDecomposition
	+ algorithm/PICA : 
		+ implements pairwise alignment based on IntervalDecompositions
	+ algorithm/CurveDistance : 
		+ interface for distance functions on curves

160518 MM
	+ lib/junit-4 : for JUnit tests
	+ test source folder
	
160515 MM
	* REIMPLEMENTATION OF CORE ALGORITHM AND DATA STRUCTURES
	+ algorithm/Curve : 
		+ holds curve data points 
		+ enables interpolation based on splines
		+ enables derivatives based on splines
	+ algorithm/AnnotatedCurve :
		+ annotation information for each coordinate
		+ filtering of annotations to derive list of CurveAnnotations
	+ algorithm/CurveAnnotation :
		+ represents one coordinate of a curve that is annotated
		+ provides type and index of the coordinate

160513 MM
	+ algorithm/ProfileUtil : former algorithm/DataPointDerivator
		+ interpolateDataPoints() : formerly DataPointDerivator.Derivate.deriveDataPoints()
	- algorithm/DataPointDerivator : renamed to ProfileUtil

160513 MM
	+ Changelog added
	+ todo list added
	+ lib/commons-math3* : apache commons-math library including sources and javadoc
	+ lib/commons-lang3* : apache commons-lang library including sources and javadoc
	+ versions/1.0.0/mica.jar : save version for comparative application
	* algorithm/Profile :
		* calculateSlopeValuesFromProfile() :
			* replaced linear slope interpolation with spline derivative computation
	* algorithm/DataPointDerivator :
		* Derivate :
			* deriveDataPoints() : now based on spline interpolation
			- insertNewDataPointsToSet() : obsolete
			- removeDataPointsFromSet() : obsolete
			- linearInterpolation() : obsolete