Gets the String term of the modification feature.
@param mf modification feature
@return modification term
509815
public String getModificationTerm(ModificationFeature mf)
	{
		Set vals = TERM_ACC.getValueFromBean(mf);
		if (vals.isEmpty()) return null;
		return vals.iterator().next().toString();
	}
502816
def _extract_mod_from_feature(mf):
        """"""
        # ModificationFeature / SequenceModificationVocabulary
        mf_type = mf.getModificationType()
        if mf_type is None:
            return None
        mf_type_terms = mf_type.getTerm().toArray()
        known_mf_type = None
        for t in mf_type_terms:
            if t.startswith('MOD_RES '):
                t = t[8:]
            mf_type_indra = _mftype_dict.get(t)
            if mf_type_indra is not None:
                known_mf_type = mf_type_indra
                break
        if not known_mf_type:
            logger.debug('Skipping modification with unknown terms: %s' %
                        ', '.join(mf_type_terms))
            return None

        mod_type, residue = known_mf_type

        # getFeatureLocation returns SequenceLocation, which is the
        # generic parent class of SequenceSite and SequenceInterval.
        # Here we need to cast to SequenceSite in order to get to
        # the sequence position.
        mf_pos = mf.getFeatureLocation()
        if mf_pos is not None:
            # If it is not a SequenceSite we can't handle it
            if not mf_pos.modelInterface.getName() == \
                'org.biopax.paxtools.model.level3.SequenceSite':
                mod_pos = None
            else:
                mf_site = cast(_bp('SequenceSite'), mf_pos)
                mf_pos_status = mf_site.getPositionStatus()
                if mf_pos_status is None:
                    mod_pos = None
                elif mf_pos_status and mf_pos_status.toString() != 'EQUAL':
                    logger.debug('Modification site position is %s' %
                                mf_pos_status.toString())
                else:
                    mod_pos = mf_site.getSequencePosition()
                    mod_pos = '%s' % mod_pos
        else:
            mod_pos = None
        mc = ModCondition(mod_type, residue, mod_pos, True)
        return mc
1201442
public String modifiers() {
        int modifiers = getModifiers();
        if (isAnnotationTypeElement() ||
                (isMethod() && containingClass().isInterface())) {
            // Remove the implicit abstract modifier.
            return Modifier.toString(modifiers & ~Modifier.ABSTRACT);
        } else {
            return Modifier.toString(modifiers);
        }
    }
73473
public String getStringProperty (final String name, final String def)
  {
    String val = m_aProps.getProperty (name, def);
    if (val == null)
      return def;
    val = val.trim ();
    return val.length () == 0 ? def : val;
  }
588995
public HashSet<String> getStringsEndingWith(String suffixStr)
    {
        HashSet<String> strHashSet = new HashSet<String>();

        if (sourceNode != null)      //if the MDAG hasn't been simplified
            getStrings(strHashSet, SearchCondition.SUFFIX_SEARCH_CONDITION, suffixStr, "", sourceNode.getOutgoingTransitions());
        else
            getStrings(strHashSet, SearchCondition.SUFFIX_SEARCH_CONDITION, suffixStr, "", simplifiedSourceNode);

        return strHashSet;
    }
1326396
private Feature getFeature(AnnotationFS annotation, FeatureDescription featureDescription) {
		if(feature == null) {
			String name = featureDescription.getName();
			feature = annotation.getType().getFeatureByBaseName(name);
		}
		return feature;
	}
775449
public String getName() {
		if (m_strFieldName != null)
			return m_strFieldName;

		String str;

		if (m_strGetName != null)
			str = m_strGetName + "()|";
		else
			str = "|";

		if (m_strSetName != null)
			return str + m_strSetName;

		return str;
	}
1230756
@Override
    public String getModuleName() {
        String moduleName = moduleRef.getName();
        if (moduleName == null || moduleName.isEmpty()) {
            moduleName = moduleNameFromModuleDescriptor;
        }
        return moduleName == null || moduleName.isEmpty() ? null : moduleName;
    }
1154335
public String getExpressionString() {
        StringBuffer buf = new StringBuffer();
        buf.append(mPrefix.getExpressionString());

        for (int i = 0; mSuffixes != null && i < mSuffixes.size(); i++) {
            ValueSuffix suffix = (ValueSuffix) mSuffixes.get(i);
            buf.append(suffix.getExpressionString());
        }

        return buf.toString();
    }
231206
public String getString() 
    {
        String strFinal = FirstMLastConverter.partsToName(m_recThis, m_iNamePrefix, m_iNameFirst, m_iNameMiddle, m_iNameSur, m_iNameSuffix, m_iNameTitle);
        int maxLength = this.getMaxLength();
        if (strFinal.length() > maxLength)
            strFinal = strFinal.substring(0, maxLength);    // Truncate to max length
        return strFinal;
    }
972172
private String getName(Description description, RoxableTest mAnnotation) {
		if (mAnnotation == null || mAnnotation.name() == null || mAnnotation.name().isEmpty()) {
			return Inflector.getHumanName(description.getMethodName());
		}
		else {
			return mAnnotation.name();
		}
	}
858162
public String getModuleName()
    {
        return ivModuleDisplayName != null ? ivModuleDisplayName :
                        ivJ2eeName != null ? ivJ2eeName.getModule() : null;
    }
914364
@Override
    public String getMethodName()
    {
        // Generally, the method name is pretty static, but for internal
        // CMR methods (with index < 0) they are dynamic, and based on
        // the signature. For performance, the substring operation is
        // deferred until the method name is actually used.             d154342.10
        if (methodName == null && methodSignature != null)
            methodName = methodSignature.substring(0, methodSignature.indexOf(":"));

        return methodName;
    }
1142880
public String getNameAsSingleString() {
    List<StringType> nameParts = new ArrayList<StringType>();
    nameParts.addAll(getPrefix());
    nameParts.addAll(getGiven());
    nameParts.add(getFamilyElement());
    nameParts.addAll(getSuffix());
    if (nameParts.size() > 0) {
      return joinStringsSpaceSeparated(nameParts);
    } else {
      return getTextElement().getValue();
    }
  }
1374989
private static String getSetterName(Method m) {
        String name = m.getName();
        if (name.startsWith("set") && (name.length() >= 4)
                && m.getReturnType().equals(void.class)
                && (m.getParameterTypes().length == 1)
        ) {
            return Character.toLowerCase(name.charAt(3)) + name.substring(4);
        }
        return null;
    }
729177
public static String toMMCIF(String categoryName, Object o) {

		StringBuilder sb = new StringBuilder();

		Class<?> c = o.getClass();


		Field[] fields = getFields(c);
		String[] names = getFieldNames(fields);

		int maxFieldNameLength = getMaxStringLength(names);

		for (int i=0;i<fields.length;i++) {
			Field f = fields[i];
			String name = names[i];

			sb.append(categoryName).append(".").append(name);

			int spacing = maxFieldNameLength - name.length() + 3;

			try {
				Object obj = f.get(o);
				String val;
				if (obj==null) {
					logger.debug("Field {} is null, will write it out as {}",name,MMCIF_MISSING_VALUE);
					val = MMCIF_MISSING_VALUE;
				} else {
					val = (String) obj;
				}
				for (int j=0;j<spacing;j++) sb.append(' ');
				sb.append(addMmCifQuoting(val));
				sb.append(newline);

			} catch (IllegalAccessException e) {
				logger.warn("Field {} is inaccessible", name);
				continue;
			} catch (ClassCastException e) {
				logger.warn("Could not cast value to String for field {}",name);
				continue;
			}

		}

		sb.append(SimpleMMcifParser.COMMENT_CHAR+newline);

		return sb.toString();
	}
125797
public String getModifiersStr() {
        final StringBuilder buf = new StringBuilder();
        TypeUtils.modifiersToString(modifiers, ModifierType.CLASS, /* ignored */ false, buf);
        return buf.toString();
    }