if (c > 128)
            return 0;
        switch (c) {
            case '\u002d': // hyphen
            case '\u2012': // figure dash << this branch is unreachable as c > 128 was excluded before
            case '\u2013': // en-dash << same 
            case '\u2014': // em-dash << same
            case '\u2212': // minus << same
                return '-'; // 002d
            default:
                return c;
        }

        if (oxNum == 0) {
            if (hybrid.equals("sp3")) { ... 
            } else if (hybrid.equals("sp2")) return 47;
        } else if (oxNum == 1 && hybrid.equals("sp3"))
            return 47;
        else if ((oxNum == 2 && hybrid.equals("sp3")) || (oxNum == 1 && hybrid.equals("sp2"))
                || (oxNum == 0 && hybrid.equals("sp"))) // << oxNum == 0 && hybrid.equals("sp") is always false as oxNum == 0 was processed above. If this condition is true, 0 will be returned instead
            return 48;
        ...

        Point3d points[] = new Point3d[0];
        if (nwanted == 1) {
            points = new Point3d[1];
            points[0] = new Point3d(aPoint);
            points[0].add(new Vector3d(length, 0.0, 0.0));
        } else if (nwanted == 2) {
            points[0] = new Point3d(aPoint); // << here points is zero-length array, so ArrayIndexOutOfBoundsException will occur. Probably points = new Point3d[2] is missing before this line
            points[0].add(new Vector3d(length, 0.0, 0.0));
            points[1] = new Point3d(aPoint);
            points[1].add(new Vector3d(-length, 0.0, 0.0));

        if (!(params[0] instanceof Integer)) {
            throw new CDKException("The parameter must be of type Integer");
        }
        if (params.length == 0) return; // << cannot be true, because params[0] was checked before. If params is empty array, we would have AIOOBE thrown on the previous condition if(!(params[0] instanceof Integer))
        maxIterations = (Integer) params[0];

        } else if ((atom.getFormalCharge() != CDKConstants.UNSET && atom.getFormalCharge() == -1)) {
            IAtomType type = getAtomType("Br.minus");
            if (isAcceptable(atom, atomContainer, type)) return type;
        } else if (atom.getFormalCharge() == 1) { // << CDKConstants.UNSET is null. If it's really possible to see null here, then you will have NPE during auto-unboxing in this comparison. If it's impossible, then previous "!= CDKConstants.UNSET" check is redundant

if (rStereo != 4 || pStereo != 4 || rStereo != 3 || pStereo != 3) { // << cannot be false as any number is either not 4 or not 3. Likely && was intended instead of ||

if (line != null) line = line.trim();
while (!line.equals(";")) { // either null-check is redundant or (more likely) NPE is possible here

while (!line.startsWith("frame:") && input.ready() && line != null) { // << line null-check after line.startsWith. Either null-check is redundant or NPE is possible here

    public IMatrix(Matrix m) {
        rows = m.rows;
        columns = m.columns;
        int i, j;
        for (i = 0; i < rows; i++)
            for (j = 0; j < columns; j++) {
                realmatrix[i][j] = m.matrix[i][j]; // << this constructor does not allocate realmatrix and imagmatrix arrays, so NPE will occur when this constructor is used
                imagmatrix[i][j] = 0d;
            }
    }

        int countSpace = 0;
        boolean foundDigit = false;
        for (int i = 0; i < strlen; i++) {
            if (!foundDigit) if (Character.isLetter(str.charAt(i))) foundDigit = true;

            if (foundDigit) {
                if (Character.isWhitespace(str.charAt(i))) {
                    if (countSpace == 0) { // << countSpace is never modified, so it's always 0 and condition is always true. Probably it's a mistake or unfinished code
                        foundSpace = true;

if (getFirstMapping() != null || !getFirstMapping().isEmpty()) { // << the second part is executed only if getFirstMapping() returned null, in which case NPE is inevitable. Likely && was intended instead of ||

List<Integer> posNumList = new ArrayList<Integer>(size); // size does not set list size, it sets the initial size of backing array

for (int i = 0; i < posNumList.size(); i++) { // << this loop is never visited as posNumList is empty
    posNumList.add(i, 0);
}

        if (lineNumber == 4 && line.length() > 7 && (line.indexOf("2000") == -1) && // MDL Mol V2000 format
                (line.indexOf("3000") == -1)) // MDL Mol V3000 format
        {
            // possibly a MDL mol file
            try {
                String atomCountString = line.substring(0, 3).trim();
                String bondCountString = line.substring(3, 6).trim();
                Integer.valueOf(atomCountString);
                Integer.valueOf(bondCountString);
                if (line.length() > 6) { // << always true as line.length() > 7 was already checked before; probably just redundant, but could be a typo

                while (last >= 0) {
                    if (atomprops[last] != 0)
                        break;
                    last--;
                }
                // matches BIOVIA syntax
                if (last >= 2 && last < atomprops.length) // << last < atomprops.length is always true as before exiting the previous loop we accessed atomprops[last]. Seems just redundant condition, but probably a mistake
                    last = 5;

addAtom("Cl", currentMolecule.isEmpty() ? null : currentMolecule.isEmpty() ? null : currentMolecule.getAtom(0), IBond.Order.SINGLE, 0); // << currentMolecule.isEmpty() is checked twice. Probably just redundant check, but something else could be intended

if (currentMolecule instanceof IAtomContainer) { // << always true except currentMolecule == null case as currentMolecule declared type is IAtomContainer. Condition could be removed or replaced with a null check if null case is possible
    logger.debug("Adding molecule to set");
    currentMoleculeSet.addAtomContainer(currentMolecule);
    logger.debug("#mols in set: " + currentMoleculeSet.getAtomContainerCount());
} else if (currentMolecule instanceof ICrystal) { // << always false as ICrystal extends IAtomContainer, so this branch is never visited. Probably 'else' is redundant
    logger.debug("Adding crystal to chemModel");
    currentChemModel.setCrystal((ICrystal) currentMolecule);
    currentChemSequence.addChemModel(currentChemModel);
}

if (object instanceof IAtomContainer) {
    root = convertor.cdkAtomContainerToCMLMolecule((IAtomContainer) object);
} else if (object instanceof ICrystal) { // << similar to previous case: this branch is unreachable
    root = convertor.cdkCrystalToCMLMolecule((ICrystal) object);

if (commonAtomCount > vfMCSSize && commonAtomCount > vfMCSSize) { // << repeated check, probably something else was intended

Integer qIndex = Integer.valueOf(getReactantMol().indexOf(qAtom));
Integer tIndex = Integer.valueOf(getProductMol().indexOf(tAtom));
if (qIndex != null && tIndex != null) { // << condition is alays true: Integer.valueOf never returns null. Probably it was intended to check for -1 as -1 is returned by indexOf when atom not found
    atomatomMapping.put(qAtom, tAtom);
    indexindexMapping.put(qIndex, tIndex);
} else {
    try {
        throw new CDKException("Atom index pointing to NULL");
    } catch (CDKException ex) {
        LOGGER.error(Level.SEVERE, null, ex);
    }
}