Examples with IntRange org.apache.commons.lang.math.IntRange used on opensource projects

Example 26 with IntRange

use of org.apache.commons.lang.math.IntRange in project incubator-systemml by apache.

the class DMLDebugger method runSystemMLDebugger.

/**
	 * Controls the communication between debugger CLI and DML runtime.  
	 */
@SuppressWarnings("deprecation")
public synchronized void runSystemMLDebugger() {
    debuggerUI.setOptions();
    debuggerUI.getDebuggerCLI();
    Thread runtime = new Thread(DMLRuntime);
    boolean isRuntimeInstruction = false;
    while (!quit) {
        try {
            //get debugger function from CLI
            getCommand();
            if (cmd != null) {
                isRuntimeInstruction = false;
                //check for help
                if (cmd.hasOption("h")) {
                    debuggerUI.getDebuggerCLI();
                } else //check for exit
                if (cmd.hasOption("q")) {
                    synchronized (DMLDebugger.class) {
                        quit = true;
                    }
                    runtime.stop();
                } else if (cmd.hasOption("r")) {
                    if (currEC != null) {
                        System.out.println("Runtime has already started. Try \"s\" to go to next line, or \"c\" to continue running your DML script.");
                    } else {
                        currEC = preEC;
                        runtime.start();
                        isRuntimeInstruction = true;
                    }
                } else if (cmd.hasOption("c")) {
                    if (currEC == null)
                        System.out.println("Runtime has not been started. Try \"r\" to start DML runtime execution.");
                    else if (!runtime.isAlive()) {
                        System.err.println("Invalid debug state.");
                    //System.out.println("Runtime terminated. Try \"-c\" to recompile followed by \"r\" to restart DML runtime execution.");
                    } else {
                        System.out.println("Resuming DML script execution ...");
                        preEC.getDebugState().setCommand(null);
                        runtime.resume();
                        isRuntimeInstruction = true;
                    }
                } else if (cmd.hasOption("si")) {
                    if (!runtime.isAlive()) {
                        currEC = preEC;
                        runtime.start();
                        isRuntimeInstruction = true;
                    }
                    preEC.getDebugState().setCommand("step_instruction");
                    runtime.resume();
                    isRuntimeInstruction = true;
                } else if (cmd.hasOption("s")) {
                    if (!runtime.isAlive()) {
                        currEC = preEC;
                        runtime.start();
                        isRuntimeInstruction = true;
                    }
                    preEC.getDebugState().setCommand("step_line");
                    runtime.resume();
                    isRuntimeInstruction = true;
                } else if (cmd.hasOption("b")) {
                    int lineNumber = dbFunctions.getValue(cmd.getOptionValues("b"), lines.length);
                    if (lineNumber > 0) {
                        if (DMLBreakpointManager.getBreakpoint(lineNumber) == null)
                            System.out.println("Sorry, a breakpoint cannot be inserted at line " + lineNumber + ". Please try a different line number.");
                        else {
                            if (DMLBreakpointManager.getBreakpoint(lineNumber).getBPInstructionStatus() != BPINSTRUCTION_STATUS.INVISIBLE) {
                                System.out.format("Breakpoint at line %d already exists.\n", lineNumber);
                            } else {
                                dbprog.accessBreakpoint(lineNumber, 0, BPINSTRUCTION_STATUS.ENABLED);
                            }
                        }
                    }
                } else if (cmd.hasOption("d")) {
                    int lineNumber = dbFunctions.getValue(cmd.getOptionValues("d"), lines.length);
                    if (lineNumber > 0 && DMLBreakpointManager.getBreakpoint(lineNumber) != null && DMLBreakpointManager.getBreakpoint(lineNumber).getBPInstructionStatus() != BPINSTRUCTION_STATUS.INVISIBLE) {
                        dbprog.accessBreakpoint(lineNumber, 1, BPINSTRUCTION_STATUS.INVISIBLE);
                    } else {
                        System.out.println("Sorry, a breakpoint cannot be deleted at line " + lineNumber + ". Please try a different line number.");
                    }
                } else if (cmd.hasOption("i")) {
                    String[] infoOptions = cmd.getOptionValues("i");
                    if (infoOptions == null || infoOptions.length == 0) {
                        System.err.println("The command \"info\" requires option. Try \"info break\" or \"info frame\".");
                    } else if (infoOptions[0].trim().equals("break")) {
                        dbFunctions.listBreakpoints(DMLBreakpointManager.getBreakpoints());
                    } else if (infoOptions[0].trim().equals("frame")) {
                        if (!runtime.isAlive())
                            System.err.println("Runtime has not been started. Try \"r\" or \"s\" to start DML runtime execution.");
                        else
                            dbFunctions.printCallStack(currEC.getDebugState().getCurrentFrame(), currEC.getDebugState().getCallStack());
                    } else {
                        System.err.println("Invalid option for command \"info\".  Try \"info break\" or \"info frame\".");
                    }
                } else if (cmd.hasOption("p")) {
                    String[] pOptions = cmd.getOptionValues("p");
                    if (pOptions == null || pOptions.length != 1) {
                        System.err.println("Incorrect options for command \"print\"");
                    } else {
                        String varName = pOptions[0].trim();
                        if (runtime.isAlive()) {
                            if (varName.contains("[")) {
                                // matrix with index: can be cell or column or row
                                try {
                                    String variableNameWithoutIndices = varName.split("\\[")[0].trim();
                                    String indexString = (varName.split("\\[")[1].trim()).split("\\]")[0].trim();
                                    String rowIndexStr = "";
                                    String colIndexStr = "";
                                    if (indexString.startsWith(",")) {
                                        colIndexStr = indexString.split(",")[1].trim();
                                    } else if (indexString.endsWith(",")) {
                                        rowIndexStr = indexString.split(",")[0].trim();
                                    } else {
                                        rowIndexStr = indexString.split(",")[0].trim();
                                        colIndexStr = indexString.split(",")[1].trim();
                                    }
                                    int rowIndex = -1;
                                    int colIndex = -1;
                                    if (!rowIndexStr.isEmpty()) {
                                        rowIndex = Integer.parseInt(rowIndexStr);
                                    }
                                    if (!colIndexStr.isEmpty()) {
                                        colIndex = Integer.parseInt(colIndexStr);
                                    }
                                    dbFunctions.print(currEC.getDebugState().getVariables(), variableNameWithoutIndices, "value", rowIndex, colIndex);
                                } catch (Exception indicesException) {
                                    System.err.println("Incorrect format for \"p\". If you are trying to print matrix variable M, you can use M[1,] or M[,1] or M[1,1] (without spaces).");
                                }
                            } else {
                                // Print entire matrix
                                dbFunctions.print(currEC.getDebugState().getVariables(), varName, "value", -1, -1);
                            }
                        } else
                            System.err.println("Runtime has not been started. Try \"r\" or \"s\" to start DML runtime execution.");
                    }
                } else if (cmd.hasOption("whatis")) {
                    String[] pOptions = cmd.getOptionValues("whatis");
                    if (pOptions == null || pOptions.length != 1) {
                        System.err.println("Incorrect options for command \"whatis\"");
                    } else {
                        String varName = pOptions[0].trim();
                        dbFunctions.print(currEC.getDebugState().getVariables(), varName, "metadata", -1, -1);
                    }
                } else if (cmd.hasOption("set")) {
                    String[] pOptions = cmd.getOptionValues("set");
                    if (pOptions == null || pOptions.length != 2) {
                        System.err.println("Incorrect options for command \"set\"");
                    } else {
                        try {
                            if (pOptions[0].contains("[")) {
                                String[] paramsToSetMatrix = new String[4];
                                paramsToSetMatrix[0] = pOptions[0].split("\\[")[0].trim();
                                String indexString = (pOptions[0].split("\\[")[1].trim()).split("\\]")[0].trim();
                                paramsToSetMatrix[1] = indexString.split(",")[0].trim();
                                paramsToSetMatrix[2] = indexString.split(",")[1].trim();
                                paramsToSetMatrix[3] = pOptions[1].trim();
                                dbFunctions.setMatrixCell(currEC.getDebugState().getVariables(), paramsToSetMatrix);
                            } else {
                                dbFunctions.setScalarValue(currEC.getDebugState().getVariables(), pOptions);
                            }
                        } catch (Exception exception1) {
                            System.out.println("Only scalar variable or a matrix cell available in current frame can be set in current version.");
                        }
                    }
                } else if (cmd.hasOption("l")) {
                    String[] pOptions = cmd.getOptionValues("l");
                    String[] argsForRange = new String[2];
                    int currentPC = 1;
                    if (runtime.isAlive()) {
                        currentPC = currEC.getDebugState().getPC().getLineNumber();
                    }
                    IntRange range = null;
                    if (pOptions == null) {
                        // Print first 10 lines
                        range = new IntRange(currentPC, Math.min(lines.length, currentPC + 10));
                    } else if (pOptions.length == 1 && pOptions[0].trim().toLowerCase().equals("all")) {
                        // Print entire program
                        range = new IntRange(1, lines.length);
                    } else if (pOptions.length == 2 && pOptions[0].trim().toLowerCase().equals("next")) {
                        int numLines = 10;
                        try {
                            numLines = Integer.parseInt(pOptions[1]);
                        } catch (Exception e1) {
                        }
                        argsForRange[0] = "" + currentPC;
                        argsForRange[1] = "" + Math.min(lines.length, numLines + currentPC);
                        range = dbFunctions.getRange(argsForRange, lines.length);
                    } else if (pOptions.length == 2 && pOptions[0].trim().toLowerCase().equals("prev")) {
                        int numLines = 10;
                        try {
                            numLines = Integer.parseInt(pOptions[1]);
                        } catch (Exception e1) {
                        }
                        argsForRange[0] = "" + Math.max(1, currentPC - numLines);
                        argsForRange[1] = "" + currentPC;
                        range = dbFunctions.getRange(argsForRange, lines.length);
                    }
                    if (range == null) {
                        System.err.println("Incorrect usage of command \"l\". Try \"l\" or \"l all\" or \"l next 5\" or \"l prev 5\".");
                    } else {
                        if (range.getMinimumInteger() > 0) {
                            dbFunctions.printLines(lines, range);
                        } else {
                            System.err.println("Sorry no lines that can be printed. Try \"l\" or \"l all\" or \"l next 5\" or \"l prev 5\".");
                        }
                    }
                } else if (cmd.hasOption("li")) {
                    String[] pOptions = cmd.getOptionValues("li");
                    String[] argsForRange = new String[2];
                    int currentPC = 1;
                    if (runtime.isAlive()) {
                        currentPC = currEC.getDebugState().getPC().getLineNumber();
                    }
                    IntRange range = null;
                    if (pOptions == null) {
                        // Print first 10 lines
                        range = new IntRange(currentPC, Math.min(lines.length, currentPC + 10));
                    } else if (pOptions.length == 1 && pOptions[0].trim().toLowerCase().equals("all")) {
                        // Print entire program
                        range = new IntRange(1, lines.length);
                    } else if (pOptions.length == 2 && pOptions[0].trim().toLowerCase().equals("next")) {
                        int numLines = 10;
                        try {
                            numLines = Integer.parseInt(pOptions[1]);
                        } catch (Exception e1) {
                        }
                        argsForRange[0] = "" + currentPC;
                        argsForRange[1] = "" + Math.min(lines.length, numLines + currentPC);
                        range = dbFunctions.getRange(argsForRange, lines.length);
                    } else if (pOptions.length == 2 && pOptions[0].trim().toLowerCase().equals("prev")) {
                        int numLines = 10;
                        try {
                            numLines = Integer.parseInt(pOptions[1]);
                        } catch (Exception e1) {
                        }
                        argsForRange[0] = "" + Math.max(1, currentPC - numLines);
                        argsForRange[1] = "" + currentPC;
                        range = dbFunctions.getRange(argsForRange, lines.length);
                    }
                    if (range == null) {
                        System.err.println("Incorrect usage of command \"li\". Try \"li\" or \"li all\" or \"li next 5\" or \"li prev 5\".");
                    } else {
                        if (range.getMinimumInteger() > 0) {
                            dbFunctions.printInstructions(lines, dbprog.getDMLInstMap(), range, false);
                        } else {
                            System.err.println("Sorry no lines that can be printed. Try \"li\" or \"li all\" or \"li next 5\" or \"li prev 5\".");
                        }
                    }
                } else if (cmd.hasOption("set_scalar")) {
                    if (!runtime.isAlive())
                        System.err.println("Runtime has not been started. Try \"r\" to start DML runtime execution.");
                    else
                        dbFunctions.setScalarValue(currEC.getDebugState().getVariables(), cmd.getOptionValues("set_scalar"));
                } else if (cmd.hasOption("m")) {
                    String varname = dbFunctions.getValue(cmd.getOptionValues("m"));
                    if (runtime.isAlive())
                        dbFunctions.printMatrixVariable(currEC.getDebugState().getVariables(), varname);
                    else
                        System.err.println("Runtime has not been started. Try \"r\" to start DML runtime execution.");
                } else if (cmd.hasOption("x")) {
                    if (!runtime.isAlive())
                        System.err.println("Runtime has not been started. Try \"r\" to start DML runtime execution.");
                    else {
                        dbFunctions.printMatrixCell(currEC.getDebugState().getVariables(), cmd.getOptionValues("x"));
                    }
                } else if (cmd.hasOption("set_cell")) {
                    if (!runtime.isAlive())
                        System.err.println("Runtime has not been started. Try \"r\" to start DML runtime execution.");
                    else {
                        dbFunctions.setMatrixCell(currEC.getDebugState().getVariables(), cmd.getOptionValues("set_cell"));
                    }
                } else {
                    System.err.println("Undefined command. Try \"help\".");
                }
                //block until runtime suspends execution or terminates 
                //while(runtime.isAlive() && !currEC.getProgram().isStopped()) {
                // To avoid race condition between submitting job and
                wait(300);
                //System.out.println(">> Before while");
                while (isRuntimeInstruction && !currEC.getDebugState().canAcceptNextCommand()) {
                    if (quit) {
                        break;
                    } else {
                        //wait
                        wait(300);
                    }
                }
            }
            wait(300);
        } catch (Exception e) {
            System.err.println("Error processing debugger command. Try \"help\".");
        }
    }
}

Example 27 with IntRange

use of org.apache.commons.lang.math.IntRange in project gatk by broadinstitute.

the class CreatePanelOfNormalsIntegrationTest method assertBasicPoNAssumptions.

private void assertBasicPoNAssumptions(final File ponFile, final File initialTargetsFileUsedToCreatePoN) {
    try (final HDF5File ponHDF5File = new HDF5File(ponFile)) {
        final HDF5PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        Assert.assertTrue(pon.getTargets().size() >= pon.getPanelTargets().size());
        Assert.assertTrue(pon.getRawTargets().size() > pon.getTargets().size());
        Assert.assertTrue(pon.getTargetNames().size() == pon.getTargets().size());
        Assert.assertTrue(pon.getPanelTargetNames().size() == pon.getPanelTargetNames().size());
        Assert.assertTrue(pon.getRawTargetNames().size() == pon.getRawTargetNames().size());
        if (initialTargetsFileUsedToCreatePoN != null) {
            final TargetCollection<Target> tc = TargetArgumentCollection.readTargetCollection(initialTargetsFileUsedToCreatePoN);
            Assert.assertEquals(pon.getRawTargets().size(), tc.targetCount());
            // Check that the raw targets are the same
            Assert.assertTrue(IntStream.of(new IntRange(0, pon.getRawTargets().size() - 1).toArray()).boxed().map(i -> pon.getRawTargets().get(i).equals(tc.target(i))).allMatch(t -> t));
        }
    }
}

Example 28 with IntRange

use of org.apache.commons.lang.math.IntRange in project gatk-protected by broadinstitute.

the class ConvertGSVariantsToSegments method calculateLog10CallQuality.

private double calculateLog10CallQuality(final double[] log10Probs, final CopyNumberTriState call) {
    final IntRange callCopyNumberRange;
    switch(call) {
        case NEUTRAL:
            callCopyNumberRange = new IntRange(neutralCopyNumber, neutralCopyNumber);
            break;
        case DELETION:
            callCopyNumberRange = new IntRange(0, neutralCopyNumber - 1);
            break;
        case DUPLICATION:
            callCopyNumberRange = new IntRange(neutralCopyNumber + 1, log10Probs.length - 1);
            break;
        default:
            throw new GATKException("unexpected call");
    }
    // We aggregate the probs of any copy number that that does not correspond
    final double log10OneMinusProbCall = MathUtils.approximateLog10SumLog10(MathUtils.log10SumLog10(log10Probs, 0, Math.min(callCopyNumberRange.getMinimumInteger(), log10Probs.length)), MathUtils.log10SumLog10(log10Probs, callCopyNumberRange.getMaximumInteger() + 1, log10Probs.length));
    final double log10ProbTotal = MathUtils.log10SumLog10(log10Probs);
    return log10OneMinusProbCall - log10ProbTotal;
}

Example 29 with IntRange

use of org.apache.commons.lang.math.IntRange in project gatk-protected by broadinstitute.

the class CreatePanelOfNormalsIntegrationTest method assertBasicPoNAssumptions.

private void assertBasicPoNAssumptions(final File ponFile, final File initialTargetsFileUsedToCreatePoN) {
    try (final HDF5File ponHDF5File = new HDF5File(ponFile)) {
        final HDF5PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        Assert.assertTrue(pon.getTargets().size() >= pon.getPanelTargets().size());
        Assert.assertTrue(pon.getRawTargets().size() > pon.getTargets().size());
        Assert.assertTrue(pon.getTargetNames().size() == pon.getTargets().size());
        Assert.assertTrue(pon.getPanelTargetNames().size() == pon.getPanelTargetNames().size());
        Assert.assertTrue(pon.getRawTargetNames().size() == pon.getRawTargetNames().size());
        if (initialTargetsFileUsedToCreatePoN != null) {
            final TargetCollection<Target> tc = TargetArgumentCollection.readTargetCollection(initialTargetsFileUsedToCreatePoN);
            Assert.assertEquals(pon.getRawTargets().size(), tc.targetCount());
            // Check that the raw targets are the same
            Assert.assertTrue(IntStream.of(new IntRange(0, pon.getRawTargets().size() - 1).toArray()).boxed().map(i -> pon.getRawTargets().get(i).equals(tc.target(i))).allMatch(t -> t));
        }
    }
}

Example 30 with IntRange

use of org.apache.commons.lang.math.IntRange in project gatk by broadinstitute.

the class ConvertGSVariantsToSegments method calculateLog10CallQuality.

private double calculateLog10CallQuality(final double[] log10Probs, final CopyNumberTriState call) {
    final IntRange callCopyNumberRange;
    switch(call) {
        case NEUTRAL:
            callCopyNumberRange = new IntRange(neutralCopyNumber, neutralCopyNumber);
            break;
        case DELETION:
            callCopyNumberRange = new IntRange(0, neutralCopyNumber - 1);
            break;
        case DUPLICATION:
            callCopyNumberRange = new IntRange(neutralCopyNumber + 1, log10Probs.length - 1);
            break;
        default:
            throw new GATKException("unexpected call");
    }
    // We aggregate the probs of any copy number that that does not correspond
    final double log10OneMinusProbCall = MathUtils.approximateLog10SumLog10(MathUtils.log10SumLog10(log10Probs, 0, Math.min(callCopyNumberRange.getMinimumInteger(), log10Probs.length)), MathUtils.log10SumLog10(log10Probs, callCopyNumberRange.getMaximumInteger() + 1, log10Probs.length));
    final double log10ProbTotal = MathUtils.log10SumLog10(log10Probs);
    return log10OneMinusProbCall - log10ProbTotal;
}