public void actionPerformed(ActionEvent e) {
progressBar.progress.setValue(LocalConfig.getInstance().getProgress());
progressBar.progress.repaint();
if (LocalConfig.getInstance().getProgress() == 100) {
progressBar.setVisible(false);
progressBar.dispose();
}
}
@Override
protected Void doInBackground() throws Exception {
int progress = 0;
TextReactionsModelReader reader = new TextReactionsModelReader();
reader.load(
GraphicalInterface.getReactionsCSVFile(), LocalConfig.getInstance().getDatabaseName());
while (progress < 100) {
try {
Thread.sleep(1000);
} catch (InterruptedException ignore) {
}
}
t.stop();
return null;
}
public void write(String file, String databaseName) {
String queryString = "jdbc:sqlite:" + databaseName + ".db";
try {
Class.forName("org.sqlite.JDBC");
} catch (ClassNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
try {
Connection conn = DriverManager.getConnection(queryString);
// String extension = ".csv";
CSVWriter writer;
try {
writer = new CSVWriter(new FileWriter(file), GraphicalInterface.getSplitCharacter());
String headerNames = "";
// start with 1 to avoid reading database id
for (int i = 1; i < GraphicalInterfaceConstants.REACTIONS_COLUMN_NAMES.length; i++) {
headerNames += GraphicalInterfaceConstants.REACTIONS_COLUMN_NAMES[i] + "#";
}
ReactionsMetaColumnManager reactionsMetaColumnManager = new ReactionsMetaColumnManager();
int metaColumnCount =
reactionsMetaColumnManager.getMetaColumnCount(
LocalConfig.getInstance().getDatabaseName());
for (int j = 1; j < metaColumnCount + 1; j++) {
headerNames +=
reactionsMetaColumnManager.getColumnName(
LocalConfig.getInstance().getDatabaseName(), j)
+ "#";
}
String[] header = (headerNames.substring(0, headerNames.length() - 1)).split("#");
writer.writeNext(header);
int numReactions = GraphicalInterface.reactionsTable.getModel().getRowCount();
for (int n = 0; n < numReactions; n++) {
int viewRow = GraphicalInterface.reactionsTable.convertRowIndexToModel(n);
String knockout = "false";
String fluxValue = "0.0";
String reactionAbbreviation = " ";
String reactionName = " ";
String reactionString = " ";
String reversible = " ";
String lowerBound = "-999999";
String upperBound = "999999";
String objective = "0.0";
String meta1 = " ";
String meta2 = " ";
String meta3 = " ";
String meta4 = " ";
String meta5 = " ";
String meta6 = " ";
String meta7 = " ";
String meta8 = " ";
String meta9 = " ";
String meta10 = " ";
String meta11 = " ";
String meta12 = " ";
String meta13 = " ";
String meta14 = " ";
String meta15 = " ";
// check if null before toString() to avoid null pointer error
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.KO_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.KO_COLUMN)
.toString()
.length()
> 0) {
knockout =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.KO_COLUMN);
} else {
knockout = "false";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.FLUX_VALUE_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.FLUX_VALUE_COLUMN)
.toString()
.length()
> 0) {
fluxValue =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.FLUX_VALUE_COLUMN);
} else {
fluxValue = "0.0";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_ABBREVIATION_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_ABBREVIATION_COLUMN)
.toString()
.length()
> 0) {
reactionAbbreviation =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_ABBREVIATION_COLUMN);
} else {
reactionAbbreviation = " ";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_NAME_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_NAME_COLUMN)
.toString()
.length()
> 0) {
reactionName =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_NAME_COLUMN);
} else {
reactionName = " ";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_STRING_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_STRING_COLUMN)
.toString()
.length()
> 0) {
reactionString =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_STRING_COLUMN);
} else {
reactionString = " ";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REVERSIBLE_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REVERSIBLE_COLUMN)
.toString()
.length()
> 0) {
reversible =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REVERSIBLE_COLUMN);
} else {
reversible = " ";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.LOWER_BOUND_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.LOWER_BOUND_COLUMN)
.toString()
.length()
> 0) {
lowerBound =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.LOWER_BOUND_COLUMN);
} else {
lowerBound = "-999999";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.UPPER_BOUND_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.UPPER_BOUND_COLUMN)
.toString()
.length()
> 0) {
upperBound =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.UPPER_BOUND_COLUMN);
} else {
upperBound = "999999";
}
}
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.BIOLOGICAL_OBJECTIVE_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.BIOLOGICAL_OBJECTIVE_COLUMN)
.toString()
.length()
> 0) {
objective =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.BIOLOGICAL_OBJECTIVE_COLUMN);
} else {
objective = "0.0";
}
}
String metaString = "";
if (metaColumnCount > 0) {
// check if null before toString() to avoid null pointer error
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META1_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META1_COLUMN)
.toString()
.length()
> 0) {
meta1 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META1_COLUMN);
}
}
metaString += meta1 + "#";
}
if (metaColumnCount > 1) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META2_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META2_COLUMN)
.toString()
.length()
> 0) {
meta2 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META2_COLUMN);
}
}
metaString += meta2 + "#";
}
if (metaColumnCount > 2) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META3_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META3_COLUMN)
.toString()
.length()
> 0) {
meta3 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META3_COLUMN);
}
}
metaString += meta3 + "#";
}
if (metaColumnCount > 3) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META4_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META4_COLUMN)
.toString()
.length()
> 0) {
meta4 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META4_COLUMN);
}
}
metaString += meta4 + "#";
}
if (metaColumnCount > 4) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META5_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META5_COLUMN)
.toString()
.length()
> 0) {
meta5 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META5_COLUMN);
}
}
metaString += meta5 + "#";
}
if (metaColumnCount > 5) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META6_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META6_COLUMN)
.toString()
.length()
> 0) {
meta6 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META6_COLUMN);
}
}
metaString += meta6 + "#";
}
if (metaColumnCount > 6) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META7_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META7_COLUMN)
.toString()
.length()
> 0) {
meta7 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META7_COLUMN);
}
}
metaString += meta7 + "#";
}
if (metaColumnCount > 7) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META8_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META8_COLUMN)
.toString()
.length()
> 0) {
meta8 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META8_COLUMN);
}
}
metaString += meta8 + "#";
}
if (metaColumnCount > 8) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META9_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META9_COLUMN)
.toString()
.length()
> 0) {
meta9 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META9_COLUMN);
}
}
metaString += meta9 + "#";
}
if (metaColumnCount > 9) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META10_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META10_COLUMN)
.toString()
.length()
> 0) {
meta10 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_META10_COLUMN);
}
}
metaString += meta10 + "#";
}
if (metaColumnCount > 10) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META11_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META11_COLUMN)
.toString()
.length()
> 0) {
meta11 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_META11_COLUMN);
}
}
metaString += meta11 + "#";
}
if (metaColumnCount > 11) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META12_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META12_COLUMN)
.toString()
.length()
> 0) {
meta12 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_META12_COLUMN);
}
}
metaString += meta12 + "#";
}
if (metaColumnCount > 12) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META13_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META13_COLUMN)
.toString()
.length()
> 0) {
meta13 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_META13_COLUMN);
}
}
metaString += meta13 + "#";
}
if (metaColumnCount > 13) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META14_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META14_COLUMN)
.toString()
.length()
> 0) {
meta14 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_META14_COLUMN);
}
}
metaString += meta14 + "#";
}
if (metaColumnCount > 14) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META15_COLUMN)
!= null) {
if (GraphicalInterface.reactionsTable
.getModel()
.getValueAt(viewRow, GraphicalInterfaceConstants.REACTION_META15_COLUMN)
.toString()
.length()
> 0) {
meta15 =
(String)
GraphicalInterface.reactionsTable
.getModel()
.getValueAt(
viewRow, GraphicalInterfaceConstants.REACTION_META15_COLUMN);
}
}
metaString += meta15 + "#";
}
if (metaString.length() > 0) {
String[] entries =
(knockout
+ "#"
+ fluxValue
+ "#"
+ reactionAbbreviation
+ "#"
+ reactionName
+ "#"
+ reactionString
+ "#"
+ reversible
+ "#"
+ lowerBound
+ "#"
+ upperBound
+ "#"
+ objective
+ "#"
+ metaString.substring(0, metaString.length() - 1))
.split("#");
writer.writeNext(entries);
} else {
String[] entries =
(knockout
+ "#"
+ fluxValue
+ "#"
+ reactionAbbreviation
+ "#"
+ reactionName
+ "#"
+ reactionString
+ "#"
+ reversible
+ "#"
+ lowerBound
+ "#"
+ upperBound
+ "#"
+ objective)
.split("#");
writer.writeNext(entries);
}
}
writer.close();
conn.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
public ReactionColumnNameInterface(final Connection con, ArrayList<String> columnNamesFromFile)
throws SQLException {
final ArrayList<Image> icons = new ArrayList<Image>();
icons.add(new ImageIcon("etc/most16.jpg").getImage());
icons.add(new ImageIcon("etc/most32.jpg").getImage());
LocalConfig.getInstance().setProgress(0);
progressBar.pack();
progressBar.setIconImages(icons);
progressBar.setSize(200, 70);
progressBar.setTitle("Loading...");
progressBar.setVisible(false);
setColumnNamesFromFile(columnNamesFromFile);
setTitle(ColumnInterfaceConstants.REACTIONS_COLUMN_NAME_INTERFACE_TITLE);
setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
cbKnockout.setEditable(true);
cbFluxValue.setEditable(true);
cbReactionAbbreviation.setEditable(true);
cbReactionName.setEditable(true);
cbReactionEquation.setEditable(true);
cbReversible.setEditable(true);
cbLowerBound.setEditable(true);
cbUpperBound.setEditable(true);
cbObjective.setEditable(true);
cbKnockout.setPreferredSize(new Dimension(250, 30));
cbKnockout.setMaximumSize(new Dimension(250, 30));
cbKnockout.setMinimumSize(new Dimension(250, 30));
cbFluxValue.setPreferredSize(new Dimension(250, 30));
cbFluxValue.setMaximumSize(new Dimension(250, 30));
cbFluxValue.setMinimumSize(new Dimension(250, 30));
cbReactionAbbreviation.setPreferredSize(new Dimension(250, 30));
cbReactionAbbreviation.setMaximumSize(new Dimension(250, 30));
cbReactionAbbreviation.setMinimumSize(new Dimension(250, 30));
cbReactionName.setPreferredSize(new Dimension(250, 30));
cbReactionName.setMaximumSize(new Dimension(250, 30));
cbReactionName.setMinimumSize(new Dimension(250, 30));
cbReactionEquation.setPreferredSize(new Dimension(250, 30));
cbReactionEquation.setMaximumSize(new Dimension(250, 30));
cbReactionEquation.setMinimumSize(new Dimension(250, 30));
cbReversible.setPreferredSize(new Dimension(250, 30));
cbReversible.setMaximumSize(new Dimension(250, 30));
cbReversible.setMinimumSize(new Dimension(250, 30));
cbLowerBound.setPreferredSize(new Dimension(250, 30));
cbLowerBound.setMaximumSize(new Dimension(250, 30));
cbLowerBound.setMinimumSize(new Dimension(250, 30));
cbUpperBound.setPreferredSize(new Dimension(250, 30));
cbUpperBound.setMaximumSize(new Dimension(250, 30));
cbUpperBound.setMinimumSize(new Dimension(250, 30));
cbObjective.setPreferredSize(new Dimension(250, 30));
cbObjective.setMaximumSize(new Dimension(250, 30));
cbObjective.setMinimumSize(new Dimension(250, 30));
JTextField fieldKnockout = (JTextField) cbKnockout.getEditor().getEditorComponent();
fieldKnockout.addKeyListener(new ComboKeyHandler(cbKnockout));
JTextField fieldFluxValue = (JTextField) cbFluxValue.getEditor().getEditorComponent();
fieldFluxValue.addKeyListener(new ComboKeyHandler(cbFluxValue));
JTextField fieldReactionAbbreviation =
(JTextField) cbReactionAbbreviation.getEditor().getEditorComponent();
fieldReactionAbbreviation.addKeyListener(new ComboKeyHandler(cbReactionAbbreviation));
JTextField fieldReactionName = (JTextField) cbReactionName.getEditor().getEditorComponent();
fieldReactionName.addKeyListener(new ComboKeyHandler(cbReactionName));
JTextField fieldReactionEquation =
(JTextField) cbReactionEquation.getEditor().getEditorComponent();
fieldReactionEquation.addKeyListener(new ComboKeyHandler(cbReactionEquation));
JTextField fieldReversible = (JTextField) cbReversible.getEditor().getEditorComponent();
fieldReversible.addKeyListener(new ComboKeyHandler(cbReversible));
JTextField fieldLowerBound = (JTextField) cbLowerBound.getEditor().getEditorComponent();
fieldLowerBound.addKeyListener(new ComboKeyHandler(cbLowerBound));
JTextField fieldUpperBound = (JTextField) cbUpperBound.getEditor().getEditorComponent();
fieldUpperBound.addKeyListener(new ComboKeyHandler(cbUpperBound));
JTextField fieldObjective = (JTextField) cbObjective.getEditor().getEditorComponent();
fieldObjective.addKeyListener(new ComboKeyHandler(cbObjective));
populateNamesFromFileBoxes(columnNamesFromFile);
// box layout
Box vb = Box.createVerticalBox();
Box hbLabels = Box.createHorizontalBox();
Box hb1 = Box.createHorizontalBox();
Box hb2 = Box.createHorizontalBox();
Box hb3 = Box.createHorizontalBox();
Box hb4 = Box.createHorizontalBox();
Box hb5 = Box.createHorizontalBox();
Box hb6 = Box.createHorizontalBox();
Box hb7 = Box.createHorizontalBox();
Box hb8 = Box.createHorizontalBox();
Box hb9 = Box.createHorizontalBox();
Box hbTop = Box.createHorizontalBox();
Box hbKnockoutLabel = Box.createHorizontalBox();
Box hbKnockout = Box.createHorizontalBox();
Box hbFluxValueLabel = Box.createHorizontalBox();
Box hbFluxValue = Box.createHorizontalBox();
Box hbReactionAbbreviationLabel = Box.createHorizontalBox();
Box hbReactionAbbreviation = Box.createHorizontalBox();
Box hbReactionNameLabel = Box.createHorizontalBox();
Box hbReactionName = Box.createHorizontalBox();
Box hbReactionEquationLabel = Box.createHorizontalBox();
Box hbReactionEquation = Box.createHorizontalBox();
Box hbReversibleLabel = Box.createHorizontalBox();
Box hbReversible = Box.createHorizontalBox();
Box hbLowerBoundLabel = Box.createHorizontalBox();
Box hbLowerBound = Box.createHorizontalBox();
Box hbUpperBoundLabel = Box.createHorizontalBox();
Box hbUpperBound = Box.createHorizontalBox();
Box hbObjectiveLabel = Box.createHorizontalBox();
Box hbObjective = Box.createHorizontalBox();
Box hbButton = Box.createHorizontalBox();
// top label
JLabel topLabel = new JLabel();
topLabel.setText(ColumnInterfaceConstants.REACTIONS_TOP_LABEL);
topLabel.setSize(new Dimension(300, 30));
// top, left, bottom. right
topLabel.setBorder(BorderFactory.createEmptyBorder(20, 30, 20, 200));
topLabel.setAlignmentX(LEFT_ALIGNMENT);
hbTop.add(topLabel);
hbTop.setAlignmentX(LEFT_ALIGNMENT);
hbLabels.add(hbTop);
// knockout Label and combo
JLabel knockoutLabel = new JLabel();
knockoutLabel.setText(ColumnInterfaceConstants.KO_LABEL);
knockoutLabel.setSize(new Dimension(300, 20));
knockoutLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 80));
knockoutLabel.setAlignmentX(LEFT_ALIGNMENT);
// knockoutLabel.setAlignmentY(TOP_ALIGNMENT);
JPanel panelKnockoutLabel = new JPanel();
panelKnockoutLabel.setLayout(new BoxLayout(panelKnockoutLabel, BoxLayout.X_AXIS));
panelKnockoutLabel.add(knockoutLabel);
panelKnockoutLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbKnockoutLabel.add(panelKnockoutLabel);
hbKnockoutLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelKnockout = new JPanel();
panelKnockout.setLayout(new BoxLayout(panelKnockout, BoxLayout.X_AXIS));
panelKnockout.add(cbKnockout);
panelKnockout.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelKnockout.setAlignmentX(RIGHT_ALIGNMENT);
hbKnockout.add(panelKnockout);
hbKnockout.setAlignmentX(RIGHT_ALIGNMENT);
hb1.add(hbKnockoutLabel);
hb1.add(hbKnockout);
// flux value label and combo
JLabel fluxValueLabel = new JLabel();
fluxValueLabel.setText(ColumnInterfaceConstants.FLUX_VALUE_LABEL);
fluxValueLabel.setSize(new Dimension(300, 20));
fluxValueLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
fluxValueLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelFluxValueLabel = new JPanel();
panelFluxValueLabel.setLayout(new BoxLayout(panelFluxValueLabel, BoxLayout.X_AXIS));
panelFluxValueLabel.add(fluxValueLabel);
panelFluxValueLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbFluxValueLabel.add(panelFluxValueLabel);
hbFluxValueLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelFluxValue = new JPanel();
panelFluxValue.setLayout(new BoxLayout(panelFluxValue, BoxLayout.X_AXIS));
panelFluxValue.add(cbFluxValue);
panelFluxValue.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelFluxValue.setAlignmentX(RIGHT_ALIGNMENT);
hbFluxValue.add(panelFluxValue);
hbFluxValue.setAlignmentX(RIGHT_ALIGNMENT);
hb2.add(hbFluxValueLabel);
hb2.add(hbFluxValue);
// reaction abbreviation label and combo
JLabel reactionAbbreviationLabel = new JLabel();
reactionAbbreviationLabel.setText(ColumnInterfaceConstants.REACTION_ABBREVIATION_LABEL);
reactionAbbreviationLabel.setSize(new Dimension(300, 20));
reactionAbbreviationLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
reactionAbbreviationLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReactionAbbreviationLabel = new JPanel();
panelReactionAbbreviationLabel.setLayout(
new BoxLayout(panelReactionAbbreviationLabel, BoxLayout.X_AXIS));
panelReactionAbbreviationLabel.add(reactionAbbreviationLabel);
panelReactionAbbreviationLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbReactionAbbreviationLabel.add(panelReactionAbbreviationLabel);
hbReactionAbbreviationLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReactionAbbreviation = new JPanel();
panelReactionAbbreviation.setLayout(new BoxLayout(panelReactionAbbreviation, BoxLayout.X_AXIS));
panelReactionAbbreviation.add(cbReactionAbbreviation);
panelReactionAbbreviation.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelReactionAbbreviation.setAlignmentX(RIGHT_ALIGNMENT);
hbReactionAbbreviation.add(panelReactionAbbreviation);
hbReactionAbbreviation.setAlignmentX(RIGHT_ALIGNMENT);
hb3.add(hbReactionAbbreviationLabel);
hb3.add(hbReactionAbbreviation);
// reaction name label and combo
JLabel reactionNameLabel = new JLabel();
reactionNameLabel.setText(ColumnInterfaceConstants.REACTION_NAME_LABEL);
reactionNameLabel.setSize(new Dimension(300, 20));
reactionNameLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
reactionNameLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReactionNameLabel = new JPanel();
panelReactionNameLabel.setLayout(new BoxLayout(panelReactionNameLabel, BoxLayout.X_AXIS));
panelReactionNameLabel.add(reactionNameLabel);
panelReactionNameLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbReactionNameLabel.add(panelReactionNameLabel);
hbReactionNameLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReactionName = new JPanel();
panelReactionName.setLayout(new BoxLayout(panelReactionName, BoxLayout.X_AXIS));
panelReactionName.add(cbReactionName);
panelReactionName.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelReactionName.setAlignmentX(RIGHT_ALIGNMENT);
hbReactionName.add(panelReactionName);
hbReactionName.setAlignmentX(RIGHT_ALIGNMENT);
hb4.add(hbReactionNameLabel);
hb4.add(hbReactionName);
// reaction equation label and combo
JLabel reactionEquationLabel = new JLabel();
reactionEquationLabel.setText(ColumnInterfaceConstants.REACTION_EQUATION_LABEL);
reactionEquationLabel.setSize(new Dimension(300, 20));
reactionEquationLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
reactionEquationLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReactionEquationLabel = new JPanel();
panelReactionEquationLabel.setLayout(
new BoxLayout(panelReactionEquationLabel, BoxLayout.X_AXIS));
panelReactionEquationLabel.add(reactionEquationLabel);
panelReactionEquationLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbReactionEquationLabel.add(panelReactionEquationLabel);
hbReactionEquationLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReactionEquation = new JPanel();
panelReactionEquation.setLayout(new BoxLayout(panelReactionEquation, BoxLayout.X_AXIS));
panelReactionEquation.add(cbReactionEquation);
panelReactionEquation.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelReactionEquation.setAlignmentX(RIGHT_ALIGNMENT);
hbReactionEquation.add(panelReactionEquation);
hbReactionEquation.setAlignmentX(RIGHT_ALIGNMENT);
hb5.add(hbReactionEquationLabel);
hb5.add(hbReactionEquation);
// reversible label and combo
JLabel reversibleLabel = new JLabel();
reversibleLabel.setText(ColumnInterfaceConstants.REVERSIBLE_LABEL);
reversibleLabel.setSize(new Dimension(300, 20));
reversibleLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
reversibleLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReversibleLabel = new JPanel();
panelReversibleLabel.setLayout(new BoxLayout(panelReversibleLabel, BoxLayout.X_AXIS));
panelReversibleLabel.add(reversibleLabel);
panelReversibleLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbReversibleLabel.add(panelReversibleLabel);
hbReversibleLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelReversible = new JPanel();
panelReversible.setLayout(new BoxLayout(panelReversible, BoxLayout.X_AXIS));
panelReversible.add(cbReversible);
panelReversible.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelReversible.setAlignmentX(RIGHT_ALIGNMENT);
hbReversible.add(panelReversible);
hbReversible.setAlignmentX(RIGHT_ALIGNMENT);
hb6.add(hbReversibleLabel);
hb6.add(hbReversible);
// lower bound label and combo
JLabel lowerBoundLabel = new JLabel();
lowerBoundLabel.setText(ColumnInterfaceConstants.LOWER_BOUND_LABEL);
lowerBoundLabel.setSize(new Dimension(300, 20));
lowerBoundLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
lowerBoundLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelLowerBoundLabel = new JPanel();
panelLowerBoundLabel.setLayout(new BoxLayout(panelLowerBoundLabel, BoxLayout.X_AXIS));
panelLowerBoundLabel.add(lowerBoundLabel);
panelLowerBoundLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbLowerBoundLabel.add(panelLowerBoundLabel);
hbLowerBoundLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelLowerBound = new JPanel();
panelLowerBound.setLayout(new BoxLayout(panelLowerBound, BoxLayout.X_AXIS));
panelLowerBound.add(cbLowerBound);
panelLowerBound.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelLowerBound.setAlignmentX(RIGHT_ALIGNMENT);
hbLowerBound.add(panelLowerBound);
hbLowerBound.setAlignmentX(RIGHT_ALIGNMENT);
hb7.add(hbLowerBoundLabel);
hb7.add(hbLowerBound);
// upper bound label and combo
JLabel upperBoundLabel = new JLabel();
upperBoundLabel.setText(ColumnInterfaceConstants.UPPER_BOUND_LABEL);
upperBoundLabel.setSize(new Dimension(300, 20));
upperBoundLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
upperBoundLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelUpperBoundLabel = new JPanel();
panelUpperBoundLabel.setLayout(new BoxLayout(panelUpperBoundLabel, BoxLayout.X_AXIS));
panelUpperBoundLabel.add(upperBoundLabel);
panelUpperBoundLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbUpperBoundLabel.add(panelUpperBoundLabel);
hbUpperBoundLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelUpperBound = new JPanel();
panelUpperBound.setLayout(new BoxLayout(panelUpperBound, BoxLayout.X_AXIS));
panelUpperBound.add(cbUpperBound);
panelUpperBound.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelUpperBound.setAlignmentX(RIGHT_ALIGNMENT);
hbUpperBound.add(panelUpperBound);
hbUpperBound.setAlignmentX(RIGHT_ALIGNMENT);
hb8.add(hbUpperBoundLabel);
hb8.add(hbUpperBound);
// objective label and combo
JLabel objectiveLabel = new JLabel();
objectiveLabel.setText(ColumnInterfaceConstants.BIOLOGICAL_OBJECTIVE_LABEL);
objectiveLabel.setSize(new Dimension(300, 20));
objectiveLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 80));
objectiveLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelObjectiveLabel = new JPanel();
panelObjectiveLabel.setLayout(new BoxLayout(panelObjectiveLabel, BoxLayout.X_AXIS));
panelObjectiveLabel.add(objectiveLabel);
panelObjectiveLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
hbObjectiveLabel.add(panelObjectiveLabel);
hbObjectiveLabel.setAlignmentX(LEFT_ALIGNMENT);
JPanel panelObjective = new JPanel();
panelObjective.setLayout(new BoxLayout(panelObjective, BoxLayout.X_AXIS));
panelObjective.add(cbObjective);
panelObjective.setBorder(BorderFactory.createEmptyBorder(0, 0, 10, 0));
panelObjective.setAlignmentX(RIGHT_ALIGNMENT);
hbObjective.add(panelObjective);
hbObjective.setAlignmentX(RIGHT_ALIGNMENT);
hb9.add(hbObjectiveLabel);
hb9.add(hbObjective);
okButton.setMnemonic(KeyEvent.VK_O);
JLabel blank = new JLabel(" ");
cancelButton.setMnemonic(KeyEvent.VK_C);
JLabel blank2 = new JLabel(" ");
nextRowButton.setMnemonic(KeyEvent.VK_N);
JPanel buttonPanel = new JPanel();
buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS));
buttonPanel.add(okButton);
buttonPanel.add(blank);
buttonPanel.add(cancelButton);
buttonPanel.add(blank2);
buttonPanel.add(nextRowButton);
buttonPanel.setBorder(BorderFactory.createEmptyBorder(10, 20, 20, 20));
hbButton.add(buttonPanel);
vb.add(hbLabels);
vb.add(hb1);
vb.add(hb2);
vb.add(hb3);
vb.add(hb4);
vb.add(hb5);
vb.add(hb6);
vb.add(hb7);
vb.add(hb8);
vb.add(hb9);
vb.add(hbButton);
add(vb);
ActionListener okButtonActionListener =
new ActionListener() {
public void actionPerformed(ActionEvent prodActionEvent) {
// add metacolumn names to db
ReactionsMetaColumnManager reactionsMetaColumnManager =
new ReactionsMetaColumnManager();
ArrayList<String> metaColumnNames = new ArrayList();
ArrayList<Integer> usedIndices = new ArrayList();
ArrayList<Integer> metaColumnIndexList = new ArrayList();
if (getColumnNamesFromFile().contains(cbKnockout.getSelectedItem())) {
LocalConfig.getInstance()
.setKnockoutColumnIndex(
getColumnNamesFromFile().indexOf(cbKnockout.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbKnockout.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbFluxValue.getSelectedItem())) {
LocalConfig.getInstance()
.setFluxValueColumnIndex(
getColumnNamesFromFile().indexOf(cbFluxValue.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbFluxValue.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbReactionAbbreviation.getSelectedItem())) {
LocalConfig.getInstance()
.setReactionAbbreviationColumnIndex(
getColumnNamesFromFile().indexOf(cbReactionAbbreviation.getSelectedItem()));
usedIndices.add(
getColumnNamesFromFile().indexOf(cbReactionAbbreviation.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbReactionName.getSelectedItem())) {
LocalConfig.getInstance()
.setReactionNameColumnIndex(
getColumnNamesFromFile().indexOf(cbReactionName.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbReactionName.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbReactionEquation.getSelectedItem())) {
LocalConfig.getInstance()
.setReactionEquationColumnIndex(
getColumnNamesFromFile().indexOf(cbReactionEquation.getSelectedItem()));
usedIndices.add(
getColumnNamesFromFile().indexOf(cbReactionEquation.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbReversible.getSelectedItem())) {
LocalConfig.getInstance()
.setReversibleColumnIndex(
getColumnNamesFromFile().indexOf(cbReversible.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbReversible.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbLowerBound.getSelectedItem())) {
LocalConfig.getInstance()
.setLowerBoundColumnIndex(
getColumnNamesFromFile().indexOf(cbLowerBound.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbLowerBound.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbUpperBound.getSelectedItem())) {
LocalConfig.getInstance()
.setUpperBoundColumnIndex(
getColumnNamesFromFile().indexOf(cbUpperBound.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbUpperBound.getSelectedItem()));
}
if (getColumnNamesFromFile().contains(cbObjective.getSelectedItem())) {
LocalConfig.getInstance()
.setBiologicalObjectiveColumnIndex(
getColumnNamesFromFile().indexOf(cbObjective.getSelectedItem()));
usedIndices.add(getColumnNamesFromFile().indexOf(cbObjective.getSelectedItem()));
}
for (int i = 0; i < getColumnNamesFromFile().size(); i++) {
if (!usedIndices.contains(i)) {
metaColumnNames.add(getColumnNamesFromFile().get(i));
metaColumnIndexList.add(
getColumnNamesFromFile().indexOf(getColumnNamesFromFile().get(i)));
}
}
reactionsMetaColumnManager.addColumnNames(
LocalConfig.getInstance().getDatabaseName(), metaColumnNames);
LocalConfig.getInstance().setReactionsMetaColumnIndexList(metaColumnIndexList);
setVisible(false);
dispose();
progressBar.setVisible(true);
t.start();
task = new Task();
task.execute();
}
};
okButton.addActionListener(okButtonActionListener);
ActionListener cancelButtonActionListener =
new ActionListener() {
public void actionPerformed(ActionEvent prodActionEvent) {
setVisible(false);
dispose();
// this is a hack, same as clear method in gui
try {
Class.forName("org.sqlite.JDBC");
DatabaseCreator databaseCreator = new DatabaseCreator();
LocalConfig.getInstance().setDatabaseName(ConfigConstants.DEFAULT_DATABASE_NAME);
Connection con =
DriverManager.getConnection(
"jdbc:sqlite:" + ConfigConstants.DEFAULT_DATABASE_NAME + ".db");
databaseCreator.createDatabase(LocalConfig.getInstance().getDatabaseName());
databaseCreator.addRows(
LocalConfig.getInstance().getDatabaseName(),
GraphicalInterfaceConstants.BLANK_DB_NUMBER_OF_ROWS,
GraphicalInterfaceConstants.BLANK_DB_NUMBER_OF_ROWS);
} catch (ClassNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
};
cancelButton.addActionListener(cancelButtonActionListener);
ActionListener nextRowButtonActionListener =
new ActionListener() {
public void actionPerformed(ActionEvent prodActionEvent) {
TextReactionsModelReader reader = new TextReactionsModelReader();
int correction = LocalConfig.getInstance().getReactionsNextRowCorrection();
if ((correction + 1) < reader.numberOfLines(GraphicalInterface.getReactionsCSVFile())) {
LocalConfig.getInstance().setReactionsNextRowCorrection(correction + 1);
System.out.println(
"corr " + LocalConfig.getInstance().getReactionsNextRowCorrection());
ArrayList<String> newColumnNamesFromFile =
reader.columnNamesFromFile(
GraphicalInterface.getReactionsCSVFile(),
LocalConfig.getInstance().getReactionsNextRowCorrection());
setColumnNamesFromFile(newColumnNamesFromFile);
populateNamesFromFileBoxes(newColumnNamesFromFile);
}
}
};
nextRowButton.addActionListener(nextRowButtonActionListener);
}
public void populateNamesFromFileBoxes(ArrayList<String> columnNamesFromFile) {
LocalConfig.getInstance().setKnockoutColumnIndex(-1);
LocalConfig.getInstance().setFluxValueColumnIndex(-1);
LocalConfig.getInstance().setReversibleColumnIndex(-1);
LocalConfig.getInstance().setLowerBoundColumnIndex(-1);
LocalConfig.getInstance().setUpperBoundColumnIndex(-1);
LocalConfig.getInstance().setBiologicalObjectiveColumnIndex(-1);
cbKnockout.removeAllItems();
cbFluxValue.removeAllItems();
cbReactionAbbreviation.removeAllItems();
cbReactionName.removeAllItems();
cbReactionEquation.removeAllItems();
cbReversible.removeAllItems();
cbLowerBound.removeAllItems();
cbUpperBound.removeAllItems();
cbObjective.removeAllItems();
// add all column names to from file comboboxes
for (int c = 0; c < columnNamesFromFile.size(); c++) {
cbKnockout.addItem(columnNamesFromFile.get(c));
cbFluxValue.addItem(columnNamesFromFile.get(c));
cbReactionAbbreviation.addItem(columnNamesFromFile.get(c));
cbReactionName.addItem(columnNamesFromFile.get(c));
cbReactionEquation.addItem(columnNamesFromFile.get(c));
cbReversible.addItem(columnNamesFromFile.get(c));
cbLowerBound.addItem(columnNamesFromFile.get(c));
cbUpperBound.addItem(columnNamesFromFile.get(c));
cbObjective.addItem(columnNamesFromFile.get(c));
}
cbKnockout.setSelectedIndex(-1);
cbFluxValue.setSelectedIndex(-1);
cbReversible.setSelectedIndex(-1);
cbLowerBound.setSelectedIndex(-1);
cbUpperBound.setSelectedIndex(-1);
cbObjective.setSelectedIndex(-1);
for (int c = 0; c < columnNamesFromFile.size(); c++) {
// filters to match column names from file to required column names in table
if ((columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.KNOCKOUT_COLUMN_FILTER[0])
== 0
|| (columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.KNOCKOUT_COLUMN_FILTER[1])
== 0) {
cbKnockout.setSelectedIndex(c);
LocalConfig.getInstance().setKnockoutColumnIndex(c);
} else if ((columnNamesFromFile.get(c).toLowerCase())
.contains(GraphicalInterfaceConstants.FLUX_VALUE_COLUMN_FILTER[0])) {
cbFluxValue.setSelectedIndex(c);
LocalConfig.getInstance().setFluxValueColumnIndex(c);
} else if ((columnNamesFromFile.get(c).toLowerCase())
.contains(GraphicalInterfaceConstants.REVERSIBLE_COLUMN_FILTER[0])) {
cbReversible.setSelectedIndex(c);
LocalConfig.getInstance().setReversibleColumnIndex(c);
} else if ((columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.LOWER_BOUND_FILTER[0])
== 0
|| (columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.LOWER_BOUND_FILTER[1])
== 0
|| (columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.LOWER_BOUND_FILTER[2])
== 0) {
cbLowerBound.setSelectedIndex(c);
LocalConfig.getInstance().setLowerBoundColumnIndex(c);
} else if ((columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.UPPER_BOUND_FILTER[0])
== 0
|| (columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.UPPER_BOUND_FILTER[1])
== 0
|| (columnNamesFromFile.get(c).toLowerCase())
.compareTo(GraphicalInterfaceConstants.UPPER_BOUND_FILTER[2])
== 0) {
cbUpperBound.setSelectedIndex(c);
LocalConfig.getInstance().setUpperBoundColumnIndex(c);
} else if ((columnNamesFromFile.get(c).toLowerCase())
.contains(GraphicalInterfaceConstants.BIOLOGICAL_OBJECTIVE_FILTER[0])) {
cbObjective.setSelectedIndex(c);
LocalConfig.getInstance().setBiologicalObjectiveColumnIndex(c);
}
}
// csv files written by TextReactionWriter will have KO and fluxValue as col 1 and 2
if ((columnNamesFromFile.get(0).toLowerCase())
.compareTo(GraphicalInterfaceConstants.KNOCKOUT_COLUMN_FILTER[0])
== 0
|| (columnNamesFromFile.get(0).toLowerCase())
.compareTo(GraphicalInterfaceConstants.KNOCKOUT_COLUMN_FILTER[1])
== 0) {
cbReactionAbbreviation.setSelectedIndex(2);
LocalConfig.getInstance().setReactionAbbreviationColumnIndex(2);
cbReactionName.setSelectedIndex(3);
LocalConfig.getInstance().setReactionNameColumnIndex(3);
cbReactionEquation.setSelectedIndex(4);
LocalConfig.getInstance().setReactionEquationColumnIndex(4);
} else {
// first two columns are recommended to be column 1 and 2: abbreviation (id), and name
cbReactionAbbreviation.setSelectedIndex(0);
LocalConfig.getInstance().setReactionAbbreviationColumnIndex(0);
cbReactionName.setSelectedIndex(1);
LocalConfig.getInstance().setReactionNameColumnIndex(1);
cbReactionEquation.setSelectedIndex(2);
LocalConfig.getInstance().setReactionEquationColumnIndex(2);
}
}