Example usage for java.util ArrayList listIterator

List of usage examples for java.util ArrayList listIterator

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Introduction

In this page you can find the example usage for java.util ArrayList listIterator.

Prototype

public ListIterator<E> listIterator()

Source Link

Document

Returns a list iterator over the elements in this list (in proper sequence).

Usage

From source file:net.sourceforge.msscodefactory.v1_10.MSSBamPg8.MSSBamPg8DictionaryTable.java

public MSSBamDictionaryBuff[] readDerivedByDictTenantIdx(MSSBamAuthorization Authorization, long DictTenantId) {
    final String S_ProcName = "readDerivedByDictTenantIdx";
    if (!schema.isTransactionOpen()) {
        throw CFLib.getDefaultExceptionFactory().newUsageException(getClass(), S_ProcName,
                "Transaction not open");
    }/*w  ww  .  ja  va  2 s  .  c  om*/
    ArrayList<String> classCodeList = new ArrayList<String>();
    String classCode;
    try {
        Connection cnx = schema.getCnx();
        String sql = S_sqlSelectDictionaryDistinctClassCode + "WHERE " + "dict.DictTenantId = "
                + Long.toString(DictTenantId) + " ";
        Statement stmt = cnx.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        ResultSet resultSet = stmt.executeQuery(sql);
        while (resultSet.next()) {
            classCode = resultSet.getString(1);
            classCodeList.add(classCode);
        }
    } catch (SQLException e) {
        throw CFLib.getDefaultExceptionFactory().newDbException(getClass(), S_ProcName, e);
    }
    ArrayList<MSSBamDictionaryBuff> resultList = new ArrayList<MSSBamDictionaryBuff>();
    ListIterator<String> classCodeIter = classCodeList.listIterator();
    while (classCodeIter.hasNext()) {
        classCode = classCodeIter.next();
        if (classCode.equals("DICT")) {
            MSSBamDictionaryBuff[] subList = readBuffByDictTenantIdx(Authorization, DictTenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("RMD")) {
            MSSBamMSSBamBuff[] subList = schema.getTableMSSBam().readBuffByDictTenantIdx(Authorization,
                    DictTenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else {
            throw CFLib.getDefaultExceptionFactory().newRuntimeException(getClass(), S_ProcName,
                    "Did not expect ClassCode \"" + classCode + "\"");
        }
    }
    return (resultList.toArray(new MSSBamDictionaryBuff[0]));

}

From source file:net.sourceforge.msscodefactory.v1_10.MSSBamPg8.MSSBamPg8DictionaryTable.java

public MSSBamDictionaryBuff[] readDerivedByScopeIdx(MSSBamAuthorization Authorization, Long ScopeId) {
    final String S_ProcName = "readDerivedByScopeIdx";
    if (!schema.isTransactionOpen()) {
        throw CFLib.getDefaultExceptionFactory().newUsageException(getClass(), S_ProcName,
                "Transaction not open");
    }// w w  w. jav a2s .  c o  m
    ArrayList<String> classCodeList = new ArrayList<String>();
    String classCode;
    try {
        Connection cnx = schema.getCnx();
        String sql = S_sqlSelectDictionaryDistinctClassCode + "WHERE "
                + ((ScopeId == null) ? "anyo.ScopeId is null " : "anyo.ScopeId = " + ScopeId.toString() + " ");
        Statement stmt = cnx.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        ResultSet resultSet = stmt.executeQuery(sql);
        while (resultSet.next()) {
            classCode = resultSet.getString(1);
            classCodeList.add(classCode);
        }
    } catch (SQLException e) {
        throw CFLib.getDefaultExceptionFactory().newDbException(getClass(), S_ProcName, e);
    }
    ArrayList<MSSBamDictionaryBuff> resultList = new ArrayList<MSSBamDictionaryBuff>();
    ListIterator<String> classCodeIter = classCodeList.listIterator();
    while (classCodeIter.hasNext()) {
        classCode = classCodeIter.next();
        if (classCode.equals("DICT")) {
            MSSBamDictionaryBuff[] subList = readBuffByScopeIdx(Authorization, ScopeId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("RMD")) {
            MSSBamMSSBamBuff[] subList = schema.getTableMSSBam().readBuffByScopeIdx(Authorization, ScopeId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else {
            throw CFLib.getDefaultExceptionFactory().newRuntimeException(getClass(), S_ProcName,
                    "Did not expect ClassCode \"" + classCode + "\"");
        }
    }
    return (resultList.toArray(new MSSBamDictionaryBuff[0]));

}

From source file:net.sourceforge.msscodefactory.v1_10.MSSBamPg8.MSSBamPg8DictionaryTable.java

public MSSBamDictionaryBuff[] readDerivedByAuthorIdx(MSSBamAuthorization Authorization, Long AuthorId) {
    final String S_ProcName = "readDerivedByAuthorIdx";
    if (!schema.isTransactionOpen()) {
        throw CFLib.getDefaultExceptionFactory().newUsageException(getClass(), S_ProcName,
                "Transaction not open");
    }/* ww  w  .  j  a  v  a  2 s  .c o m*/
    ArrayList<String> classCodeList = new ArrayList<String>();
    String classCode;
    try {
        Connection cnx = schema.getCnx();
        String sql = S_sqlSelectDictionaryDistinctClassCode + "WHERE "
                + ((AuthorId == null) ? "anyo.AuthorId is null "
                        : "anyo.AuthorId = " + AuthorId.toString() + " ");
        Statement stmt = cnx.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        ResultSet resultSet = stmt.executeQuery(sql);
        while (resultSet.next()) {
            classCode = resultSet.getString(1);
            classCodeList.add(classCode);
        }
    } catch (SQLException e) {
        throw CFLib.getDefaultExceptionFactory().newDbException(getClass(), S_ProcName, e);
    }
    ArrayList<MSSBamDictionaryBuff> resultList = new ArrayList<MSSBamDictionaryBuff>();
    ListIterator<String> classCodeIter = classCodeList.listIterator();
    while (classCodeIter.hasNext()) {
        classCode = classCodeIter.next();
        if (classCode.equals("DICT")) {
            MSSBamDictionaryBuff[] subList = readBuffByAuthorIdx(Authorization, AuthorId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("RMD")) {
            MSSBamMSSBamBuff[] subList = schema.getTableMSSBam().readBuffByAuthorIdx(Authorization, AuthorId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else {
            throw CFLib.getDefaultExceptionFactory().newRuntimeException(getClass(), S_ProcName,
                    "Did not expect ClassCode \"" + classCode + "\"");
        }
    }
    return (resultList.toArray(new MSSBamDictionaryBuff[0]));

}

From source file:net.floodlightcontroller.devicemanager.internal.DeviceManagerImpl.java

@Override
public Command reconcileFlows(ArrayList<OFMatchReconcile> ofmRcList) {
    ListIterator<OFMatchReconcile> iter = ofmRcList.listIterator();
    while (iter.hasNext()) {
        OFMatchReconcile ofm = iter.next();

        // Remove the STOPPed flow.
        if (Command.STOP == reconcileFlow(ofm)) {
            iter.remove();//from w  w  w  .j a  v  a  2  s .c om
        }
    }

    if (ofmRcList.size() > 0) {
        return Command.CONTINUE;
    } else {
        return Command.STOP;
    }
}

From source file:net.sourceforge.msscodefactory.v1_10.MSSBamPg8.MSSBamPg8LegalEntityTable.java

public MSSBamLegalEntityBuff[] readDerivedByTenantIdx(MSSBamAuthorization Authorization, long TenantId) {
    final String S_ProcName = "readDerivedByTenantIdx";
    if (!schema.isTransactionOpen()) {
        throw CFLib.getDefaultExceptionFactory().newUsageException(getClass(), S_ProcName,
                "Transaction not open");
    }/* w w  w. j ava 2s  .c om*/
    ArrayList<String> classCodeList = new ArrayList<String>();
    String classCode;
    try {
        Connection cnx = schema.getCnx();
        String sql = S_sqlSelectLegalEntityDistinctClassCode + "WHERE " + "anyo.TenantId = "
                + Long.toString(TenantId) + " ";
        Statement stmt = cnx.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        ResultSet resultSet = stmt.executeQuery(sql);
        while (resultSet.next()) {
            classCode = resultSet.getString(1);
            classCodeList.add(classCode);
        }
    } catch (SQLException e) {
        throw CFLib.getDefaultExceptionFactory().newDbException(getClass(), S_ProcName, e);
    }
    ArrayList<MSSBamLegalEntityBuff> resultList = new ArrayList<MSSBamLegalEntityBuff>();
    ListIterator<String> classCodeIter = classCodeList.listIterator();
    while (classCodeIter.hasNext()) {
        classCode = classCodeIter.next();
        if (classCode.equals("LENT")) {
            MSSBamLegalEntityBuff[] subList = readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("COM")) {
            MSSBamCompanyBuff[] subList = schema.getTableCompany().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("USR")) {
            MSSBamUserBuff[] subList = schema.getTableUser().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else {
            throw CFLib.getDefaultExceptionFactory().newRuntimeException(getClass(), S_ProcName,
                    "Did not expect ClassCode \"" + classCode + "\"");
        }
    }
    return (resultList.toArray(new MSSBamLegalEntityBuff[0]));

}

From source file:com.aol.framework.helper.report.CustomizedReporter.java

synchronized private void generateModuleWiseTestReport(String testName, List<ISuite> suites, String newFileName,
        String passedModule, String nodeIp) throws IOException {
    final PrintWriter pw = TestHelper.createFileWriter(TestHelper.customReportDir + newFileName);

    startHtmlPage(pw);/*from  www . jav  a 2 s . c  om*/

    pw.println("<button class=\"sexybutton sexysimple sexylarge sexyblack\" onClick=\"location.href='"
            + passedModule + "-Overall-customized-report.html"
            + "'\"><span class=\"prev\">Back to Modulewise Test Execution Summary</span></button>");

    pw.println(
            "<br/><br/><br/><fieldset><legend><b>Modulewise Execution Details</b></legend><br/><table class=\"details\" cellspacing=0 cellpadding=0><tr><td><b>Test Name: </b></td><td>"
                    + testName + "</td></tr>");

    pw.println("<tr><td><b>Node IP: </b></td><td>" + nodeIp + "</td></tr></table></fieldset><br/><br/>");
    pw.println("<table id=\"myTable\" width=\"100%\" cellspacing=0 cellpadding=0 class=\"tablesorter\">");
    pw.println("<thead><tr><th>Module Name</th><th># Passed</th>" + "<th># Failed</th><th># Warning</th>"
            + "<th># Skipped</th><th># Total</th><th>Success Rate</th></tr></thead>");

    HashMap<String, ArrayList<ITestNGMethod>> moduleMap = new HashMap<String, ArrayList<ITestNGMethod>>();

    ITestContext overview = null;

    for (ISuite suite : suites) {
        Map<String, ISuiteResult> tests = suite.getResults();
        for (ISuiteResult r : tests.values()) {
            overview = r.getTestContext();
            if ((overview.getName()).equalsIgnoreCase(testName)) {
                ITestNGMethod[] testngMethods = overview.getAllTestMethods();

                ArrayList<HashMap<String, ITestNGMethod>> moduleMethods = new ArrayList<HashMap<String, ITestNGMethod>>();

                for (ITestNGMethod testngMethod : testngMethods) {
                    String[] groups = testngMethod.getGroups();
                    for (String group : groups) {
                        for (String module : TestHelper.MODULES) {
                            if (group.equalsIgnoreCase(module)) {
                                HashMap<String, ITestNGMethod> tempMap = new HashMap<String, ITestNGMethod>();
                                tempMap.put(module, testngMethod);
                                moduleMethods.add(tempMap);
                            }
                        }
                    }
                }

                for (String module : TestHelper.MODULES) {
                    ArrayList<ITestNGMethod> moduleTestMethods = new ArrayList<ITestNGMethod>();

                    Iterator<HashMap<String, ITestNGMethod>> it = moduleMethods.iterator();

                    while (it.hasNext()) {
                        String moduleName = "";
                        ITestNGMethod testMethod = null;

                        HashMap<String, ITestNGMethod> moduleWithTestMethod = it.next();
                        if (moduleWithTestMethod.containsKey(module)) {
                            moduleName = module;
                            testMethod = moduleWithTestMethod.get(module);
                        }

                        if (module.equalsIgnoreCase(moduleName)) {
                            moduleTestMethods.add(testMethod);
                        }
                    }

                    moduleMap.put(module, moduleTestMethods);
                }
            }
        }
    }

    Set<String> keySet = moduleMap.keySet();
    Iterator<String> it = keySet.iterator();

    for (ISuite suite : suites) {
        Map<String, ISuiteResult> tests = suite.getResults();
        for (ISuiteResult r : tests.values()) {
            overview = r.getTestContext();
            if ((overview.getName()).equalsIgnoreCase(testName)) {
                while (it.hasNext()) {
                    String moduleName = it.next();

                    int totalPassedMethods = 0;
                    int totalFailedMethods = 0;
                    int totalAutomationErrors = 0;
                    int totalSkippedMethods = 0;
                    int totalSkippedConfigurations = 0;
                    int totalFailedConfigurations = 0;

                    ArrayList<ITestNGMethod> values = moduleMap.get(moduleName);
                    ListIterator<ITestNGMethod> it2 = values.listIterator();

                    while (it2.hasNext()) {
                        ITestNGMethod method = it2.next();

                        int failedMethods = overview.getFailedTests().getResults(method).size();
                        int failedAutomationErrors = overview.getFailedButWithinSuccessPercentageTests()
                                .getResults(method).size();
                        int passedMethods = overview.getPassedTests().getResults(method).size();
                        int skippedMethods = overview.getSkippedTests().getResults(method).size();
                        int failedConfiguration = overview.getFailedConfigurations().getResults(method).size();
                        int skippedConfiguration = overview.getSkippedConfigurations().getResults(method)
                                .size();

                        totalPassedMethods += passedMethods;
                        totalFailedMethods += failedMethods;
                        totalAutomationErrors += failedAutomationErrors;
                        totalSkippedMethods += skippedMethods;
                        totalFailedConfigurations += failedConfiguration;
                        totalSkippedConfigurations += skippedConfiguration;

                    }

                    if (values.size() > 0) {
                        String fileName = testName + "-" + moduleName + "-customized-report.html";
                        try {
                            generateModuleTestMethodSummary(testName, moduleName, suites, fileName, values,
                                    nodeIp);
                        } catch (IOException e) {
                            e.printStackTrace();
                        }

                        int totalMethods = totalPassedMethods + totalFailedMethods + totalAutomationErrors
                                + totalSkippedMethods;

                        NumberFormat nf = NumberFormat.getInstance();
                        nf.setMaximumFractionDigits(2);
                        nf.setGroupingUsed(false);

                        String passPercentage = getPercentage(nf, totalPassedMethods, totalMethods);

                        generateModulesRow(pw, fileName, moduleName, totalPassedMethods, totalFailedMethods,
                                totalAutomationErrors, totalSkippedMethods, totalSkippedConfigurations,
                                totalFailedConfigurations, totalMethods, passPercentage);
                    }
                }
                break;
            }
        }
    }

    pw.println("</table>");
    endHtmlPage(pw);
    pw.flush();
    pw.close();
}

From source file:net.sourceforge.msscodefactory.v1_10.MSSBamPg8.MSSBamPg8BaseDomainTable.java

public MSSBamBaseDomainBuff[] readDerivedByTenantIdx(MSSBamAuthorization Authorization, long TenantId) {
    final String S_ProcName = "readDerivedByTenantIdx";
    if (!schema.isTransactionOpen()) {
        throw CFLib.getDefaultExceptionFactory().newUsageException(getClass(), S_ProcName,
                "Transaction not open");
    }/*from w ww  .  ja  v a 2s .  co  m*/
    ArrayList<String> classCodeList = new ArrayList<String>();
    String classCode;
    try {
        Connection cnx = schema.getCnx();
        String sql = S_sqlSelectBaseDomainDistinctClassCode + "WHERE " + "anyo.TenantId = "
                + Long.toString(TenantId) + " ";
        Statement stmt = cnx.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        ResultSet resultSet = stmt.executeQuery(sql);
        while (resultSet.next()) {
            classCode = resultSet.getString(1);
            classCodeList.add(classCode);
        }
    } catch (SQLException e) {
        throw CFLib.getDefaultExceptionFactory().newDbException(getClass(), S_ProcName, e);
    }
    ArrayList<MSSBamBaseDomainBuff> resultList = new ArrayList<MSSBamBaseDomainBuff>();
    ListIterator<String> classCodeIter = classCodeList.listIterator();
    while (classCodeIter.hasNext()) {
        classCode = classCodeIter.next();
        if (classCode.equals("BDM")) {
            MSSBamBaseDomainBuff[] subList = readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("DOM")) {
            MSSBamDomainBuff[] subList = schema.getTableDomain().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("LENT")) {
            MSSBamLegalEntityBuff[] subList = schema.getTableLegalEntity().readBuffByTenantIdx(Authorization,
                    TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("COM")) {
            MSSBamCompanyBuff[] subList = schema.getTableCompany().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("USR")) {
            MSSBamUserBuff[] subList = schema.getTableUser().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("PRJ")) {
            MSSBamProjectBuff[] subList = schema.getTableProject().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("VER")) {
            MSSBamVersionBuff[] subList = schema.getTableVersion().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("MJV")) {
            MSSBamMajorVersionBuff[] subList = schema.getTableMajorVersion().readBuffByTenantIdx(Authorization,
                    TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("MNV")) {
            MSSBamMinorVersionBuff[] subList = schema.getTableMinorVersion().readBuffByTenantIdx(Authorization,
                    TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("TLD")) {
            MSSBamTLDBuff[] subList = schema.getTableTLD().readBuffByTenantIdx(Authorization, TenantId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else {
            throw CFLib.getDefaultExceptionFactory().newRuntimeException(getClass(), S_ProcName,
                    "Did not expect ClassCode \"" + classCode + "\"");
        }
    }
    return (resultList.toArray(new MSSBamBaseDomainBuff[0]));

}

From source file:net.sourceforge.msscodefactory.v1_10.MSSBamPg8.MSSBamPg8LegalEntityTable.java

public MSSBamLegalEntityBuff[] readDerivedByScopeIdx(MSSBamAuthorization Authorization, Long ScopeId) {
    final String S_ProcName = "readDerivedByScopeIdx";
    if (!schema.isTransactionOpen()) {
        throw CFLib.getDefaultExceptionFactory().newUsageException(getClass(), S_ProcName,
                "Transaction not open");
    }//w ww  . j  a v a2  s  .  c o  m
    ArrayList<String> classCodeList = new ArrayList<String>();
    String classCode;
    try {
        Connection cnx = schema.getCnx();
        String sql = S_sqlSelectLegalEntityDistinctClassCode + "WHERE "
                + ((ScopeId == null) ? "anyo.ScopeId is null " : "anyo.ScopeId = " + ScopeId.toString() + " ");
        Statement stmt = cnx.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        ResultSet resultSet = stmt.executeQuery(sql);
        while (resultSet.next()) {
            classCode = resultSet.getString(1);
            classCodeList.add(classCode);
        }
    } catch (SQLException e) {
        throw CFLib.getDefaultExceptionFactory().newDbException(getClass(), S_ProcName, e);
    }
    ArrayList<MSSBamLegalEntityBuff> resultList = new ArrayList<MSSBamLegalEntityBuff>();
    ListIterator<String> classCodeIter = classCodeList.listIterator();
    while (classCodeIter.hasNext()) {
        classCode = classCodeIter.next();
        if (classCode.equals("LENT")) {
            MSSBamLegalEntityBuff[] subList = readBuffByScopeIdx(Authorization, ScopeId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("COM")) {
            MSSBamCompanyBuff[] subList = schema.getTableCompany().readBuffByScopeIdx(Authorization, ScopeId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else if (classCode.equals("USR")) {
            MSSBamUserBuff[] subList = schema.getTableUser().readBuffByScopeIdx(Authorization, ScopeId);
            for (int subListIdx = 0; subListIdx < subList.length; subListIdx++) {
                resultList.add(subList[subListIdx]);
            }
        } else {
            throw CFLib.getDefaultExceptionFactory().newRuntimeException(getClass(), S_ProcName,
                    "Did not expect ClassCode \"" + classCode + "\"");
        }
    }
    return (resultList.toArray(new MSSBamLegalEntityBuff[0]));

}

From source file:ffx.potential.MolecularAssembly.java

/**
 * <p>/*  w  ww.ja va2s  .c o m*/
 * sidePolymerCOM</p>
 */
public void sidePolymerCOM() {
    ArrayList residues = getResidueList();
    Residue r;

    ListIterator li;

    for (li = residues.listIterator(); li.hasNext();) {
        r = (Residue) li.next();
        r.logSideChainCOM();
    }
}

From source file:ipnat.skel.Strahler.java

/**
 * This method is called when the plugin is loaded.
 *
 * @param arg//from www. j  a va2 s . c  o m
 *            the arguments as specified in {@code plugins.config}
 *
 */
@Override
public void run(final String arg) {

    // Retrieve analysis image and its ROI
    srcImp = WindowManager.getCurrentImage();
    if (!validRequirements(srcImp))
        return;

    title = srcImp.getTitle();
    rootRoi = srcImp.getRoi();
    validRootRoi = (rootRoi != null && rootRoi.getType() == Roi.RECTANGLE);

    // TODO: 3D Roots are special. We need to:
    // 1) Check if ROI is associated with all slices or just one
    // 2) Ignore counts above/below the ROI, as needed
    // 3) Extend ip operations to stack
    if (srcImp.getNSlices() > 1) {
        final String warning = "3D images are currently supported with the following limitations:\n"
                + "    - 'Root-protecting' ROIs are not yet supported\n"
                + "    - Lengths are estimated from Z-projections\n \n"
                + "These issues will be addressed in future releases.";
        if (IJ.macroRunning())
            IJ.log(warning);
        else
            IJ.showMessage("Warning", warning);
        validRootRoi = false;
    }

    // Retrieve grayscale image for intensity-based pruning of skel. loops
    if (!getSettings())
        return;

    // Work on a skeletonized copy since we'll be modifing the image
    if (rootRoi != null)
        srcImp.killRoi();
    final ImagePlus imp = srcImp.duplicate();
    if (rootRoi != null)
        srcImp.setRoi(rootRoi);
    ip = imp.getProcessor();
    skeletonizeWithoutHermits(imp);

    // Initialize ResultsTable: main and detailed info
    final ResultsTable rt = Utils.getTable(STRAHLER_TABLE);
    final ResultsTable logrt = Utils.getTable(VERBOSE_TABLE);

    // Analyze root
    ImagePlus rootImp;
    ImageProcessor rootIp = null;
    SkeletonResult rootResult = null;
    ArrayList<Point> rootEndpointsList = null;
    int nRootEndpoints = 0, nRootJunctions = 0;

    if (validRootRoi && verbose) {

        // Duplicate entire canvas. Ignore tree(s) outside ROI
        rootImp = imp.duplicate();
        rootIp = rootImp.getProcessor();
        rootIp.setValue(0.0);
        rootIp.fillOutside(rootRoi);

        // Get root properties
        final AnalyzeSkeleton_ root = new AnalyzeSkeleton_();
        root.setup("", rootImp);
        rootResult = root.run(pruneChoice, false, false, grayscaleImp, true, false);
        rootImp.flush();

        // We assume ROI contains only end-point branches, slab voxels and
        // no junction points. We'll thus remove end-points at ROI
        // boundaries
        nRootJunctions = sum(rootResult.getJunctions());
        rootEndpointsList = rootResult.getListOfEndPoints();
        final ListIterator<Point> it = rootEndpointsList.listIterator();
        final Rectangle r = rootRoi.getBounds();
        while (it.hasNext()) {
            final Point p = it.next();
            if (p.x == r.x || p.y == r.y || p.x == (int) (r.x + r.getWidth() - 1)
                    || p.y == (int) (r.y + r.getHeight() - 1))
                it.remove();
        }
        rootResult.setListOfEndPoints(rootEndpointsList);
        nRootEndpoints = rootEndpointsList.size();

    }

    // Initialize display images. Use Z-projections to populate
    // iteration stack when dealing with 3D skeletons
    final int nSlices = imp.getNSlices();
    ZProjector zp = null;

    final ImageStack iterationStack = new ImageStack(imp.getWidth(), imp.getHeight());
    if (nSlices > 1) {
        zp = new ZProjector(imp);
        zp.setMethod(ZProjector.MAX_METHOD);
        zp.setStartSlice(1);
        zp.setStopSlice(nSlices);
    }

    // Initialize AnalyzeSkeleton_
    final AnalyzeSkeleton_ as = new AnalyzeSkeleton_();
    as.setup("", imp);

    // Perform the iterative pruning
    int order = 1, nEndpoints = 0, nJunctions = 0, nJunctions2 = 0;
    ArrayList<Point> endpointsList = null, junctionsList = null;
    String errorMsg = "";

    do {

        IJ.showStatus("Retrieving measurements for order " + order + "...");
        IJ.showProgress(order, getMaxOrder());

        // (Re)skeletonize image
        if (order > 1)
            skeletonizeWithoutHermits(imp);

        // Get properties of loop-resolved tree(s)
        final SkeletonResult sr = as.run(pruneChoice, false, false, grayscaleImp, true, false);
        nEndpoints = sum(sr.getEndPoints());
        nJunctions = sum(sr.getJunctions());

        if (order == 1) {
            // Remember initial properties
            endpointsList = sr.getListOfEndPoints();
            junctionsList = sr.getListOfJunctionVoxels();

            // Do not include root in 1st order calculations
            nEndpoints -= nRootEndpoints;
            nJunctions -= nRootJunctions;
        }

        // Is it worth proceeding?
        if (nEndpoints == 0 || nJunctions2 == nJunctions) {
            errorMsg = "Error! Iteration " + order + " aborted: ";
            errorMsg += (nEndpoints == 0) ? "No end-poins found" : "Unsolved loop(s) detected";
            break;
        }

        // Add current tree(s) to debug animation
        ImageProcessor ipd;
        if (nSlices > 1) {
            zp.doProjection();
            ipd = zp.getProjection().getProcessor();
        } else {
            ipd = ip.duplicate();
        }
        iterationStack.addSlice("Order " + IJ.pad(order, 2), ipd);

        // Report properties of pruned structures
        if (verbose) {
            logrt.incrementCounter();
            logrt.addValue("Image", title);
            logrt.addValue("Structure", "Skel. at iteration " + Integer.toString(order));
            logrt.addValue("Notes", errorMsg);
            logrt.addValue("# Trees", sr.getNumOfTrees());
            logrt.addValue("# Branches", sum(sr.getBranches()));
            logrt.addValue("# End-points", nEndpoints);
            logrt.addValue("# Junctions", nJunctions);
            logrt.addValue("# Triple points", sum(sr.getTriples()));
            logrt.addValue("# Quadruple points", sum(sr.getQuadruples()));
            logrt.addValue("Average branch length", average(sr.getAverageBranchLength()));
        }

        // Remember main results
        nJunctions2 = nJunctions;

        // Eliminate end-points
        as.run(pruneChoice, true, false, grayscaleImp, true, false, rootRoi);

    } while (order++ <= getMaxOrder() && nJunctions > 0);

    // Set counter to the de facto order
    order -= 1;

    // Append root properties to log table
    if (validRootRoi && verbose) {

        // Check if ROI contains unexpected structures
        final String msg = (nRootJunctions > 0) ? "Warning: ROI contains ramified root(s)"
                : "Root-branches inferred from ROI";
        logrt.incrementCounter();
        logrt.addValue("Image", title);
        logrt.addValue("Structure", "Root");
        logrt.addValue("Notes", msg);
        logrt.addValue("# Trees", rootResult.getNumOfTrees());
        logrt.addValue("# Branches", sum(rootResult.getBranches()));
        logrt.addValue("# End-points", nRootEndpoints);
        logrt.addValue("# Junctions", nRootJunctions);
        logrt.addValue("# Triple points", sum(rootResult.getTriples()));
        logrt.addValue("# Quadruple points", sum(rootResult.getQuadruples()));
        logrt.addValue("Average branch length", average(rootResult.getAverageBranchLength()));

    }

    // Safety check
    if (iterationStack == null || iterationStack.getSize() < 1) {
        error("Enable \"detailed\" mode and check " + VERBOSE_TABLE + " for details.");
        return;
    }

    // Create iteration stack
    final Calibration cal = srcImp.getCalibration();
    final ImagePlus imp2 = new ImagePlus("StrahlerIteration_" + title, iterationStack);
    imp2.setCalibration(cal);
    if (outIS) {
        if (validRootRoi) {
            iterationStack.addSlice("Root", rootIp);
            paintPoints(iterationStack, rootEndpointsList, 255, "Root end-points");
            imp2.setRoi(rootRoi);
        }
        paintPoints(iterationStack, endpointsList, 255, "End-points");
        paintPoints(iterationStack, junctionsList, 255, "Junction-points");
    }

    // Generate Strahler mask
    zp = new ZProjector(imp2);
    zp.setMethod(ZProjector.SUM_METHOD);
    zp.setStartSlice(1);
    zp.setStopSlice(order);
    zp.doProjection();
    final ImageProcessor ip3 = zp.getProjection().getProcessor().convertToShortProcessor(false);
    clearPoints(ip3, junctionsList); // disconnect branches
    ip3.multiply(1 / 255.0); // map intensities to Strahler orders
    final ImagePlus imp3 = new ImagePlus("StrahlerMask_" + title, ip3);
    imp3.setCalibration(cal);

    // Measure segmented orders
    double prevNbranches = Double.NaN;
    for (int i = 1; i <= order; i++) {

        // Segment branches by order
        final ImagePlus maskImp = imp3.duplicate(); // Calibration is
        // retained
        IJ.setThreshold(maskImp, i, i);
        IJ.run(maskImp, "Convert to Mask", "");

        // Analyze segmented order
        final AnalyzeSkeleton_ maskAs = new AnalyzeSkeleton_();
        maskAs.setup("", maskImp);
        final SkeletonResult maskSr = maskAs.run(pruneChoice, false, false, grayscaleImp, true, false);
        maskImp.flush();

        // Since all branches are disconnected at this stage, the n. of
        // branches is
        // the same as the # the trees unless zero-branches trees exist,
        // i.e., trees
        // with no slab voxels (defined by just an end-point). We will
        // ignore those
        // trees if the user requested it
        final int nBranches = (erodeIsolatedPixels) ? sum(maskSr.getBranches()) : maskSr.getNumOfTrees();

        // Log measurements
        rt.incrementCounter();
        rt.addValue("Image", title);
        rt.addValue("Strahler Order", i);
        rt.addValue("# Branches", nBranches);
        rt.addValue("Ramification ratios", prevNbranches / nBranches);
        rt.addValue("Average branch length", average(maskSr.getAverageBranchLength()));
        rt.addValue("Unit", cal.getUnit());
        String noteMsg = "";
        if (i == 1) {
            noteMsg = (erodeIsolatedPixels) ? "Ignoring" : "Including";
            noteMsg += " single-point arbors...";
        }
        rt.addValue("Notes", noteMsg);

        // Remember results for previous order
        prevNbranches = nBranches;

    }

    // Append any errors to last row
    rt.addValue("Notes", errorMsg);

    // Display outputs
    if (!tabular) {
        if (outIS)
            imp2.show();
        ip3.setMinAndMax(0, order);
        ColorMaps.applyMagmaColorMap(imp3, 200, false);
        if (validRootRoi)
            imp3.setRoi(rootRoi);
        imp3.show();
        addCalibrationBar(imp3, Math.min(order, 5), "Black");
    }
    if (verbose)
        logrt.show(VERBOSE_TABLE);
    rt.show(STRAHLER_TABLE);

    IJ.showProgress(0, 0);
    IJ.showTime(imp, imp.getStartTime(), "Strahler Analysis concluded... ");
    imp.flush();

}