Examples with Function org.cytoscape.equations.Function used on opensource projects

Example 1 with Function

use of org.cytoscape.equations.Function in project cytoscape-impl by cytoscape.

the class EquationParserImpl method parseFunctionCall.

/**
 *   Implements func_call --> ident "(" ")" | ident "(" expr {"," expr} ")".
 */
private AbstractNode parseFunctionCall() {
    Token token = tokeniser.getToken();
    final int functionNameStartPos = tokeniser.getStartPos();
    if (token != Token.IDENTIFIER)
        throw new IllegalStateException(functionNameStartPos + ": function name expected.");
    final String originalName = tokeniser.getIdent();
    final String functionNameCandidate = originalName.toUpperCase();
    if (functionNameCandidate.equals("DEFINED"))
        return parseDefined();
    final Function func = nameToFunctionMap.get(functionNameCandidate);
    if (func == null) {
        if (tokeniser.getToken() == Token.OPEN_PAREN)
            throw new IllegalStateException(functionNameStartPos + ": call to unknown function " + originalName + "().");
        else
            throw new IllegalStateException(functionNameStartPos + ": unknown text \"" + originalName + "\", maybe you forgot to put quotes around this text?");
    }
    token = tokeniser.getToken();
    final int openParenPos = tokeniser.getStartPos();
    if (token != Token.OPEN_PAREN)
        throw new IllegalStateException(openParenPos + ": expected '(' after function name \"" + functionNameCandidate + "\".");
    // Parse the comma-separated argument list.
    final ArrayList<Class<?>> argTypes = new ArrayList<Class<?>>();
    ArrayList<AbstractNode> args = new ArrayList<AbstractNode>();
    int sourceLocation;
    for (; ; ) {
        token = tokeniser.getToken();
        sourceLocation = tokeniser.getStartPos();
        if (token == Token.CLOSE_PAREN)
            break;
        tokeniser.ungetToken(token);
        final AbstractNode exprNode = parseExpr();
        argTypes.add(exprNode.getType());
        args.add(exprNode);
        token = tokeniser.getToken();
        sourceLocation = tokeniser.getStartPos();
        if (token != Token.COMMA)
            break;
    }
    final Class<?> returnType = func.validateArgTypes(argTypes.toArray(new Class<?>[argTypes.size()]));
    if (returnType == null)
        throw new IllegalStateException((openParenPos + 1) + ": invalid number or type of arguments in call to " + functionNameCandidate + "().");
    if (token != Token.CLOSE_PAREN)
        throw new IllegalStateException(sourceLocation + ": expected the closing parenthesis of a call to " + functionNameCandidate + ".");
    AbstractNode[] nodeArray = new AbstractNode[args.size()];
    return new FuncCallNode(functionNameStartPos, func, returnType, args.toArray(nodeArray));
}

Example 2 with Function

use of org.cytoscape.equations.Function in project cytoscape-impl by cytoscape.

the class InterpreterImpl method call.

private void call() throws EmptyStackException, IllegalStateException, FunctionError {
    // 1. get the function
    final Object o = argumentStack.pop();
    if (!(o instanceof Function))
        throw new IllegalStateException("expected a column function after the CALL opcode but found \"" + o.getClass() + "\" instead.");
    final Function func = (Function) o;
    // 2. get and validate the argument count
    final int argCount;
    try {
        argCount = (Integer) argumentStack.pop();
    } catch (final Exception e) {
        throw new IllegalStateException("invalid argument count type following a CALL opcode.");
    }
    final int MIN_ARG_COUNT = 0;
    // This is an arbitrary limit and exists only to find bugs.
    final int MAX_ARG_COUNT = 100;
    // Should it prove to be too low we could easily make it much bigger.
    if (argCount < MIN_ARG_COUNT || argCount > MAX_ARG_COUNT)
        throw new IllegalStateException("invalid argument count type following a CALL opcode (range must be in [" + MIN_ARG_COUNT + ", " + MAX_ARG_COUNT + "]).");
    // 3. collect the actual arguments
    final Object[] args = new Object[argCount];
    for (int argNo = 0; argNo < argCount; ++argNo) args[argNo] = argumentStack.pop();
    // 4. now actually call the function
    argumentStack.push(func.evaluateFunction(args));
}

Example 3 with Function

use of org.cytoscape.equations.Function in project cytoscape-impl by cytoscape.

the class FormulaBuilderDialog method initComponents.

private void initComponents() {
    final JLabel fnIconLabel = new JLabel("f(x)");
    Font iconFont = null;
    try {
        iconFont = Font.createFont(Font.TRUETYPE_FONT, getClass().getResourceAsStream("/fonts/jsMath-cmti10.ttf"));
        iconFont = iconFont.deriveFont(36.0f);
        fnIconLabel.setFont(iconFont);
    } catch (Exception e) {
        throw new RuntimeException("Error loading font", e);
    }
    final JPanel buttonPanel = LookAndFeelUtil.createOkCancelPanel(getOkButton(), getCancelButton(), "Column_Data_Functions_and_Equations");
    final JPanel contents = new JPanel();
    final GroupLayout layout = new GroupLayout(contents);
    contents.setLayout(layout);
    layout.setAutoCreateContainerGaps(true);
    layout.setAutoCreateGaps(true);
    layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING, true).addComponent(getFunctionPanel(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addGroup(layout.createSequentialGroup().addComponent(fnIconLabel, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getFormulaTextField(), 380, 520, Short.MAX_VALUE)).addComponent(getApplyToPanel(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(buttonPanel, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE));
    layout.setVerticalGroup(layout.createSequentialGroup().addComponent(getFunctionPanel()).addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(fnIconLabel, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getFormulaTextField(), 60, 60, Short.MAX_VALUE)).addComponent(getApplyToPanel()).addComponent(buttonPanel));
    getContentPane().add(contents);
    LookAndFeelUtil.setDefaultOkCancelKeyStrokes(getRootPane(), getOkButton().getAction(), getCancelButton().getAction());
    getRootPane().setDefaultButton(getOkButton());
    pack();
    setResizable(false);
    if (((DefaultListModel<Function>) getFunctionList().getModel()).size() > 0)
        getFunctionList().setSelectedIndex(0);
}

Example 4 with Function

use of org.cytoscape.equations.Function in project cytoscape-impl by cytoscape.

the class FormulaBuilderDialog method getFunctionList.

private JList<Function> getFunctionList() {
    if (functionList == null) {
        DefaultListModel<Function> model = new DefaultListModel<>();
        functionList = new JList<>(model);
        functionList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
        functionList.addListSelectionListener(new ListSelectionListener() {

            @Override
            public void valueChanged(ListSelectionEvent e) {
                functionSelected();
            }
        });
        functionList.setCellRenderer(new DefaultListCellRenderer() {

            @Override
            public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                final Function fn = (Function) value;
                this.setText(fn.getName());
                this.setToolTipText(fn.getFunctionSummary());
                return this;
            }
        });
        final EquationParser parser = compiler.getParser();
        final List<Function> functions = new ArrayList<>(parser.getRegisteredFunctions());
        final Collator collator = Collator.getInstance(Locale.getDefault());
        Collections.sort(functions, new Comparator<Function>() {

            @Override
            public int compare(Function f1, Function f2) {
                return collator.compare(f1.getName(), f2.getName());
            }
        });
        final Class<?> requestedReturnType = getAttributeType(targetAttrName);
        int index = 0;
        for (final Function fn : functions) {
            if (returnTypeIsCompatible(requestedReturnType, fn.getReturnType()))
                model.add(index++, fn);
        }
    }
    return functionList;
}

Example 5 with Function

use of org.cytoscape.equations.Function in project cytoscape-impl by cytoscape.

the class InterpreterTest method testFunctionWithBadRuntimeReturnType.

@Test
public void testFunctionWithBadRuntimeReturnType() throws Exception {
    final Function badReturnFunction = new BadReturnFunction();
    if (// Avoid duplicate registration!
    parser.getFunction(badReturnFunction.getName()) == null)
        parser.registerFunctionInternal(badReturnFunction);
    final Map<String, Class<?>> attribNameToTypeMap = new HashMap<String, Class<?>>();
    assertTrue(compiler.compile("=BAD()", attribNameToTypeMap));
    final Map<String, IdentDescriptor> nameToDescriptorMap = new HashMap<String, IdentDescriptor>();
    try {
        interpreter.execute(compiler.getEquation(), nameToDescriptorMap);
    } catch (final IllegalStateException e) {
    // If we get here, everything is as expected and we let the test pass!
    }
}