0.24 UML 1.4 false false false false false true false true 1 ArgoUML (using Netbeans XMI Writer version 1.0) 0.24(5) revised on $Date: 2006-11-06 19:55:22 +0100 (Mon, 06 Nov 2006) $ Dependency Operation Operation sourcePortFig="Fig5.0" destPortFig="Fig7.0" sourceFigNode="Fig5" destFigNode="Fig7" sourcePortFig="Fig20.0" destPortFig="Fig20" sourceFigNode="Fig20" destFigNode="Fig20" DNA addSegment(spline : B_Spline,options : Dictionary) : void getSegments() : List deleteSegment(segment : Segment) : void getStrands() : List getStrandByName(name : String) : Strand deleteStrand(name : String) : void joinStrands(strand1 : String,strand2 : String,options : Dictionary) : void breakStrand(strandName : String,index : Integer,options : Dictionary) : void draw() : void getNewStrandName() : String getNextStrandColor() : Color name : String rootSegmentBlock : SegmentBlock strandNameMap : Dictionary relations? : List plane : Plane Segment getSpline() : B_Spline setSpline(spline : B_Spline) : void getLength() : float <<factory>> getBasePair(index : Integer,basePairModel : int) : BasePair <<factory>> getBasePairs(basePairModel : int) : List setBasePair(primaryStrand : Strand,index : Integer,basePair : BasePair) : void draw() : void getEndPoints() : List setEndPoints() : List strands : List startPhaseAngle : float spline : B_Spline relations : List chunk : Chunk rise : float basesPerTurn : float Strand getSequence(startIndex : int,endIndex : int) : String setSequence(sequence : String) : void getSequenceLength() : Integer getLength() : float getBaseLetter(index : Integer) : String setBaseLetter(index : Integer,baseLetter : String) : void getStrandRelations() : List addStrandRelation(relation : SequenceRelation) : void draw() : void name : String baseFrameCoordinates : List sequence : String segments : List relations : List chunk : Chunk BasePair getBaseLetters() : List getFrameCoordinates() : List getModelCoordinates() : List baseLetters : List baseFrameCoordinates : List modelCoordinates : List DNA_Utility getComplementSequence() : void getReverseSequence() : void replaceUnrecognized() : void getBaseRise() : float Drawable_orSomething draw() : void color : List displayStyle : Enumeration sourcePortFig="Fig2.0" destPortFig="Fig4.0" sourceFigNode="Fig2" destFigNode="Fig4" sourcePortFig="Fig3.0" destPortFig="Fig4.0" sourceFigNode="Fig3" destFigNode="Fig4" sourcePortFig="Fig4.0" destPortFig="Fig3.0" sourceFigNode="Fig4" destFigNode="Fig3" sourcePortFig="Fig2.0" destPortFig="Fig7.0" sourceFigNode="Fig2" destFigNode="Fig7" sourcePortFig="Fig3.0" destPortFig="Fig7.0" sourceFigNode="Fig3" destFigNode="Fig7" sourcePortFig="Fig4.0" destPortFig="Fig7.0" sourceFigNode="Fig4" destFigNode="Fig7" BasePairModeller setModelCoordinates(basePair : BasePair,basePairModel : int) : void setBaseFrame(basePair : BasePair,basePairModel : int) : void basePairModels : List PAM3_Model PAM5_Model AtomisticDNA_Model SegmentBlock sourcePortFig="Fig2.0" destPortFig="Fig18.0" sourceFigNode="Fig2" destFigNode="Fig18" SegmentBlock treeAPI() : void segments : List strands : List sourcePortFig="Fig20.0" destPortFig="Fig3.0" sourceFigNode="Fig20" destFigNode="Fig3" Note: SegmentBlocks (Groups?) EITHER parent more SegmentBlocks, OR have Segments and Strands. sourcePortFig="Fig20.0" destPortFig="Fig7.0" sourceFigNode="Fig20" destFigNode="Fig7" SequenceRelation getRelationIndices(strandIndex : int) : List getStrand(strandIndex : int) : Strand relationIndices : List strands : List sourcePortFig="Fig4.0" destPortFig="Fig24.0" sourceFigNode="Fig4" destFigNode="Fig24" Note: APIs are illustrative, not complete. Solid diamond - composition Hollow diamond - aggregation/collection sourcePortFig="Fig3.0" destPortFig="Fig5.0" sourceFigNode="Fig3" destFigNode="Fig5" GeometryRelation getSegment(segmentIndex : int) : Segment segments : List Relation setRelations(relations : int) : void getRelations() : int relationFlags : int sourcePortFig="Fig3.0" destPortFig="Fig29.0" sourceFigNode="Fig3" destFigNode="Fig29" sourcePortFig="Fig29.0" destPortFig="Fig30.0" sourceFigNode="Fig29" destFigNode="Fig30" sourcePortFig="Fig24.0" destPortFig="Fig30.0" sourceFigNode="Fig24" destFigNode="Fig30" BaseFrameModel BasePairModel toModel(baseFrameCoordinates : List) : List toBaseFrame(modelCoordinates : List) : List sourcePortFig="Fig34.0" destPortFig="Fig35.0" sourceFigNode="Fig34" destFigNode="Fig35" sourcePortFig="Fig15.0" destPortFig="Fig35.0" sourceFigNode="Fig15" destFigNode="Fig35" sourcePortFig="Fig16.0" destPortFig="Fig35.0" sourceFigNode="Fig16" destFigNode="Fig35" sourcePortFig="Fig17.0" destPortFig="Fig35.0" sourceFigNode="Fig17" destFigNode="Fig35" sourcePortFig="Fig14.0" destPortFig="Fig34.0" sourceFigNode="Fig14" destFigNode="Fig34" sourcePortFig="Fig14.0" destPortFig="Fig15.0" sourceFigNode="Fig14" destFigNode="Fig15" sourcePortFig="Fig14.0" destPortFig="Fig16.0" sourceFigNode="Fig14" destFigNode="Fig16" sourcePortFig="Fig14.0" destPortFig="Fig17.0" sourceFigNode="Fig14" destFigNode="Fig17" sourcePortFig="Fig3.0" destPortFig="Fig14.0" sourceFigNode="Fig3" destFigNode="Fig14" uses as a Singleton generates via factory method sourcePortFig="Fig29.0" destPortFig="Fig3.0" sourceFigNode="Fig29" destFigNode="Fig3" sourcePortFig="Fig24.0" destPortFig="Fig4.0" sourceFigNode="Fig24" destFigNode="Fig4" Strand relations (Enumeration): -Complimentary -Not (very) complimentary -Equal -Equal length -Fixed -Fixed length sourcePortFig="Fig20" destPortFig="Fig4" sourceFigNode="Fig20" destFigNode="Fig4"