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Package hSimulator.library |
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Class hSimulator.library.Model extends Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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double numMoleculesInAMole
String modelSpecification
Map<K,V> mapCompartmentVolumes
LinkedHashMap<K,V> mapAbundances
variableName + variableCompartmentSeparator + compartmentName
.LinkedHashMap
because variable
ordering is used to compute the stoichiometric matrix.Double
objects for compatibility
issues with the other data structures implemented in the library.
String volumeUM
String timeUM
int[][] stoichiometricRMatrix
mapAbundances
).
int[][] stoichiometricPMatrix
mapAbundances
).
int[][] stoichiometricMatrix
mapAbundances
).
double[] rates
stoichiometricMatrix
).
double[] rVolumes
stoichiometricMatrix
).
The array provides the reaction volume of ech reaction defined in the model
Class hSimulator.library.SimulatedTS extends Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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double timeSampling
double filledTime
int filledTimeDecimalDigits
filledTime
(to prevent errors during put()).
String timeUM
List<E> timeList
List<E> stateList
int[] savedVarsIndex
List<E> savedVars
variableName + Model.variableCompartmentSeparator + compartmentName
.
double computationTime
int optimizedSize
double lastStateTime
double[] lastState
boolean isLastStateFiltered
boolean wasLastStateInserted
Class hSimulator.library.SimulationStoppedException extends Exception implements Serializable |
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Serialized Fields |
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SimulatedTS partialResults
null
).
Package hSimulator.simulator.gui |
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Class hSimulator.simulator.gui.AboutFrame extends JFrame implements Serializable |
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Serialized Fields |
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JEditorPane detailText
JLabel jLabel1
JPanel jPanel1
JScrollPane jScrollPane2
Class hSimulator.simulator.gui.AppFrame extends JFrame implements Serializable |
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Serialized Fields |
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org.fife.ui.rsyntaxtextarea.RSyntaxTextArea textArea
UndoManager undoManager
File f
String filename
JFileChooser chooser
Model m
String tMaxString
String tsSamplingString
String init
String modelName
String modelNameXls
String modelAlgorithm
SimulatedTS ts
Simulator s
boolean isAlreadyOneClicked
boolean alreadySaved
boolean logScale
boolean paused
org.jfree.chart.ChartPanel chPanel1
Thread thread
Thread thread1
AppFrame.UpdatePercentage updatePercentage
String filePath
File file1
String userhome
org.jfree.chart.JFreeChart chart
org.jfree.chart.ChartPanel chPanel
Model m1
JButton advancedOptions
ButtonGroup buttonGroup1
ButtonGroup buttonGroup2
JMenuItem checkMenu
JButton checkModel
JButton copy
JMenuItem copyMenuItem
JButton cut
JMenuItem cutMenuItem
JMenuItem decMenuItem
JButton decreaseFontSize
JRadioButton dmBtn
JRadioButton eulerBtn
JRadioButton hrssaBtn
JMenuItem incMenuItem
JButton increaseFontSize
JMenu jMenu1
JMenu jMenu2
JMenu jMenu3
JMenu jMenu4
JMenuBar jMenuBar1
JMenuItem jMenuItem1
JMenuItem jMenuItem2
JMenuItem jMenuItem5
JMenuItem jMenuItem7
JMenuItem jMenuItem8
JMenuItem jMenuItem9
JPanel jPanel1
JPanel jPanel2
JPanel jPanel3
JPanel jPanel5
JSeparator jSeparator1
JPopupMenu.Separator jSeparator2
JPopupMenu.Separator jSeparator4
JPopupMenu.Separator jSeparator5
JPopupMenu.Separator jSeparator6
JPopupMenu.Separator jSeparator7
JPopupMenu.Separator jSeparator8
JPopupMenu.Separator jSeparator9
JSplitPane jSplitPane1
JToolBar jToolBar1
JToolBar jToolBar2
JToolBar jToolBar5
JRadioButtonMenuItem logScaleOption
JButton newModel
JRadioButtonMenuItem nonLogScaleOption
JButton openModel
JButton paste
JMenuItem pasteMenuItem
JButton pauseSimulation
JPanel plotPanel
JMenuItem printPlot
JProgressBar progressBar
JButton redo
JMenuItem redoMenuItem
JRadioButton rk45Btn
JRadioButton rssaBtn
JButton runSimulation
JButton saveModel
JMenuItem saveModelAsMenu
JMenuItem saveModelMenu
JMenuItem saveResults
JMenuItem showPlot
JToolBar simToolbar
JButton stopSimulation
JTextField tMax
JLabel tMaxLabel
JPanel textPanel
JTextField tsSampling
JLabel tsSamplingLabel
JButton undo
JMenuItem undoMenuItem
Class hSimulator.simulator.gui.OptionDM extends JFrame implements Serializable |
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Serialized Fields |
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JButton applyM
JButton jButton1
JLabel jLabel1
JLabel jLabel2
JPanel jPanel1
JPanel jPanel2
JPanel jPanel3
JTextField nSimDM
JTextField nThread
Class hSimulator.simulator.gui.OptionRK45 extends JFrame implements Serializable |
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Serialized Fields |
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JButton applyV
JButton cancel
JTextField initialDt
JLabel jLabel7
JLabel jLabel8
JPanel jPanel1
JPanel jPanel30
JPanel jPanel31
JTextField maxErr
Class hSimulator.simulator.gui.OptionsEuler extends JFrame implements Serializable |
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Serialized Fields |
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JButton applyV
JButton close
JTextField dt
JLabel jLabel5
JPanel jPanel1
JPanel jPanel6
Class hSimulator.simulator.gui.OptionsHRSSA extends JFrame implements Serializable |
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Serialized Fields |
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JButton Cancel
JButton applyV
JTextField deltaHRSSA
JTextField dtHRSSA
JTextField epsilonHRSSA
JTextField gammaHRSSA
JLabel jLabel1
JLabel jLabel10
JLabel jLabel11
JLabel jLabel14
JLabel jLabel2
JLabel jLabel3
JLabel jLabel9
JPanel jPanel1
JPanel jPanel11
JPanel jPanel12
JPanel jPanel13
JPanel jPanel16
JPanel jPanel2
JPanel jPanel3
JPanel jPanel4
JPanel jPanel5
JTextField nSimHRSSA
JTextField nThread2
JTextField thetaHRSSA
Class hSimulator.simulator.gui.OptionsRSSA extends JFrame implements Serializable |
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Serialized Fields |
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JButton applyV
JButton cancel
JTextField deltaRSSA
JTextField epsilonRSSA
JLabel jLabel1
JLabel jLabel2
JLabel jLabel3
JLabel jLabel4
JPanel jPanel1
JPanel jPanel14
JPanel jPanel2
JPanel jPanel3
JPanel jPanel4
JPanel jPanel6
JTextField nSimRSSA
JTextField nThread
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