ChangeLog.txt

Version 1.4a
SVDetection
- Fixed minor bug in inversion detection
DataQualityCheck
- Added handling to IOException in reading files
DataTools
- Removed unused concatin and concatout option parsing
ExtendOptionParser
- Added support for future OMTools GUI
MAFReader
SegmentIdentifierWriter
CollinearBlockReader
MultipleAlignmentPerformanceAnalysis
- Set some options to be required

Version 1.4
Modified classes:
UnweightedRange
- Fixed bug in canStitch and stitchUnweightedRange methods
- length method now returns max-min+1 instead of max-min
WeightedRange
- Fixed bug in stitchWeightedRange method
- Added toString method
GenomicPosNode
- Added overlap method
- Added contains method
- Use Regex for string parsing
OMTools
- Added support to ExtendOptionParser.manualGeneration
- Added noverbose and randseed parameters
KmerCluster
- Rewrite to support strand-sensitive clustering
DataFormat
- Added support to compressed file
Identifiable
- Added convertToMap method
OMReader
- Added support to compressed file
- Added methods: readAll, getStream, getFileStream
OMWriter
- Added support to compressed file
- Modified writeAll methods to accept more general parameters
AnnotationNode
- Added methods: getRegion, setRegion
BEDNode
- Added constructor
BEDReader
- Added assignOptions
BEDWriter
- Rewriter to extend from OMWriter
GFFNode
- Added constructor
- Added setRegion
GFFWriter
- Fixed bug in writing GFFNode with non-null score but null frame
BnxDataNode
- Added support to bnx version 1.2
DataNode
- Added hashCode and equals
- Remove getErrorKmerWord method
DataSignalCountNode
- Added an incomplete method for future use
OptMapDataGenerator
- Move SimuDataNode out as an independent class
OptMapDataReader
- Modified to support new bnx format
OptMapDataWriter
- Modified to support new cmap and bnx format
- Modified writeAll methods to accept more general parameters
OptMapResultReader
- modified oma and omd parsing for fragmentInfo incorporation
- Modified to support new xmap format
OMBlastCore
- Added supprot to allowDiffRefQuery parameter
OMBlastMapper
- Added supprot to allowDiffRefQuery parameter
Kmer
- Removed unused variables, methods and constructors
- Added methods: getReverse, getForwardSizes, getReverseSizes, getAverageSizes
- Used different way to generate hashCode
Seed
- Removed support to error-containing seeds (Rewrite getCigar method)
ExtendOptionParser
- Added support to manualGeneration option
CollinearBlock
- Rewrite
CollinearBlockOrder
- Added support to assignReadOptions and assignWriterOptions
CollinearBlockReader
- Remove unused variables
CollinearBlockWriter
- Remove unused variables
GroupingEntry
- Accept more general parameters
DataTools
- Added parameter staticid
ResultTools
- Added parameters qprefix, rprefix
OMView
- Added support to MultipleOpticalMapsBlockControlPanel/MultipleOpticalMapsBlockView, CompressionFormat
- Now accepted SV input
- Added new ambiguousFileLoader support viewin
ViewSetting
- Added view settings: mabMoleculeSpace, showCoverage, showCoverageAxis, coverageAxisUnit, coverageAxisColor, maxDisplayCoverage, separateAlignmentDisplay, useVariableColor, hideBlockThreshold, hideOverlapBlocks, useVariabilityColor, collapseSameGroupQuery, blockConnectionLineWidth
- SVObjectSize changed to minSpaceSize
- Use ColorStringParser for fields parsing
- Settings import can be space-separated files instead of strict tab-separated files
AlignmentView
- Added support to separateAlignmentDisplay
AnchorView
- Fixed minor bug: replace maMoleculeSpace with moleculeSpace
MultipleOpticalMapsView
- Support new display features and bug fixing
RegionalView
- Added support to coverage
VCoverage
- Rewrite coverage display
VData
- Added getData method
VMapMolecule
- Rewriter color display 
VVariability
- Added empty constructor
- Added getAverageVariability method
StreamFastaNode
- Added support to seq extraction even when start > stop (No reverse complement)
ImageSaveFormat
- Added file extension check

Moved classes:
- Moved src/aldenjava/opticalmapping/visualizer/utils/VPartialMoleculeInfo.java to src/aldenjava/opticalmapping/multiplealignment/BlockInfo.java
- Moved src/aldenjava/opticalmapping/multiplealignment/SegmentIdentifier.java to src/aldenjava/opticalmapping/data/data/SegmentIdentifier.java
- Moved classes from aldenjava/opticalmapping/application/svdetection to aldenjava/opticalmapping/svdetection

New classes: 
CompressedFilenameUtils
CompressionFormat
- Added support to compression file
- FileNameCompressionExtensionFilter
ColorStringParser
- As an independent color string parser
ClusteringFormat
- Added format to identify clustering files
DataQualityCheck
- Added class for data quality output
MAFEntry
MAFNode
MAFReader
- Support for .maf files
SegmentIdentifierFormat
SegmentIdentifierReader
SegmentIdentifierWriter
- Support for segment identifier I/O
RandomSeed
- Added support to random seed parameters in OMTools
BlockConnectionGraphGeneration
BlockInfo
EntryConnection
EntryMatch
GroupingEntryChain
MADependentDirectedGraph
MADirectedGraph
MAMergeGraph
MultipleAlignment
MultipleAlignmentPerformanceAnalysis
- Multiple alignment-related classes
MultipleOpticalMapsBlockControlPanel
MultipleOpticalMapsBlockView
- MultipleOpticalMapsBlockView support
VBlockSpace
- Better display support for MultipleOpticalMapsView
AlignmentHighlight
CBLTools
QueryReverse
FrequentKmerHighlight
TWINResultRepeatRemover
- New scripts
SeparateBNXScan
- New scripts

Version 1.3a
Add support for AGP file, support old option names

Modified classes:
AnnotationFormat
- Added AGP file format
ExtendOptionParser
- Added alias option
ResultClusterModule
- Added alternative options (old option names)
OMView
- Added alternative options (old option names)
- Added support on anchor-region input
ViewSetting
- Added view settings: gapStrokeWidth, gapStrokeColor, annotationTextLength, annotationBlockHeight
- Reorganized options
VAnno
VIndel
VInversion
VRearrangement
VTranslocation
- Modified to use new ViewSetting
- Do not display tool tip when length <= 0

New classes:
AGPReader
AGPNode
- Added class for AGP file support



Version 1.3
Add SVDetection module, improve OMView function, fix bugs in other classes

Modified classes:
OMTools
- Added SVDetection in the menu
MultipleAlignmentFormat
- Added static method isValidCollinearBlockFormat
OptMapResultWriter
- Fix spelling error
OMBlastCore
- Added option allowEqualRefQuery
OMBlastMapper
- Added option allowEqualRefQuery
ProgressPrinter
- Added update method
KmerCluster
- Added support for forward/reverse clustering
CollinearBlock
- Retain the name in GroupingEntry in toSingleSegmentCollinearBlocks method, instead of creating a new name
- Added reverse and getSize method
CollinearBlockReader
- Rewrite for format change of multiple alignment
CollinearBlockWriter
- Rewrite for format change of multiple alignment
GroupingEntry
- Rewrite to use Map instead of List for better performance
SingleGroup
- Added constructor
DataStatistics
- Rewrite the DataStatistics class
ResultStatistics
- Fixed bug on not able to import alignment results without data incorporated in the same file
- Fixed bug on incorrect aligned molecules in alignment files with with translocation.
EnzymeSiteNode
- Added warning for incorrect enzyme name
ResultTools
- Fixed bug on not resetting minjoinscore to 0
DataModule
- Added support for collinear block order
OMView
- Rewrite change setting on developer options
- Added output option menu
- Rewrite loading of collinear block order
- Fixed bug on displaying the data selection menu when no data is loaded as molecules / reference
- Enable options at command line: dnaratio, zoom and viewunmap, and viewsettingin for loading developer options
- Enable a hidden option (datacolormap) that is used to recolor the molecules. Experimental. 
- Fixed bug on not loading annotations in start-up of regional view
- Accepts loading of multiple alignment (cbl) without the order file (cbo)
ViewSetting
- Added options: 
	coverageHeight
	variabilityHeight
	maxViewVariability
	objBorderX
	objBorderY
	defaultLeftSpaceAfterGoto
	defaultTopSpaceAfterGoto
	coverageBGColor	
	coverageColor
	variationColor1
	variationColor2
	displayRuler (Moved option to ViewSetting from VRuler)
	rulerHeight
	rulerSmallMark (Moved option to ViewSetting from VRuler)
	rulerLargeMark (Moved option to ViewSetting from VRuler)
	rulerSmallMarkColor
	rulerLargeMarkColor
	rulerBodyColor
	displayQueryName
	queryNameColor
	maBGColor1
	maBGColor2
- Changed minSVObjectSize to SVObjectSize
- Rewrite changeSetting method to allow input of all variable types in ViewSetting
- Added displaySetting options (for output options in OMView menu)
VPartialMoleculeInfo
- Added reverse method
AlignmentView
- Disable gotoMenu
AnchorView
- Display query names
- Added support for gotoMenu
MoleculeView
- Moved previous goto options into the gotoMenu
- Added support for data color. Experimental.
MultipleOpticalMapsView
- A rewrite of the whole class
- A different block layout algorithm
- Displaying query names
- Support for gotoMenu
- Use VMultiAlignMolecule instead of VMolecule
- Support for new collinear block ordering
- Added variability and coverage calculation
- Update reverse function
- Removed sort and save function temporarily
RegionalView
- Display query names
- Added support for gotoMenu
ScrollablePanel
- Added support for gotoMenu
AnnotationPanel
- Disable gotoMenu
VIndel
- Fixed bug in small gap size
- Tool tip text update upon change in ref / mol length
VInversion
- Fixed bug in small gap size
VMapMolecule
- Added support for data color. Experimental.
VRearrangement
- Fixed bug in small gap size
VRuler
- Moved options to ViewSetting
VSpace
- change constructor to use setRefDNALength and setMoleDNALength
VTranslocation
- Update on minSVObjectSize to SVObjectSize


New classes: 
SVDetection
- A class to call SV from alignment results
LocalConsensusPattern
- A class with a static method to generate local consensus pattern, used in reconstructing inserted patterns
DataSignalCountNode
- A class used in signal count in SVDetection
CollinearBlockOrder
- A class for new query ordering in multiple alignment
VCoverage
- A new VObject that represents the coverage ub MultipleOpticalMapsView
VVariability
- A new VObject that represents the variability in MultipleOpticalMapsView
ElementsGroup
IntegerKeyFactory
KeyFactory
NumberOperation
UnweightedRange
WeightedRange
- A set of classes of UnweightedRange and WeightedRange

Example file
Updated Ecoli_MA.cbl