A C D E F G I K L M N O P Q R S T V W

A

ACESERV_MSGDATA - Static variable in interface acedb.Constants

ACESERV_MSGENCORE - Static variable in interface acedb.Constants

ACESERV_MSGFAIL - Static variable in interface acedb.Constants

ACESERV_MSGKILL - Static variable in interface acedb.Constants

ACESERV_MSGOK - Static variable in interface acedb.Constants

ACESERV_MSGREQ - Static variable in interface acedb.Constants

Ace - class acedb.Ace.

Ace class, A key interface to ACEDB.

Ace(String, int, String, String) - Constructor for class acedb.Ace

Constructing an Ace object.

AceEmptyMessageException - exception acedb.AceEmptyMessageException.

AceException - exception acedb.AceException.

Exceptins thrown by Ace and Aceobj class

AceException() - Constructor for class acedb.AceException

AceException(String) - Constructor for class acedb.AceException

AceObjectNotFoundException - exception acedb.AceObjectNotFoundException.

AceObjectNotFoundException(String) - Constructor for class acedb.AceObjectNotFoundException

Aceclient - class acedb.Aceclient.

Aceclient(String, int, String, String) - Constructor for class acedb.Aceclient

create a client object that is not connected yet.

Aceclient() - Constructor for class acedb.Aceclient

Default constructors, emtpy client

Aceclient(String, int) - Constructor for class acedb.Aceclient

create a client with anonymous user.

Aceconnect - class acedb.Aceconnect.

The Aceconnect class is the driver for interacting the socket aceserver.

Aceconnect(Socket) - Constructor for class acedb.Aceconnect

Aceobj - class acedb.Aceobj.

The Aceobj objects are constructed by the Ace class.

Aceobj() - Constructor for class acedb.Aceobj

Construct an empty object.

Aceobj(String) - Constructor for class acedb.Aceobj

Construct a full Aceobj from the acedump, should implement construction one line at time ON-DEMAND for efficiency.

Aceobj(Aceobj.AceobjNode) - Constructor for class acedb.Aceobj

construct an object from a tree node.

Aceobj.AceobjNode - class acedb.Aceobj.AceobjNode.

Aceobj.AceobjNode() - Constructor for class acedb.Aceobj.AceobjNode

Default constructor with all members set to null.

Aceobj.AceobjNode(String) - Constructor for class acedb.Aceobj.AceobjNode

Constructs AceobjNode from String like ?Sequence?X97021?.

Aceobj.AceobjNode(String, Aceobj.AceobjNode) - Constructor for class acedb.Aceobj.AceobjNode

constructor, also set parent node as parent

Aceobj.AceobjNode(Object, Aceobj.AceobjNode) - Constructor for class acedb.Aceobj.AceobjNode

Aceobj.DumpStore - class acedb.Aceobj.DumpStore.

for storing the aceDump temperarily

Aceobj.DumpStore(String) - Constructor for class acedb.Aceobj.DumpStore

Constructing the object from a acedump string.

absolute(int) - Method in class acedb.Result

acedb - package acedb

addChild(String) - Method in class acedb.Aceobj.AceobjNode

Add a node to the buttom of this one with str containing the Java String representation of the node.

addSibling(String) - Method in class acedb.Aceobj.AceobjNode

add a node to the right of this one.

at(String) - Method in class acedb.Aceobj

take a tag path separated by dot (.).

C

Constants - interface acedb.Constants.

these constants will speed up a little bit, if used in comparason

chopComment(String) - Static method in class acedb.Ace

remove the comment info at the end of the ace output.

close() - Method in class acedb.Ace

close() - Method in class acedb.Aceclient

close() - Method in class acedb.Aceconnect

Close the socket and associated streams.

close() - Method in class acedb.Result

close() - Method in class acedb.SeqResult

D

down - Variable in class acedb.Aceobj.AceobjNode

down() - Method in class acedb.Aceobj

similar to right(), return a subtree of the parent

dumpSocketInfo() - Method in class acedb.Aceconnect

for debuging

E

exec(String) - Method in class acedb.Ace

Execute database commands and return the whole result as String.

execCommand(String) - Method in class acedb.Aceconnect

Send query command to Saceserver and return the Status of the command execution; use getMessage() to get the message.

execData(String) - Method in class acedb.Aceconnect

I don't know what type of data should be send through this channel.

execQuery(String) - Method in class acedb.Ace

Execute a AQL query and reture a RESULT_FORWARD Result object.

execQuery(String, int) - Method in class acedb.Ace

use to get random access results if rltProperty == RESULT_RANDOM.

F

fasta2String(String) - Static method in class acedb.Ace

helper function to convert the ace fasta dump into String discarding header line

fetch(String, String) - Method in class acedb.Ace

retrieve an Aceobj from the server.

fetch(Aceobj) - Method in class acedb.Ace

follow an Aceobj into the database and retrieve a new object.

fetchMany(String, Vector) - Method in class acedb.Ace

fetch all objects in objlist into an Objset object, then use the next method to iterate through the objcets in the set.

fetchMany(String) - Method in class acedb.Ace

keys must be formated as "Keyset-read = CLASS key1;key2;...; .

fetchManyString(String, Vector) - Method in class acedb.Ace

fetch all the object in objlist as a large string containing all object.

find(Aceobj.AceobjNode, String) - Static method in class acedb.Aceobj

A search function, not to be used by the public.

first() - Method in class acedb.Result

for random access only.

G

get(String) - Method in class acedb.Aceobj

Search the object for the tag.

getAceClass() - Method in class acedb.Aceobj

return the Ace class type such as Sequence, Paper, int,.

getCDS(String) - Method in class acedb.Ace

obtain the CDS sequence from an mRNA object

getColumnCount() - Method in class acedb.Result

returns number of columns returns by AQL

getColumnType(int) - Method in class acedb.Result

returns column type at cnum as a String.

getConnect() - Method in class acedb.Aceclient

Creates a new Aceconnect object based on the information storeed in the Aceclient object.

getConnectCount() - Method in class acedb.Aceclient

getCurrentRow() - Method in class acedb.Result

return the rows that have been accessed through next().

getDBInfo() - Method in class acedb.Ace

get a summary of info about the underlying acedb.

getDBTitle() - Method in class acedb.Ace

obtain the title of the underlying acedb.

getDNA(String) - Method in class acedb.Ace

Retrieve the sequence string only, without \n and header no white characters left.

getDouble(int) - Method in class acedb.Result

getFastaDNA(String) - Method in class acedb.Ace

Retrieve DNA sequence as fasta formated, 50 nt per line, with the header > seqName.

getFastaPeptide(String) - Method in class acedb.Ace

Retrieve Peptide sequence as fasta formated, 50 aa per line, with the header > seqName.

getFloat(int) - Method in class acedb.Result

getHost() - Method in class acedb.Aceclient

getInt(int) - Method in class acedb.Result

retruns the column at col as an integer.

getMessage() - Method in class acedb.Aceconnect

returns the message body as String.

getMsgType() - Method in class acedb.Aceconnect

The client only consructs ACESERV_MSGREQ, ACESERV_MSGENCORE for requesting information.

getMsgTypeInt() - Method in class acedb.Aceconnect

returns the message type as int defined in Constants.java

getName() - Method in class acedb.SeqResult

return the name of the current sequence

getPeptide(String) - Method in class acedb.Ace

Retrieve the peptide string only, without \n and header no white characters left.

getPort() - Method in class acedb.Aceclient

getRowArray() - Method in class acedb.Result

returns row as an array of Strings

getRowCount() - Method in class acedb.Result

return the total rows in this result only if Result is set to be random access.

getRowString() - Method in class acedb.Result

return the whole row as a single String object.

getSeqSet(String) - Method in class acedb.Ace

Must be called after a regular query that returns sequence sets such as an aql statement or keyset statement.

getSeqSet(String, Vector) - Method in class acedb.Ace

returns a SeqResult object from a list of protein or sequence names.

getSequence() - Method in class acedb.SeqResult

return the String of the sequence

getStatus() - Method in class acedb.Ace

getString(int) - Method in class acedb.Result

return unquoted String.

getTabCount() - Method in class acedb.Aceobj.DumpStore

Get the next horizontal branch as AceobjNode (pointer), if no more branch left returns null.

getUser() - Method in class acedb.Aceclient

I

isClosed() - Method in class acedb.Aceconnect

to see that this connection is closed or not

isEmpty() - Method in class acedb.Result

Simply inform you whether you have obtained some results or not.

isTag() - Method in class acedb.Aceobj.AceobjNode

isTag() - Method in class acedb.Aceobj

K

keyset(String, Vector) - Method in class acedb.Ace

Use the tace Keyset-Read command to import a keyset into the server database with class=type and all the keys from keys vector.

keyset(String) - Method in class acedb.Ace

send a keyset to the server with keys containing the String of keys separated with ";".

L

last() - Method in class acedb.Result

login(String, String) - Method in class acedb.Aceconnect

signing on to the server.

M

make(String) - Method in class acedb.Aceobj

make an object out of ace dump string.

N

name() - Method in class acedb.Aceobj

return the value of the class, such as Sequence, Paper, etc

next() - Method in class acedb.Objset

Fetch the next Aceobj, one pass only; FORWARD_ONLY iteration!.

next() - Method in class acedb.Result

if there is more results, after calling next you can retrieve the result with getXXXX methods.

next() - Method in class acedb.SeqResult

starts with end = -1, begin=0, in each iteration begin is on >

nextForward() - Method in class acedb.Result

move pointer to the next item in result; this is a FORWARD_ONLY iterator.

nextline() - Method in class acedb.Aceobj.DumpStore

obtain the next line of text.

O

Objset - class acedb.Objset.

Objset(String) - Constructor for class acedb.Objset

Construct an Objset object from a ace object string dump with the show -j command.

P

parent - Variable in class acedb.Aceobj.AceobjNode

print(Aceobj.AceobjNode) - Static method in class acedb.Aceobj

dump out the node type:value, same format as ACE model.

print() - Method in class acedb.Aceobj

print the object tree, row first.

Q

QUERY_LIMIT - Static variable in class acedb.Ace

quit() - Method in class acedb.Aceconnect

Terminate the server.

R

RESULT_BACKWARD - Static variable in interface acedb.Constants

RESULT_FORWARD - Static variable in interface acedb.Constants

RESULT_RANDOM - Static variable in interface acedb.Constants

Result - class acedb.Result.

provide a pointer iteration through the result.

Result() - Constructor for class acedb.Result

construct an empty Result object if return 0 objects.

Result(String) - Constructor for class acedb.Result

the String r should be the whole message body obtained from the Ace or Aceclient class Should not be used outside the package.

Result(String, Aceconnect) - Constructor for class acedb.Result

Construct a new Result object from String r.

Result(String, boolean) - Constructor for class acedb.Result

Construct a random access result from a complete query result.

resultProperty - Variable in class acedb.Result

to mark the type of result, currently RESULT_FORWARD, RESULT_RANDOM.

reverseComplement(String) - Static method in class acedb.Ace

helper function, should be in a separete package

right - Variable in class acedb.Aceobj.AceobjNode

right() - Method in class acedb.Aceobj

low level tree traversal, will not follow into the database.

rootBranch() - Method in class acedb.Aceobj.DumpStore

make the root branch from the first line of the Ace object dump in the Java format.

S

SeqResult - class acedb.SeqResult.

class SeqResult used to retrieve a set of DNA sequences It was yesterday and today that I wrote this class.

SeqResult(String) - Constructor for class acedb.SeqResult

SeqResult(String, Aceconnect) - Constructor for class acedb.SeqResult

searchDown(Aceobj.AceobjNode, String) - Method in class acedb.Aceobj

search the immediate right tags downward.

sendCommand(String) - Method in class acedb.Aceconnect

Sends commands to server and read the header from the socket.

sendData(String) - Method in class acedb.Aceconnect

Send data to be parsed into the server database.

shutdown() - Method in class acedb.Aceconnect

Tell the server to shutdown.

socketIns - Variable in class acedb.Aceconnect

T

tags() - Method in class acedb.Aceobj

return the top level tags as a vector.

toString() - Method in class acedb.Aceobj.AceobjNode

toString() - Method in class acedb.Aceobj

return the root's value as string

type - Variable in class acedb.Aceobj.AceobjNode

A tre node with Ace class name, tags, build-in type derived from ace show -j option from tace.

type() - Method in class acedb.Aceobj

return the ace class type

V

value - Variable in class acedb.Aceobj.AceobjNode

W

writeFasta(PrintWriter, String) - Static method in class acedb.Ace

defalt line 50 nt per line

writeFasta(PrintWriter, String, int) - Static method in class acedb.Ace

writeFasta(PrintStream, String) - Static method in class acedb.Ace

writeFasta(PrintStream, String, int) - Static method in class acedb.Ace

helper function to dump sequence string into pw, lineLen bases per line

A C D E F G I K L M N O P Q R S T V W