FragSpec Class

Member Function Documentation

FragSpec::FragSpec(PolChemDefCstSPtr pol_chem_def_csp, QString name, QString formula = QString(), FragEnd frag_end = FRAG_END_NONE, const QString &comment = QString())

Constructs a FragSpec instance.

pol_chem_def_csp Polymer chemistry definition. Cannot be nullptr.

name Name. Cannot be empty.

formula Formula. Defaults to the null string.

frag_end Fragmentation end. Defaults to FRAG_END_NONE.

comment Comment. Defaults to the null string.

FragSpec::FragSpec(PolChemDefCstSPtr pol_chem_def_csp, QString name, QString formula)

Constructs a fragmentation specification.

pol_chem_def_csp Polymer chemistry definition. Cannot be nullptr.

name Name. Cannot be empty.

formula Formula.

FragSpec::FragSpec(const FragSpec &other)

Constructs a FragSpec instance as a copy of other.

[virtual noexcept] FragSpec::~FragSpec()

Destroys this FragSpec instance.

void FragSpec::appendRule(FragRule *frag_rule)

Adds the frag_rule FragRule instance to the member list of FragRule instances.

QString FragSpec::comment() const

Returns the comment.

See also setComment().

QString *FragSpec::formatXmlFgsElement(int offset, const QString &indent = QString(" "))

Formats a string representing this FragSpec instance suitable to use as an XML element.

The typical fragmentation specification element that is generated in this function looks like this:

<fgs>
<name>a</name>
<end>LE</end>
<formula>-C1O1</formula>
<fgr>
<name>a-fgr-1</name>
<formula>+H200</formula>
<prev-mnm-code>E</prev-mnm-code>
<curr-mnm-code>D</curr-mnm-code>
<next-mnm-code>F</next-mnm-code>
<comment>comment here!</comment>
</fgr>
<fgr>
<name>a-fgr-2</name>
<formula>+H100</formula>
<prev-mnm-code>F</prev-mnm-code>
<curr-mnm-code>D</curr-mnm-code>
<next-mnm-code>E</next-mnm-code>
<comment>comment here!</comment>
</fgr>
</fgs>

The formatting of the XML element takes into account offset and indent by prepending the string with offset * indent character substring.

indent defaults to two spaces.

Returns a dynamically allocated string that needs to be freed after use.

QString FragSpec::formula() const

Returns the Formula as a string.

FragEnd FragSpec::fragEnd() const

Returns the fragmentation end.

See also setFragEnd().

void FragSpec::insertRuleAt(int index, FragRule *frag_rule)

Inserts in the member list of FragRule instances at index the frag_rule FragRule instance.

[static] int FragSpec::isNameInList(const QString &name, const QList<FragSpec *> &frag_spec_list, FragSpec *other = nullptr)

Searches by name for a FragSpec in the frag_spec_list.

If such fragmentation specification is found, and if other is non-0, the found fragmentation specification's data are copied into other.

Returns the index of the found FragSpec instance or -1 if none is found or if name is empty.

void FragSpec::removeRuleAt(int index)

Removes from the member list of FragRule instances the item at index index.

bool FragSpec::renderXmlFgsElement(const QDomElement &element, int version)

Parses a fragmentation specification XML element using a versioned function.

Upon parsing and validation of the parsed data, the member data are updated, thus essentially initializing this FragSpec instance.

Returns true if parsing and formula validation were successful, false otherwise.

QList<FragRule *> &FragSpec::ruleList()

Returns the list of FragRule instances.

void FragSpec::setComment(const QString &comment)

Sets the comment.

See also comment().

void FragSpec::setFragEnd(FragEnd frag_end)

Sets the fragmentation end to frag_end.

See also fragEnd().

bool FragSpec::validate()

Validates the FragSpec.

The validation involves checking that:

• The name is not empty.
• The fragmentation end must have been set.
• The FragRule instances (if any) are valid.
• The Formula is valid.

Returns true upon success, false otherwise.

FragSpec &FragSpec::operator=(const FragSpec &other)

Assigns other to this FragSpec instance.

Returns a reference to this FragSpec.