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AMOS::Index_t Class Reference

An association index between two types of AMOS objects. More...

#include <Index_AMOS.hh>

Inheritance diagram for AMOS::Index_t:

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List of all members.

Public Types

typedef HASHMAP::hash_multimap<
ID_t, ID_t >::iterator 
iterator
 Un-mutable index iterator, only itr -> second can be modified.
typedef HASHMAP::hash_multimap<
ID_t, ID_t >::const_iterator 
const_iterator
 constant index iterator

Public Member Functions

 Index_t ()
 Constructs an empty Index_t object.
 Index_t (NCode_t a, NCode_t b)
 Constructs an Index_t of a certain type.
 Index_t (const Index_t &source)
 Copy constructor.
 ~Index_t ()
 Destroys a Index_t object.
iterator begin ()
 Returns a iterator to the beginning of the index.
const_iterator begin () const
void buildContigFeature (const std::string bankname)
 Builds the index with Contig_t Feature_t's.
void buildContigScaffold (const std::string bankname)
 Builds the index with Contig_t to Scaffold_t mappings.
void buildReadContig (const std::string bankname)
 Builds the index with Read_t to Contig_t mappings.
void buildReadLibrary (const std::string bankname)
 Builds the index with Read_t to Library_t mappings.
void buildReadMate (const std::string bankname)
 Builds the index with mated Read_t's.
void buildScaffoldFeature (const std::string bankname)
 Builds the index with Scaffold_t Feature_t's.
iterator end ()
 Returns a iterator to the end of the index.
const_iterator end () const
bool empty () const
 Returns true if the index is empty.
virtual void clear ()
 Clears all object data, reinitializes the object.
Size_t count (ID_t key) const
 Returns the number of IDs associated with a particular key.
virtual NCode_t getNCode () const
 Get the AMOS NCode type identifier.
Size_t getSize () const
 Returns the number of ID pairs in the index.
std::pair< NCode_t, NCode_tgetType () const
 Get the index type as a pair of NCodes.
void insert (ID_t key, ID_t value)
 Inserts a new IID pair into the index.
void insert (std::pair< ID_t, ID_t > iids)
bool isMulti (ID_t key) const
 Returns true if count is > 1 for a particular key.
ID_t lookup (ID_t key) const
 Look up a single IID by its index key.
std::pair< iterator, iteratorlookupAll (ID_t key)
 Look up a list of IIDs by their index key.
std::pair< const_iterator,
const_iterator
lookupAll (ID_t key) const
virtual void readMessage (const Message_t &msg)
 Reads in data from a Message object.
Size_t remove (ID_t key)
 Remove all IIDs associated with a particular key.
void remove (iterator itr)
 Remove a single ID pair.
void setType (std::pair< NCode_t, NCode_t > type)
 Set the index type as a pair of NCodes.
void setType (NCode_t a, NCode_t b)
virtual void writeMessage (Message_t &msg) const
 Writes data to a Message object.
const std::string & getComment () const
 Get the comment string.
const Status_t getStatus () const
 Get the status value.
void setComment (const std::string &comment)
 Set the comment string.
void setStatus (Status_t status)
 Set the status value.
const std::string & getEID () const
 Get the external ID.
ID_t getIID () const
 Get the internal ID.
bool isRemoved () const
 Check if the object is waiting to be removed from the bank.
bool isModified () const
 Check if the object has been modified.
bool isFlagA () const
 Check the value of flag A.
bool isFlagB () const
 Check the value of flag B.
void setEID (const std::string &eid)
 Set the external ID.
void setFlagA (bool flag)
 Set flag A.
void setFlagB (bool flag)
 Set flag B.
void setIID (ID_t iid)
 Set the internal ID.

Static Public Attributes

const NCode_t NCODE = M_INDEX
 The NCode type identifier for this object.

Protected Member Functions

virtual void readRecord (std::istream &fix, std::istream &var)
 Read selected class members from a biserial record.
virtual void writeRecord (std::ostream &fix, std::ostream &var) const
 Write selected class members to a biserial record.

Protected Attributes

ID_t iid_m
 internal ID (integer AMOS identifier)
std::string eid_m
 external ID (anything you want sans newlines)
BankFlags_t flags_m
 bank flags, derived classes may use "nibble"

Detailed Description

An association index between two types of AMOS objects.

Provides an efficient means for storing/retrieving inter-object relationships, e.g. read to mated read. Since most objects only store a minimal set of references, it can be akward and costly to identify related objects not directly linked with an IID reference. The Index_t provides a way to amortize this cost by storing the association information directly for future, repeated use. When in memory, it is essentially a watered-down version of an STL multimap.

Definition at line 33 of file Index_AMOS.hh.


Member Typedef Documentation

typedef HASHMAP::hash_multimap<ID_t, ID_t>::const_iterator AMOS::Index_t::const_iterator
 

constant index iterator

Definition at line 62 of file Index_AMOS.hh.

Referenced by begin(), buildContigScaffold(), buildReadContig(), end(), writeMessage(), and writeRecord().

typedef HASHMAP::hash_multimap<ID_t, ID_t>::iterator AMOS::Index_t::iterator
 

Un-mutable index iterator, only itr -> second can be modified.

Definition at line 59 of file Index_AMOS.hh.

Referenced by begin(), end(), and remove().


Constructor & Destructor Documentation

AMOS::Index_t::Index_t  )  [inline]
 

Constructs an empty Index_t object.

Sets all members to zero or NULL Definition at line 70 of file Index_AMOS.hh.

References AMOS::NULL_NCODE.

AMOS::Index_t::Index_t NCode_t  a,
NCode_t  b
[inline]
 

Constructs an Index_t of a certain type.

Definition at line 79 of file Index_AMOS.hh.

References AMOS::NCode_t.

AMOS::Index_t::Index_t const Index_t source  )  [inline]
 

Copy constructor.

Definition at line 89 of file Index_AMOS.hh.

AMOS::Index_t::~Index_t  )  [inline]
 

Destroys a Index_t object.

Definition at line 98 of file Index_AMOS.hh.


Member Function Documentation

const_iterator AMOS::Index_t::begin  )  const [inline]
 

Definition at line 119 of file Index_AMOS.hh.

References begin(), and const_iterator.

iterator AMOS::Index_t::begin  )  [inline]
 

Returns a iterator to the beginning of the index.

Iterator is of the type hash_multimap<ID_t, ID_t>::iterator. Access TO and FROM IIDs with 'itr -> first' and 'itr -> second' respectively.

Returns:
An iterator to the beginning of the index
Definition at line 112 of file Index_AMOS.hh.

References iterator.

Referenced by begin(), buildContigScaffold(), buildReadContig(), writeMessage(), and writeRecord().

void Index_t::buildContigFeature const std::string  bankname  ) 
 

Builds the index with Contig_t Feature_t's.

Builds the index with contig features, i.e. the index will contain a set of all associated features for each contig IID. Will throw an exception if there was any trouble opening and reading from the banks.

Parameters:
bankname Name of the bank directory to index
Exceptions:
ArgumentException_t 
IOException_t 
Returns:
void
Definition at line 22 of file Index_AMOS.cc.

References AMOS::B_READ, clear(), AMOS::IBankable_t::getIID(), insert(), AMOS::NULL_ID, and setType().

void Index_t::buildContigScaffold const std::string  bankname  ) 
 

Builds the index with Contig_t to Scaffold_t mappings.

Builds the index with contig to scaffold links, i.e. the index will reference the containing scaffold(s) for each contig IID. Will throw an exception if there was any trouble opening and reading from the banks.

Parameters:
bankname Name of the bank directory to index
Exceptions:
ArgumentException_t 
IOException_t 
Returns:
void
Definition at line 45 of file Index_AMOS.cc.

References AMOS::B_READ, begin(), clear(), const_iterator, end(), AMOS::IBankable_t::getIID(), insert(), AMOS::NULL_ID, and setType().

void Index_t::buildReadContig const std::string  bankname  ) 
 

Builds the index with Read_t to Contig_t mappings.

Builds the index with read to contig links, i.e. the index will reference the containing contig(s) for each read IID. Will throw an exception if there was any trouble opening and reading from the banks.

Parameters:
bankname Name of the bank directory to index
Exceptions:
ArgumentException_t 
IOException_t 
Returns:
void
Definition at line 71 of file Index_AMOS.cc.

References AMOS::B_READ, begin(), clear(), const_iterator, end(), AMOS::IBankable_t::getIID(), insert(), AMOS::NULL_ID, and setType().

void Index_t::buildReadLibrary const std::string  bankname  ) 
 

Builds the index with Read_t to Library_t mappings.

Builds the index with read to library links, i.e. the index will reference the parent library for each read IID. Will throw an exception if there was any trouble opening and reading from the banks.

Parameters:
bankname Name of the bank directory to index
Exceptions:
ArgumentException_t 
IOException_t 
Returns:
void
Definition at line 97 of file Index_AMOS.cc.

References AMOS::B_READ, clear(), AMOS::IBankable_t::getIID(), insert(), AMOS::NULL_ID, and setType().

void Index_t::buildReadMate const std::string  bankname  ) 
 

Builds the index with mated Read_t's.

Builds the index with read mates, i.e. the index will reference the the mate of each read IID. Will throw an exception if there was any trouble opening and reading from the banks.

Exceptions:
ArgumentException_t 
IOException_t 
Returns:
void
Definition at line 123 of file Index_AMOS.cc.

References clear(), insert(), AMOS::NULL_ID, and setType().

void Index_t::buildScaffoldFeature const std::string  bankname  ) 
 

Builds the index with Scaffold_t Feature_t's.

Builds the index with scaffold features, i.e. the index will contain a set of all associated features for each scaffold IID. Will throw an exception if there was any trouble opening and reading from the banks.

Parameters:
bankname Name of the bank directory to index
Exceptions:
ArgumentException_t 
IOException_t 
Returns:
void
Definition at line 147 of file Index_AMOS.cc.

References AMOS::B_READ, clear(), AMOS::IBankable_t::getIID(), insert(), AMOS::NULL_ID, and setType().

virtual void AMOS::Index_t::clear  )  [inline, virtual]
 

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.

Definition at line 246 of file Index_AMOS.hh.

References AMOS::Universal_t::clear(), and AMOS::NULL_NCODE.

Referenced by buildContigFeature(), buildContigScaffold(), buildReadContig(), buildReadLibrary(), buildReadMate(), buildScaffoldFeature(), readMessage(), readRecord(), and writeMessage().

Size_t AMOS::Index_t::count ID_t  key  )  const [inline]
 

Returns the number of IDs associated with a particular key.

Returns:
The number of IDs associated with a particular key
Definition at line 260 of file Index_AMOS.hh.

References AMOS::ID_t, and AMOS::Size_t.

Referenced by isMulti().

bool AMOS::Index_t::empty  )  const [inline]
 

Returns true if the index is empty.

Returns:
True if the index is empty, else false
Definition at line 239 of file Index_AMOS.hh.

const_iterator AMOS::Index_t::end  )  const [inline]
 

Definition at line 228 of file Index_AMOS.hh.

References const_iterator, and end().

iterator AMOS::Index_t::end  )  [inline]
 

Returns a iterator to the end of the index.

Iterator is of the type hash_multimap<ID_t, ID_t>::iterator. Access TO and FROM IIDs with 'itr -> first' and 'itr -> second' respectively.

Returns:
A iterator to the end of the index
Definition at line 221 of file Index_AMOS.hh.

References iterator.

Referenced by buildContigScaffold(), buildReadContig(), end(), writeMessage(), and writeRecord().

const std::string& AMOS::Universal_t::getComment  )  const [inline, inherited]
 

Get the comment string.

Returns:
The comment string
Definition at line 110 of file Universal_AMOS.hh.

Referenced by AMOS::operator<<().

const std::string& AMOS::IBankable_t::getEID  )  const [inline, inherited]
 

Get the external ID.

Returns:
The external ID
Definition at line 156 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m.

Referenced by AMOS::Contig_t::writeUMD().

ID_t AMOS::IBankable_t::getIID  )  const [inline, inherited]
 

Get the internal ID.

Returns:
The internal ID
Definition at line 167 of file Bank_AMOS.hh.

References AMOS::ID_t, and AMOS::IBankable_t::iid_m.

Referenced by buildContigFeature(), buildContigScaffold(), buildReadContig(), buildReadLibrary(), buildScaffoldFeature(), and AMOS::operator<<().

virtual NCode_t AMOS::Index_t::getNCode  )  const [inline, virtual]
 

Get the AMOS NCode type identifier.

Returns:
The AMOS NCode type identifier

Reimplemented from AMOS::Universal_t.

Definition at line 267 of file Index_AMOS.hh.

References AMOS::NCode_t.

Size_t AMOS::Index_t::getSize  )  const [inline]
 

Returns the number of ID pairs in the index.

Returns:
The number of ID pairs in the index
Definition at line 278 of file Index_AMOS.hh.

References AMOS::Size_t.

Referenced by readMessage(), writeMessage(), and writeRecord().

const Status_t AMOS::Universal_t::getStatus  )  const [inline, inherited]
 

Get the status value.

Returns:
The status value
Definition at line 121 of file Universal_AMOS.hh.

References AMOS::Status_t.

std::pair<NCode_t, NCode_t> AMOS::Index_t::getType  )  const [inline]
 

Get the index type as a pair of NCodes.

Get the index type as a pair of NCodes for the FROM and TO type respectively.

Returns:
The index type
Definition at line 292 of file Index_AMOS.hh.

void AMOS::Index_t::insert std::pair< ID_t, ID_t iids  )  [inline]
 

Definition at line 315 of file Index_AMOS.hh.

References insert().

void AMOS::Index_t::insert ID_t  key,
ID_t  value
[inline]
 

Inserts a new IID pair into the index.

Inserts a new IID pair into the index. Index keys are allowed to have multiple, not necessarily unique, values.

Parameters:
key The index key
value The new index value
Returns:
void
Definition at line 308 of file Index_AMOS.hh.

References AMOS::ID_t.

Referenced by buildContigFeature(), buildContigScaffold(), buildReadContig(), buildReadLibrary(), buildReadMate(), buildScaffoldFeature(), insert(), readMessage(), and readRecord().

bool AMOS::IBankable_t::isFlagA  )  const [inline, inherited]
 

Check the value of flag A.

Returns:
The value of flag A
Definition at line 210 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isFlagB  )  const [inline, inherited]
 

Check the value of flag B.

Returns:
The value of flag B
Definition at line 221 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isModified  )  const [inline, inherited]
 

Check if the object has been modified.

Returns:
true if modified, otherwise false
Definition at line 199 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

bool AMOS::Index_t::isMulti ID_t  key  )  const [inline]
 

Returns true if count is > 1 for a particular key.

Returns:
True if count is > 1 for a particular key
Definition at line 326 of file Index_AMOS.hh.

References count(), and AMOS::ID_t.

bool AMOS::IBankable_t::isRemoved  )  const [inline, inherited]
 

Check if the object is waiting to be removed from the bank.

Note:
Useful for debugging only
Returns:
true if removed, otherwise false
Definition at line 188 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

ID_t AMOS::Index_t::lookup ID_t  key  )  const [inline]
 

Look up a single IID by its index key.

Look up a single IID by its index key, even though multiple IDs make be associated with the same key. If multiple IDs exist for the same key, a single value will be picked (in no guaranteed fasion) and returned

Parameters:
key The key to lookup
Returns:
An IID value associated with the given key
Definition at line 342 of file Index_AMOS.hh.

References AMOS::ID_t.

std::pair<const_iterator, const_iterator> AMOS::Index_t::lookupAll ID_t  key  )  const [inline]
 

Definition at line 366 of file Index_AMOS.hh.

References AMOS::ID_t.

std::pair<iterator, iterator> AMOS::Index_t::lookupAll ID_t  key  )  [inline]
 

Look up a list of IIDs by their index key.

Look up all IIDs associated with the same index key. A begin and end iterator will be returned, representing the bounds of the value list. Like standard STL begin/end iterators, the begin iterator will point to the first object and the end iterator will point one past the end object.

Parameters:
key The key to lookup
Returns:
A pair of iterators bounding the values with the given key
Definition at line 359 of file Index_AMOS.hh.

References AMOS::ID_t.

void Index_t::readMessage const Message_t msg  )  [virtual]
 

Reads in data from a Message object.

Reads the data contained in a Message object and stores it in the Messagable object. Will not complain if incoming message is of the wrong type, will only try and suck out the fields it recognizes. All previous data in the Messagable object will be cleared or overwritten.

Parameters:
msg The Message to read from
Precondition:
The expected fields are formatted properly
Exceptions:
ArgumentException_t 
Returns:
void

Reimplemented from AMOS::Universal_t.

Definition at line 170 of file Index_AMOS.cc.

References AMOS_THROW_ARGUMENT, clear(), AMOS::Encode(), AMOS::F_MAP, AMOS::F_OBJECT, AMOS::F_SIZE, getSize(), insert(), AMOS::NCODE_SIZE, AMOS::Universal_t::readMessage(), and AMOS::Size_t.

void Index_t::readRecord std::istream &  fix,
std::istream &  var
[protected, virtual]
 

Read selected class members from a biserial record.

Reads the fixed and variable length streams from a biserial record and initializes the class members to the values stored within. Used in translating a biserial IBankable object, and needed to retrieve objects from a bank.

Note:
This method must be able to interpret the biserial record produced by its related function writeRecord.
Parameters:
fix The fixed length stream (stores all fixed length members)
var The variable length stream (stores all var length members)
Precondition:
The get pointer of fix is at the beginning of the record

The get pointer of var is at the beginning of the record

Returns:
void

Reimplemented from AMOS::Universal_t.

Definition at line 230 of file Index_AMOS.cc.

References clear(), insert(), AMOS::Pos_t, AMOS::readLE(), AMOS::Universal_t::readRecord(), and AMOS::Size_t.

void AMOS::Index_t::remove iterator  itr  )  [inline]
 

Remove a single ID pair.

Parameters:
itr An iterator pointing to the pair to remove
Returns:
void
Definition at line 397 of file Index_AMOS.hh.

References iterator.

Size_t AMOS::Index_t::remove ID_t  key  )  [inline]
 

Remove all IIDs associated with a particular key.

Will remove the index key and all values associated with that key. Returns the number of ID pairs removed.

Parameters:
key The key to remove
Returns:
The number of ID pairs removed
Definition at line 385 of file Index_AMOS.hh.

References AMOS::ID_t, and AMOS::Size_t.

void AMOS::Universal_t::setComment const std::string &  comment  )  [inline, inherited]
 

Set the comment string.

Parameters:
comment The new comment string
Returns:
void
Definition at line 144 of file Universal_AMOS.hh.

void AMOS::IBankable_t::setEID const std::string &  eid  )  [inline, inherited]
 

Set the external ID.

Will only use the characters up to but not including the first newline.

Returns:
void
Definition at line 234 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.

Referenced by AMOS::Contig_t::readUMD().

void AMOS::IBankable_t::setFlagA bool  flag  )  [inline, inherited]
 

Set flag A.

Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag B.

Parameters:
flag The new flag A value
Returns:
void
Definition at line 254 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setFlagB bool  flag  )  [inline, inherited]
 

Set flag B.

Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag A.

Parameters:
flag The new flag B value
Returns:
void
Definition at line 270 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setIID ID_t  iid  )  [inline, inherited]
 

Set the internal ID.

Parameters:
iid The new internal ID
Returns:
void
Definition at line 282 of file Bank_AMOS.hh.

References AMOS::ID_t, and AMOS::IBankable_t::iid_m.

void AMOS::Universal_t::setStatus Status_t  status  )  [inline, inherited]
 

Set the status value.

Parameters:
status The new status value
Returns:
void
Definition at line 156 of file Universal_AMOS.hh.

References AMOS::Status_t.

Referenced by AMOS::Universal_t::readMessage().

void AMOS::Index_t::setType NCode_t  a,
NCode_t  b
[inline]
 

Definition at line 419 of file Index_AMOS.hh.

References AMOS::NCode_t, and setType().

void AMOS::Index_t::setType std::pair< NCode_t, NCode_t type  )  [inline]
 

Set the index type as a pair of NCodes.

Set the index type as a pair of NCodes for the FROM and TO type respectively.

Parameters:
type The new index type
Returns:
void
Definition at line 412 of file Index_AMOS.hh.

Referenced by buildContigFeature(), buildContigScaffold(), buildReadContig(), buildReadLibrary(), buildReadMate(), buildScaffoldFeature(), and setType().

void Index_t::writeMessage Message_t msg  )  const [virtual]
 

Writes data to a Message object.

Writes the data contained in a Messagable object to a Message object. All previous data in the Message will be cleared or overwritten.

Parameters:
msg The Message to write to
Returns:
void

Reimplemented from AMOS::Universal_t.

Definition at line 252 of file Index_AMOS.cc.

References begin(), clear(), const_iterator, AMOS::Decode(), end(), AMOS::F_MAP, AMOS::F_OBJECT, AMOS::F_SIZE, getSize(), AMOS::NL_CHAR, AMOS::NULL_NCODE, AMOS::NULL_STRING, AMOS::Size_t, and AMOS::Universal_t::writeMessage().

void Index_t::writeRecord std::ostream &  fix,
std::ostream &  var
const [protected, virtual]
 

Write selected class members to a biserial record.

Writes the fixed and variable length streams to a biserial record. Used in generating a biserial IBankable object, and needed to commit objects to a bank. Should not write the flags, EID, or IID of the object because the bank will handle the storage of these fields on its own.

Note:
This method must be able to produce a biserial record that can be read by its related funtion readRecord.
Parameters:
fix The fixed length stream (stores all fixed length members)
var The variable length stream (stores all var length members)
Returns:
void

Reimplemented from AMOS::Universal_t.

Definition at line 296 of file Index_AMOS.cc.

References begin(), const_iterator, end(), getSize(), AMOS::Size_t, AMOS::writeLE(), and AMOS::Universal_t::writeRecord().


Member Data Documentation

std::string AMOS::IBankable_t::eid_m [protected, inherited]
 

external ID (anything you want sans newlines)

Definition at line 66 of file Bank_AMOS.hh.

Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::getEID(), and AMOS::IBankable_t::setEID().

BankFlags_t AMOS::IBankable_t::flags_m [protected, inherited]
 

bank flags, derived classes may use "nibble"

Definition at line 68 of file Bank_AMOS.hh.

Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::IBankable_t::setFlagA(), and AMOS::IBankable_t::setFlagB().

ID_t AMOS::IBankable_t::iid_m [protected, inherited]
 

internal ID (integer AMOS identifier)

Definition at line 64 of file Bank_AMOS.hh.

Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), and AMOS::IBankable_t::setIID().

const NCode_t Index_t::NCODE = M_INDEX [static]
 

The NCode type identifier for this object.

Reimplemented from AMOS::Universal_t.

Definition at line 18 of file Index_AMOS.cc.


The documentation for this class was generated from the following files:
Generated on Tue May 17 15:19:47 2005 for libAMOS by doxygen 1.3.8