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Summary Period: 2005-10-12 to 2005-09-29 (Commits 217-266 of 266)

schmidt 2005-10-12 13:17

added Swiss-Prot support

5520 lines of code changed in:

• studioBase/src/bea/engine/swissProt: PropertyComparison.html (new 25), PropertyComparison.java (new 722), PropertyComparisonN.java (new 329), SwissProtAnalysesMain.java (new 38), SwissProtEngineResult.java (new 133)
• studioBase/src/bea/input/classes/swissProt: SwissProt.html (new 29), SwissProt.java (new 548)
• studioBase/src/bea/input/classes/swissProt/internals: Description.java (new 83), Domain.java (new 43), FeatureTable.java (new 36), Keywords.java (new 37), Literature.java (new 45), Organelle.java (new 49), OrganismClassification.java (new 103), OrganismSpecies.java (new 36), Reference.java (new 74), SortHashtable.java (new 179), SwissProtFileReader.java (new 200), SwissProtFlatFileReader.java (new 242), SwissProtSequenceParser.java (new 104), SwissProtXMLFileReader.java (new 373)
• studioBase/src/bea/input/swissProt: ISwissProt.java (new 49), ISwissProtFileReader.java (new 32)
• studioBase/src/bea/util/graph: Edge.java (new 49), Graph.java (new 165), Graph2.java (new 200), IEdge.java (new 31), IGraph.java (new 33), IGraph2.java (new 24), INode.java (new 24), Node.java (new 85), Node2.java (new 98)
• studioBase/src/bea/vis/swissprot: EC_Visualization.java (new 282), HierarchicalSwissProtVisualisation.java (new 397), StandardSwissProtVisualisation.java (new 371), SwissProtVisualisation.java (new 252)

schmidt 2005-10-10 16:36

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9 lines of code changed in:

• studioBase/src/bea/input/classes: FlatFile.java (+9 -2)

schmidt 2005-10-10 14:54

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6 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+6 -6)

schmidt 2005-10-10 14:45

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32 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+32 -5)

schmidt 2005-10-10 14:39

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4 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+4 -14)

schmidt 2005-10-10 12:58

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23 lines of code changed in:

• studioBase/src/bea/input/classes: SeqProperties.java (+23 -9)

schmidt 2005-10-10 12:50

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2 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+2 -1)

schmidt 2005-10-10 12:25

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81 lines of code changed in:

• studioBase/src/bea/engine/seqproperties: AaDistribution.java (+47 -50), AaDistributionDimer.java (+4 -1), AaDistributionTriplets.java (+4 -1), AaFrequences.java (+4 -1), LengthAgainstHyphob.java (+3 -1)
• studioBase/src/bea/input/classes: SeqProperties.java (+19 -8)

schmidt 2005-10-07 17:10

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0 lines of code changed in:

• studioBase/src/afilter: FilterTest.java (del), FuncatLabel.java (del)

schrader 2005-10-07 17:02

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0 lines of code changed in:

• studioBase/src/com/eteks/jeks: CircularityException.java (del), FileFilterCSV.java (del), FileFilterExcel.java (del), FilteFilterEngineResults.java (del), IllegalCellException.java (del), JeksCell.java (del), JeksCellEditor.java (del), JeksCellRenderer.java (del), JeksCellSet.java (del), JeksCodec.java (del), JeksExpression.java (del), JeksExpressionParser.java (del), JeksExpressionSyntax.java (del), JeksFrame.java (del), JeksFunctionParser.java (del), JeksFunctionSyntax.java (del), JeksInterpreter.java (del), JeksParameter.java (del), JeksTable.java (del), JeksTableModel.java (del), Makefile (del), ReferringCellsListener.java (del), ResourceSyntax.java (del), Updater.java (del)
• studioBase/src/com/eteks/jeks/dv: JerksNode.java (del), JerksTableListener.java (del), Makefile (del), UnitTest_JerksNode.java (del), UnitTest_JerksTableListener.java (del)
• studioBase/src/com/eteks/jeks/hsa: CellTypeAlgorithm.java (del), Makefile (del), Table.java (del), Unit.java (del), UnitChecker.java (del)
• studioBase/src/com/eteks/jeks/resources: appendix2.png (del), appendix3.png (del), appendix4.png (del), empty_cells.png (del), ex1.png (del), ex2.png (del), help.html (del), help_fr.html (del), jeks.gif (del), jeks.properties (del), jeks_fr.properties (del), jeksicon.gif (del), jeksscreen.jpg (del), logoeteks.gif (del), referred_cells.png (del), referring_cells.png (del), syntax.properties (del), syntax_fr.properties (del), unit_checking.png (del), unreferenced_cells.png (del), whitelogo.png (del)
• studioBase/src/com/eteks/parser: AbstractSyntax.java (del), CalculatorParser.java (del), CompilationException.java (del), CompiledExpression.java (del), CompiledFunction.java (del), DefaultSyntax.java (del), DoubleInterpreter.java (del), ExpressionParameter.java (del), ExpressionParser.java (del), Function.java (del), FunctionParser.java (del), IncompatibleTypesException.java (del), Interpreter.java (del), JavaSyntax.java (del), JerksFunctions.java (del), Makefile (del), MathMLInterpreter.java (del), Parser.java (del), PascalSyntax.java (del), StringToFunctionException.java (del), Syntax.java (del), WrapperInterpreter.java (del)
• studioBase/src/com/eteks/parser/node: BinaryOperatorNode.java (del), CommonFunctionNode.java (del), ConditionNode.java (del), ConstantNode.java (del), ExpressionNode.java (del), ExpressionParameterNode.java (del), FunctionNode.java (del), FunctionParameterNode.java (del), LiteralNode.java (del), Makefile (del), ParameterizedNode.java (del), UnaryOperatorNode.java (del)
• studioBase/src/com/eteks/tools/awt: Curve2DDisplay.java (del), Curve3DDisplay.java (del), GridBagConstraints2.java (del), Makefile (del), SplashScreenWindow.java (del)
• studioBase/src/com/eteks/tools/calculator: JeksCalculator.java (del), Makefile (del)
• studioBase/src/com/eteks/tools/d3d: CoordinatesArray.java (del), Makefile (del), Matrix3D.java (del), Point3D.java (del), Point3D2D.java (del), Polygon3D.java (del), Vector3D.java (del)
• studioBase/src/com/eteks/tools/swing: HTMLDocumentViewer.java (del), Makefile (del)
• studioBase/src/toolbarButtonGraphics/general: Copy16.gif (del), Cut16.gif (del), Delete16.gif (del), DependCell16.gif (del), Header16.gif (del), Help16.gif (del), New16.gif (del), Open16.gif (del), Paste16.gif (del), Referred16.gif (del), Referring16.gif (del), Save16.gif (del), Unit16.gif (del), Unreferenced16.gif (del)

schmidt 2005-10-07 16:32

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107 lines of code changed in:

• studioBase/src/afilter: FilterTest.java (-19)
• studioBase/src/bea/engine: CompareNumericDistributions.java (-1), Engine.java (-5)
• studioBase/src/bea/engine/genericxml: GenericXMLCompare.java (+1 -4)
• studioBase/src/bea/engine/pedant: FuncatCompare13.java (-3), FuncatCompare20.java (-3), ScopClassDistribution.java (-1)
• studioBase/src/bea/engine/seqproperties: AaDistribution.java (-1), AaDistributionDimer.java (-1), AaDistributionTriplets.java (-1), FastaSaver.java (+1 -4), HydrophobicityCompare.java (-1), LengthCompare.java (-1), MassCompare.java (-1), PICompare.java (-1)
• studioBase/src/bea/engine/seqproperties/mapper: BlastDialog.java (+2 -5), SimapMd5.java (+3 -3)
• studioBase/src/bea/input: IAnnotationData.java (-1), ITango.java (-2)
• studioBase/src/bea/input/classes: Annotation.java (+5 -7), FlatFile.java (-6), GenBankRemote.java (+2 -15), GenericProperty.java (+1), GenericXMLFile.java (-4), Input.java (-10), Pedant.java (-2), PedantFilter.java (-2), PedantWithFilter.java (-1), SeqProperties.java (+1 -13)
• studioBase/src/bea/rinterface: RParser.java (-2)
• studioBase/src/bea/statistic: Test.java (-1)
• studioBase/src/bea/ui: AaDialog.java (-1), DataTable.java (+2 -20), SaveUI.java (-5)
• studioBase/src/bea/util: DynamicLoading.java (-7)
• studioBase/src/bea/vis: IVisualisation.java (-2), IVisualisationGnuplot.java (-6), IVisualisationR.java (-4), Viewer.java (-3), ViewerMenuBar.java (-16), ViewerPopupMenu.java (-18), VisualisationR.java (-2)
• studioBase/src/bea/vis/generic: ScatterPlotFancy.java (-1)
• studioBase/src/com/eteks/jeks: JeksCellEditor.java (+1 -1), JeksCellRenderer.java (+1 -1), JeksCodec.java (+14 -18), JeksExpression.java (+5 -5), JeksExpressionParser.java (+14 -13), JeksExpressionSyntax.java (+1 -1), JeksFrame.java (-2), JeksFunctionParser.java (+1 -1), JeksFunctionSyntax.java (+1 -1), JeksInterpreter.java (+1 -1), JeksParameter.java (+1 -1), JeksTable.java (+10 -12), JeksTableModel.java (+3 -5), ReferringCellsListener.java (+2 -2), ResourceSyntax.java (+1 -1)
• studioBase/src/com/eteks/jeks/dv: JerksNode.java (+2 -2), JerksTableListener.java (+7 -6), UnitTest_JerksNode.java (-2)
• studioBase/src/com/eteks/jeks/hsa: CellTypeAlgorithm.java (+1 -1), Table.java (+1 -1), Unit.java (+1 -1), UnitChecker.java (+1 -1)
• studioBase/src/com/eteks/parser: AbstractSyntax.java (+1 -1), CalculatorParser.java (+1 -1), CompiledExpression.java (+1 -1), ExpressionParser.java (+1 -1), FunctionParser.java (+7 -7), JerksFunctions.java (+1 -2)
• studioBase/src/com/eteks/parser/node: ExpressionParameterNode.java (+1 -1), FunctionNode.java (+1 -1)
• studioBase/src/com/eteks/tools/awt: Curve2DDisplay.java (+1 -1), Curve3DDisplay.java (+1 -1), SplashScreenWindow.java (+2 -3)
• studioBase/src/com/eteks/tools/calculator: JeksCalculator.java (+1 -1)
• studioBase/src/com/eteks/tools/swing: HTMLDocumentViewer.java (+1 -1)

schrader 2005-10-07 16:17

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1 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+1)

schrader 2005-10-07 16:05

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6 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+6 -1)

schrader 2005-10-07 14:43

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11 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+11 -4)

schmidt 2005-10-07 13:53

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482 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+482 -459)

schrader 2005-10-07 13:25

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3 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+3 -3)

schrader 2005-10-07 11:19

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28 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+28 -22)

schmidt 2005-10-07 11:09

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35 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+4 -1)
• studioBase/src/bea/ui: DataTable.java (+31 -47)

schmidt 2005-10-06 17:57

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26 lines of code changed in:

• studioBase/src/bea/vis: VisualisationR.java (+26 -32)

schmidt 2005-10-06 16:09

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59 lines of code changed in:

• studioBase/src/bea/engine/pedant: ScopClassDistribution.java (+15 -40)
• studioBase/src/bea/engine/seqproperties/mapper: Blast.java (+3), BlastDialog.java (+27 -15)
• studioBase/src/bea/input: IPedant.java (+6)
• studioBase/src/bea/input/classes: Pedant.java (+8)

schmidt 2005-10-06 13:49

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52 lines of code changed in:

• studioBase/src/bea/engine/pedant: FuncatCompare13.java (+15), FuncatCompare20.java (+2), ScopClassDistribution.java (+16 -2)
• studioBase/src/bea/input: IFuncat.java (+7), IPedant.java (+3)
• studioBase/src/bea/input/classes: Pedant.java (+9 -4)

schmidt 2005-10-06 12:29

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59 lines of code changed in:

• studioBase/src/bea/input/classes: FlatFile.java (+59 -11)

schrader 2005-10-06 11:11

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7 lines of code changed in:

• studioBase/src/bea/ui: DataTable.java (+7 -4)

schrader 2005-10-05 13:17

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6 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+6 -3)

schmidt 2005-10-04 19:02

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8 lines of code changed in:

• studioBase/src/bea/engine/seqproperties: FastaSaver.java (+8 -1)

schmidt 2005-10-04 18:25

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38 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions.java (+1 -1)
• studioBase/src/bea/input/classes: FlatFile.java (+3 -1), GenBankRemote.java (+1 -1), GenericXMLFile.java (+1 -1)
• studioBase/src/bea/ui: DialogFactory.java (+32 -8)

schrader 2005-10-04 16:35

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7 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+7 -1)

schrader 2005-10-04 16:13

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9 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+9 -2)

schrader 2005-10-04 14:21

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2 lines of code changed in:

• studioBase/src/bea/input/classes: SeqProperties.java (+2 -2)

schrader 2005-10-04 13:30

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14 lines of code changed in:

• studioBase/src/com/eteks/jeks: JeksFrame.java (+14 -18)

schrader 2005-10-04 13:21

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39 lines of code changed in:

• studioBase/src/bea/ui: DataTable.java (+3 -1)
• studioBase/src/com/eteks/jeks: JeksFrame.java (+36 -11)

schmidt 2005-10-04 11:29

jerks table viewer temporarily included

110 lines of code changed in:

• studioBase/src/com/eteks/jeks: CircularityException.java (new), FileFilterCSV.java (new), FileFilterExcel.java (new), FilteFilterEngineResults.java (new), IllegalCellException.java (new), JeksCell.java (new), JeksCellEditor.java (new 1), JeksCellRenderer.java (new 1), JeksCellSet.java (new), JeksCodec.java (new 18), JeksExpression.java (new 5), JeksExpressionParser.java (new 13), JeksExpressionSyntax.java (new 1), JeksFrame.java (new 11), JeksFunctionParser.java (new 1), JeksFunctionSyntax.java (new 1), JeksInterpreter.java (new 1), JeksParameter.java (new 1), JeksTable.java (new 12), JeksTableModel.java (new 5), Makefile (new), ReferringCellsListener.java (new 2), ResourceSyntax.java (new 1), Updater.java (new)
• studioBase/src/com/eteks/jeks/dv: JerksNode.java (new 2), JerksTableListener.java (new 6), Makefile (new), UnitTest_JerksNode.java (new 2), UnitTest_JerksTableListener.java (new)
• studioBase/src/com/eteks/jeks/hsa: CellTypeAlgorithm.java (new 1), Makefile (new), Table.java (new 1), Unit.java (new 1), UnitChecker.java (new 1)
• studioBase/src/com/eteks/jeks/resources: appendix2.png (changed), appendix3.png (changed), appendix4.png (changed), empty_cells.png (changed), ex1.png (changed), ex2.png (changed), help.html (new), help_fr.html (new), jeks.gif (changed), jeks.properties (new), jeks_fr.properties (new), jeksicon.gif (changed), jeksscreen.jpg (changed), logoeteks.gif (changed), referred_cells.png (changed), referring_cells.png (changed), syntax.properties (new), syntax_fr.properties (new), unit_checking.png (changed), unreferenced_cells.png (changed), whitelogo.png (changed)
• studioBase/src/com/eteks/parser: AbstractSyntax.java (new 1), CalculatorParser.java (new 1), CompilationException.java (new), CompiledExpression.java (new 1), CompiledFunction.java (new), DefaultSyntax.java (new), DoubleInterpreter.java (new), ExpressionParameter.java (new), ExpressionParser.java (new 1), Function.java (new), FunctionParser.java (new 7), IncompatibleTypesException.java (new), Interpreter.java (new), JavaSyntax.java (new), JerksFunctions.java (new 2), Makefile (new), MathMLInterpreter.java (new), Parser.java (new), PascalSyntax.java (new), StringToFunctionException.java (new), Syntax.java (new), WrapperInterpreter.java (new)
• studioBase/src/com/eteks/parser/node: BinaryOperatorNode.java (new), CommonFunctionNode.java (new), ConditionNode.java (new), ConstantNode.java (new), ExpressionNode.java (new), ExpressionParameterNode.java (new 1), FunctionNode.java (new 1), FunctionParameterNode.java (new), LiteralNode.java (new), Makefile (new), ParameterizedNode.java (new), UnaryOperatorNode.java (new)
• studioBase/src/com/eteks/tools/awt: Curve2DDisplay.java (new 1), Curve3DDisplay.java (new 1), GridBagConstraints2.java (new), Makefile (new), SplashScreenWindow.java (new 3)
• studioBase/src/com/eteks/tools/calculator: JeksCalculator.java (new 1), Makefile (new)
• studioBase/src/com/eteks/tools/d3d: CoordinatesArray.java (new), Makefile (new), Matrix3D.java (new), Point3D.java (new), Point3D2D.java (new), Polygon3D.java (new), Vector3D.java (new)
• studioBase/src/com/eteks/tools/swing: HTMLDocumentViewer.java (new 1), Makefile (new)
• studioBase/src/toolbarButtonGraphics/general: Copy16.gif (changed), Cut16.gif (changed), Delete16.gif (changed), DependCell16.gif (changed), Header16.gif (changed), Help16.gif (changed), New16.gif (changed), Open16.gif (changed), Paste16.gif (changed), Referred16.gif (changed), Referring16.gif (changed), Save16.gif (changed), Unit16.gif (changed), Unreferenced16.gif (changed)

schrader 2005-10-04 11:10

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33 lines of code changed in:

• studioBase/src/bea/vis: ViewerImagePanel.java (+1 -1)

schmidt 2005-10-02 20:51

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17 lines of code changed in:

• studioBase/src/bea/rinterface: RCfgCheck.java (+15 -9)
• studioBase/src/bea/ui: SaveUI.java (+2)

schmidt 2005-10-02 17:17

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6 lines of code changed in:

• studioBase/src/bea/engine/seqproperties: FastaSaver.html (+1 -1)

schmidt 2005-10-02 16:42

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7 lines of code changed in:

• studioBase/src/bea/engine: CompareNumericDistributions_whole.html (+1 -2)
• studioBase/src/bea/input/classes: GenericXMLFile.html (+6 -7)

schmidt 2005-10-02 16:27

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187 lines of code changed in:

• studioBase/src: annoTest.tab (del), annoTest.xml (del)
• studioBase/src/bea/engine: CompareNumericDistributions.java (+84 -5), CompareNumericDistributions_hist.html (new 31), CompareNumericDistributions_whole.html (new 14), Engine.java (+8 -28)
• studioBase/src/bea/engine/genericxml: GenericXMLCompare.html (+18 -1)
• studioBase/src/bea/engine/seqproperties/mapper: Blast.html (new 8), EqualTotal.html (new 4), SimapMd5.html (new 4)
• studioBase/src/bea/input/classes: GenBankRemote.html (+2 -2), Input.java (+3 -22)

schmidt 2005-10-02 13:34

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33 lines of code changed in:

• studioBase/src/bea/engine: EngineResults.java (+1)
• studioBase/src/bea/input/classes: Pedant.java (+24 -2)
• studioBase/src/bea/statistic: Test.java (+8)

schmidt 2005-10-01 23:23

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28 lines of code changed in:

• studioBase/src/bea/engine: EngineResults.java (+11), IEngineResults.java (+17)

schmidt 2005-10-01 21:35

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0 lines of code changed in:

• studioBase/src/bea/engine/seqproperties: PIabs.java (-1)

schmidt 2005-10-01 21:10

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47 lines of code changed in:

• studioBase/src/bea/input/classes: Pedant.java (+40 -20), PedantWithFilter.java (+7 -3)

schmidt 2005-09-30 20:33

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657 lines of code changed in:

• studioBase/src: AnnotationTest.java (del)
• studioBase/src/bea/engine/seqproperties: FastaSaver.java (+2 -1)
• studioBase/src/bea/engine/seqproperties/mapper: Blast.java (+1 -1), EqualTotal.java (+1 -1), SimapMd5.java (+1 -1)
• studioBase/src/bea/input/classes: Pedant.java (+647 -639)
• studioBase/src/bea/ui: DataTable.java (+5 -1)
• studioBase/src/bew/examples: TestMapper.java (del), TupelIter.java (del)

schmidt 2005-09-30 19:29

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104 lines of code changed in:

• studioBase/src/bea/input/classes: GenBankRemote.java (+103 -117), SeqProperties.java (+1)

schmidt 2005-09-30 18:33

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244 lines of code changed in:

• studioBase/src/bea/input/classes: GenBankRemote.java (+155 -16)
• studioBase/src/bea/util: LazyCollection.java (new 89), ttt.java (del)

schmidt 2005-09-30 14:15

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82 lines of code changed in:

• studioBase/src/bea/input/classes: GenBankRemote.java (new 82)

schmidt 2005-09-30 11:07

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179 lines of code changed in:

• studioBase/src/bea/engine/seqproperties: FastaSaver.java (new 97)
• studioBase/src/bea/engine/seqproperties/mapper: Blast.java (+3 -3), BlastDialog.java (+1 -1), SimapMd5.java (new 78)

schmidt 2005-09-29 20:46

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351 lines of code changed in:

• studioBase/src/bea/engine/seqproperties/mapper: Blast.java (+16 -10), BlastDialog.java (new 308), BlastDialogReturn.java (new 27)

schmidt 2005-09-29 19:16

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253 lines of code changed in:

• studioBase/src/bea/engine/seqproperties/map: Blast.java (del), EqualTotal.java (del)
• studioBase/src/bea/engine/seqproperties/mapper: Blast.java (new 161), EqualTotal.java (new 90)
• studioBase/src/bew/examples: TestMapper.java (+2 -2)

schmidt 2005-09-29 19:00

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16 lines of code changed in:

• studioBase/src/bea/ui: DataTable.java (+16 -3)

schmidt 2005-09-29 18:46

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20 lines of code changed in:

• studioBase/src/bea/engine: IEngine2.java (+9 -1)
• studioBase/src/bea/engine/seqproperties/map: Blast.java (new), EqualTotal.java (new)
• studioBase/src/bea/input/classes: FlatFile.java (+9 -1)
• studioBase/src/bew/examples: TestMapper.java (new 2), TupelIter.java (new)

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