Serialized Form


Package hSimulator.library

Class hSimulator.library.Model extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

numMoleculesInAMole

double numMoleculesInAMole
Number of variable molecules in a mole (Avogadro's number).


modelSpecification

String modelSpecification
Textual specification of the model provided by the user.


mapCompartmentVolumes

Map<K,V> mapCompartmentVolumes
Map that associates to each compartment name its volume.


mapAbundances

LinkedHashMap<K,V> mapAbundances
Map that associates to each variable ID its abundance (number of molecules). Variable IDs has to be indicated according to the following notation: variableName + variableCompartmentSeparator + compartmentName.
This map is implemented by a LinkedHashMap because variable ordering is used to compute the stoichiometric matrix.
Variable abundances are stored in Double objects for compatibility issues with the other data structures implemented in the library.


volumeUM

String volumeUM
Global unit of measurement for volume.


timeUM

String timeUM
Global unit of measurement for time.


stoichiometricRMatrix

int[][] stoichiometricRMatrix
Stoichiometric matrix of reactants (variable order is that specified in mapAbundances).


stoichiometricPMatrix

int[][] stoichiometricPMatrix
Stoichiometric matrix of products (variable order is that specified in mapAbundances).


stoichiometricMatrix

int[][] stoichiometricMatrix
Stoichiometric matrix (variable order is that specified in mapAbundances).


rates

double[] rates
Reaction rates (reaction order is that specified in stoichiometricMatrix).


rVolumes

double[] rVolumes
Reaction volumes (reaction order is that specified in stoichiometricMatrix). The array provides the reaction volume of ech reaction defined in the model

Class hSimulator.library.SimulatedTS extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

timeSampling

double timeSampling
Time sampling used for storing the time series.


filledTime

double filledTime
Last time instant stored in the time series.


filledTimeDecimalDigits

int filledTimeDecimalDigits
Number of significant decimal digits of filledTime (to prevent errors during put()).


timeUM

String timeUM
Global unit of measurement for time.


timeList

List<E> timeList
List of stored time instants.


stateList

List<E> stateList
List of system states.


savedVarsIndex

int[] savedVarsIndex
Index of saved systems variables (with respect to the variable ordering used in the stoichiometric matrix).


savedVars

List<E> savedVars
List of IDs of saved systems variables. Variable IDs are indicated according to the following notation: variableName + Model.variableCompartmentSeparator + compartmentName.


computationTime

double computationTime
Time (in seconds) spent for computing the stored time series.


optimizedSize

int optimizedSize
Number of states that can be efficiently stored in this data structure.


lastStateTime

double lastStateTime
Time instant of the last state that has been put.


lastState

double[] lastState
Last state that has been put.


isLastStateFiltered

boolean isLastStateFiltered
Indicates if the last state that has been put contains only the variable TS that has to be stored.


wasLastStateInserted

boolean wasLastStateInserted
Stores if the last state that has been put has been actually saved or not in the data structure.

Class hSimulator.library.SimulationStoppedException extends Exception implements Serializable

Serialized Fields

partialResults

SimulatedTS partialResults
Partial simulation results computed before this exception has been thrown (can be null).


Package hSimulator.simulator.gui

Class hSimulator.simulator.gui.AboutFrame extends JFrame implements Serializable

Serialized Fields

detailText

JEditorPane detailText

jLabel1

JLabel jLabel1

jPanel1

JPanel jPanel1

jScrollPane2

JScrollPane jScrollPane2

Class hSimulator.simulator.gui.AppFrame extends JFrame implements Serializable

Serialized Fields

textArea

org.fife.ui.rsyntaxtextarea.RSyntaxTextArea textArea

undoManager

UndoManager undoManager

f

File f

filename

String filename

chooser

JFileChooser chooser

m

Model m

tMaxString

String tMaxString

tsSamplingString

String tsSamplingString

init

String init

modelName

String modelName

modelNameXls

String modelNameXls

modelAlgorithm

String modelAlgorithm

ts

SimulatedTS ts

s

Simulator s

isAlreadyOneClicked

boolean isAlreadyOneClicked

alreadySaved

boolean alreadySaved

logScale

boolean logScale

paused

boolean paused

chPanel1

org.jfree.chart.ChartPanel chPanel1

thread

Thread thread

thread1

Thread thread1

updatePercentage

AppFrame.UpdatePercentage updatePercentage

filePath

String filePath

file1

File file1

userhome

String userhome

chart

org.jfree.chart.JFreeChart chart

chPanel

org.jfree.chart.ChartPanel chPanel

m1

Model m1

advancedOptions

JButton advancedOptions

buttonGroup1

ButtonGroup buttonGroup1

buttonGroup2

ButtonGroup buttonGroup2

checkMenu

JMenuItem checkMenu

checkModel

JButton checkModel

copy

JButton copy

copyMenuItem

JMenuItem copyMenuItem

cut

JButton cut

cutMenuItem

JMenuItem cutMenuItem

decMenuItem

JMenuItem decMenuItem

decreaseFontSize

JButton decreaseFontSize

dmBtn

JRadioButton dmBtn

eulerBtn

JRadioButton eulerBtn

hrssaBtn

JRadioButton hrssaBtn

incMenuItem

JMenuItem incMenuItem

increaseFontSize

JButton increaseFontSize

jMenu1

JMenu jMenu1

jMenu2

JMenu jMenu2

jMenu3

JMenu jMenu3

jMenu4

JMenu jMenu4

jMenuBar1

JMenuBar jMenuBar1

jMenuItem1

JMenuItem jMenuItem1

jMenuItem2

JMenuItem jMenuItem2

jMenuItem5

JMenuItem jMenuItem5

jMenuItem7

JMenuItem jMenuItem7

jMenuItem8

JMenuItem jMenuItem8

jMenuItem9

JMenuItem jMenuItem9

jPanel1

JPanel jPanel1

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jPanel5

JPanel jPanel5

jSeparator1

JSeparator jSeparator1

jSeparator2

JPopupMenu.Separator jSeparator2

jSeparator4

JPopupMenu.Separator jSeparator4

jSeparator5

JPopupMenu.Separator jSeparator5

jSeparator6

JPopupMenu.Separator jSeparator6

jSeparator7

JPopupMenu.Separator jSeparator7

jSeparator8

JPopupMenu.Separator jSeparator8

jSeparator9

JPopupMenu.Separator jSeparator9

jSplitPane1

JSplitPane jSplitPane1

jToolBar1

JToolBar jToolBar1

jToolBar2

JToolBar jToolBar2

jToolBar5

JToolBar jToolBar5

logScaleOption

JRadioButtonMenuItem logScaleOption

newModel

JButton newModel

nonLogScaleOption

JRadioButtonMenuItem nonLogScaleOption

openModel

JButton openModel

paste

JButton paste

pasteMenuItem

JMenuItem pasteMenuItem

pauseSimulation

JButton pauseSimulation

plotPanel

JPanel plotPanel

printPlot

JMenuItem printPlot

progressBar

JProgressBar progressBar

redo

JButton redo

redoMenuItem

JMenuItem redoMenuItem

rk45Btn

JRadioButton rk45Btn

rssaBtn

JRadioButton rssaBtn

runSimulation

JButton runSimulation

saveModel

JButton saveModel

saveModelAsMenu

JMenuItem saveModelAsMenu

saveModelMenu

JMenuItem saveModelMenu

saveResults

JMenuItem saveResults

showPlot

JMenuItem showPlot

simToolbar

JToolBar simToolbar

stopSimulation

JButton stopSimulation

tMax

JTextField tMax

tMaxLabel

JLabel tMaxLabel

textPanel

JPanel textPanel

tsSampling

JTextField tsSampling

tsSamplingLabel

JLabel tsSamplingLabel

undo

JButton undo

undoMenuItem

JMenuItem undoMenuItem

Class hSimulator.simulator.gui.OptionDM extends JFrame implements Serializable

Serialized Fields

applyM

JButton applyM

jButton1

JButton jButton1

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

jPanel1

JPanel jPanel1

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

nSimDM

JTextField nSimDM

nThread

JTextField nThread

Class hSimulator.simulator.gui.OptionRK45 extends JFrame implements Serializable

Serialized Fields

applyV

JButton applyV

cancel

JButton cancel

initialDt

JTextField initialDt

jLabel7

JLabel jLabel7

jLabel8

JLabel jLabel8

jPanel1

JPanel jPanel1

jPanel30

JPanel jPanel30

jPanel31

JPanel jPanel31

maxErr

JTextField maxErr

Class hSimulator.simulator.gui.OptionsEuler extends JFrame implements Serializable

Serialized Fields

applyV

JButton applyV

close

JButton close

dt

JTextField dt

jLabel5

JLabel jLabel5

jPanel1

JPanel jPanel1

jPanel6

JPanel jPanel6

Class hSimulator.simulator.gui.OptionsHRSSA extends JFrame implements Serializable

Serialized Fields

Cancel

JButton Cancel

applyV

JButton applyV

deltaHRSSA

JTextField deltaHRSSA

dtHRSSA

JTextField dtHRSSA

epsilonHRSSA

JTextField epsilonHRSSA

gammaHRSSA

JTextField gammaHRSSA

jLabel1

JLabel jLabel1

jLabel10

JLabel jLabel10

jLabel11

JLabel jLabel11

jLabel14

JLabel jLabel14

jLabel2

JLabel jLabel2

jLabel3

JLabel jLabel3

jLabel9

JLabel jLabel9

jPanel1

JPanel jPanel1

jPanel11

JPanel jPanel11

jPanel12

JPanel jPanel12

jPanel13

JPanel jPanel13

jPanel16

JPanel jPanel16

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jPanel4

JPanel jPanel4

jPanel5

JPanel jPanel5

nSimHRSSA

JTextField nSimHRSSA

nThread2

JTextField nThread2

thetaHRSSA

JTextField thetaHRSSA

Class hSimulator.simulator.gui.OptionsRSSA extends JFrame implements Serializable

Serialized Fields

applyV

JButton applyV

cancel

JButton cancel

deltaRSSA

JTextField deltaRSSA

epsilonRSSA

JTextField epsilonRSSA

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

jLabel3

JLabel jLabel3

jLabel4

JLabel jLabel4

jPanel1

JPanel jPanel1

jPanel14

JPanel jPanel14

jPanel2

JPanel jPanel2

jPanel3

JPanel jPanel3

jPanel4

JPanel jPanel4

jPanel6

JPanel jPanel6

nSimRSSA

JTextField nSimRSSA

nThread

JTextField nThread