None
+ +COMMON-LISP
This package contains all the symbols (and definitions) of the CLARITY library.
+ +None.
+ + +None.
+ + +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +
The following entries are part of the CLARITY + dictionary.
+ + +Questions? Queries? Suggestions? Comments? Please direct them + at me. +
+ +News in chronological order, most recent on top. +
+ +
CLARITY
+
+ align-charts cl-handle timecourse-id-1 timecourse-id-2 ++ + +
cl-handle---a cl-handle
+
timecourse-id-1---an integer
+
timecourse-id-2---an integer
+
+
The generic function align-charts aligns two datasets, given their timecourse data ids. + It takes three parameters, cl-handle, which preserves the session; and timecourse-id-1 and timecourse-id-2, + which are the numerical ids identifying the timecourse datasets in the database. The function returns a hash table + containing alignments hashed by score.
+ + ++
+
+ align-charts (cl-handle clarity-handle) (timecourse-id-1 integer) (timecourse-id-2 integer) ++ + +
cl-prompt: (clarity:align-charts cl-handle 6 8) ++ +
None.
+ +None.
+ +SCORE-PAIR
+ SCORE-PAIR-CONSENSUS
+ ALIGN-TO-CONSENSUS
+ STRING-ALIGNMENT
None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ align-to-consensus cl-handle timecourse-id consensus-id ++ + +
cl-handle---a cl-handle
+
timecourse-id---an integer
+
consensus-id---an integer
+
+
The generic function align-to-consensus aligns a timecourse dataset to a consensus of sequences. + It takes three parameters, cl-handle, which preserves the session; timecourse-id which identifies the timecourse data + and consensus id which is the numerical id identifying the consensus sequences (note that consensus id is interchangeable with + tree id in this case) in the database. The function returns a hash table containing alignments hashed by score.
+ + ++
+
+ align-to-consensus (cl-handle clarity-handle) (timecourse-id integer) (consensus-id integer) ++ + +
cl-prompt: (clarity:align-to-consensus cl-handle 6 8) ++ +
None.
+ +None.
+ +SCORE-PAIR
+ SCORE-PAIR-CONSENSUS
+ ALIGN-CHARTS
+ STRING-ALIGNMENT
None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
alignment-item, STRUCTURE-OBJECT, T +
+ +The alignment-item structure is used to store information for terms about to be aligned. The dataset-id will be either + a timecourse dataset id or a tree node id depending on whether the the node the item belongs to is an internal (consensus) node + or a leaf node. Chart-id is the id of the item in the gantt_chart table. String is the gantt chart as created with the ganttify function.
+ +The constructor for this class is new-alignment-item. The accessors alignment-item-dataset-id, alignment-item-chart-id + alignment-item-term-name and alignment-item-string can be used to read or write their respective fields.
+ + +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
ALIGNMENT, STRUCTURE-OBJECT, T +
+ +The alignment class stores pairs of instances of the alignment-item class as well as the score of the aligned items. + The constructor for this class is new-alignment. The accessors alignment-score and alignment items can be used to read or write + their respective fields.
+ + +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ build-consensus cl-handle data-left data-right ++ + +
cl-handle---a clarity-handle
+
data-left---an integer
+
data-right---an integer
+
+
The generic function build-consensus takes two nodes, computes their consensus sequence, and then stores it in the database. + It takes three parameters, clarity-handle, which identifies the clarity database; data-left, which may be either a timecourse_id + or a consensus id and sdata-right, which is a timecourse id.
+ + ++
+
+ build-consensus (cl-handle clarity-handle) (data-left integer) (data-right integer) ++ + +
cl-prompt: (clarity:build-consensus cl-handle 7 9)+ +
None.
+ +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ connect db-spec + => database-connection ++ + +
db spec---a string
+
(optional) connection--- a string
+
+
+
The generic function connect sets up a connection to an underlying CLARITY database for the handle. + It takes two parameter, clarity handle, to preserve one's session, and db-spec + a database connection string.
+ + ++
+
+ connect (clarity-handle-object clarity-handle) (dp-spec string) + => database-connection ++ + + +
+
+ connect (clarity-handle-object clarity-handle) (dp-spec string)) + => database-connection ++ + +
This uses the method sqlcon in place of a connection string. In this case, db spec would be the null + string, "".
+cl-prompt: (clarity:connect myclarityhandle "data source name/user/password") +#<CLARITY:CLARITY-HANDLE 2061155C> connecting as "data source name/user" +#<SQL::ODBC-DATABASE "data source name/user" 205F450C>+ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ ganttify clarity-handle filename filedate ++ + +
clarity handle---a clarity-handle
+
filename--- a string or path
+
filedate--- a string
+
+
+
The generic function ganttify ganttifys a datafile into the database. It calls the functions ganttify, store-gantt-charts as well as store-numerical-data. + The function then pops up a confirmer, where a user may select to add the data to the tree. + It takes three parameters, clarity handle, to preserve one's session, filename + the location of the data to be ganttifyed and filedate the creation date of the file.
+ + ++
+
+ ganttify (clarity-handle-object clarity-handle) (filename string) (filedate string) ++ + + +
cl-prompt: (clarity:ganttify myclarityhandle "C:/Files/myfile.txt" "MO/DAY/YR")+ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ get-all-data cl-handle ++ + +
cl-handle---a clarity-handle
+
+
The generic function get-all-data gets all of the rows in the timecourse data table of the database. + It takes one parameter, cl-handle, which preserves the session and identifies the database.
+ + ++
+
+ get-all-data (cl-handle clarity-handle) ++ + +
cl-prompt: (clarity:get-all-data cl-handle) ++ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ get-children node-id ++ + +
node-id---an integer
+
+
+
The generic function get-children gets left and right child of node in a phylogenetic tree. + It takes one parameter, node-id, the unique identifier of the node in the tree and returns the + ids of the nodes two children, or nil if it is a leaf node.
+ + ++
+
+ get-children (node-id integer) ++ + +
cl-prompt: (clarity:get-children 6) +cl-prompt: (8 12)+ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ get-consensus-terms cl-handle node-id term-name sequence ++ + +
cl-handle---a clarity-handle
+
node-id---an integer
+
+
+
The generic function get-consensus-terms gets the corresponding consensus terms from the database for a + node in the tree. It takes two parameters, clarity-handle, which identifies the clarity database; and node-id, the + integer id of the tree node for which to find the terms. It returns a list of the ontology terms that are in the + consensus.
+ + ++
+
+ get-consensus-terms (cl-handle clarity-handle) (node-id integer) ++ + +
cl-prompt: (clarity:get-consensus-terms cl-handle 7)
+cl-prompt: '("Apoptosis" "M phase of mitotic cell cycle" "pathogenesis")
+
+ None.
+ +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ get-data-terms cl-handle node-id term-name sequence ++ + +
cl-handle---a clarity-handle
+
data-id---an integer
+
+
+
The generic function get-data-terms gets the corresponding consensus terms from the database for a + node in the tree. It takes two parameters, clarity-handle, which identifies the clarity database; and data-id, the + integer id of the timecourse dataset for which to find the terms. It returns a list of the ontology terms that are in the + consensus.
+ + ++
+
+ get-data-terms (cl-handle clarity-handle) (data-id integer) ++ + +
cl-prompt: (clarity:get-data-terms cl-handle 9)
+cl-prompt: '("Apoptosis" "M phase of mitotic cell cycle" "pathogenesis")
+
+ None.
+ +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ get-node-terms node-id ++ + +
node-id---an integer
+
+
The generic function get-node-terms gets all of the terms associated with a tree node in the phylogenetic tree. + It takes one parameter, node-id, the unique identifier of the node in the tree and returns the + terms associated with the node. These terms will be part of the dataset associated with the node if it is a leaf + or part of the consensus sequence associated with the node if it is internal.
+ + ++
+
+ get-node-terms (node-id integer) ++ + +
cl-prompt: (clarity:get-node-terms 6)
+cl-prompt: ("cell death" "M phase" "mitotic anaphase A")
+
+ None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ get-root cl-handle ++ + +
cl-handle---a clarity-handle
+
+
The generic function get-root returns the tree id of the root node in the phylogenetic tree. It takes one parameter, + clarity-handle, which identifies the clarity database.
+ + ++
+
+ get-root (cl-handle clarity-handle) ++ + +
cl-prompt: (clarity:get-root cl-handle) +cl-prompt: 8+ +
None.
+ +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ insert-node cl-handle new-node-id sibling-node-id ++ + +
cl-handle---a clarity-handle
+
new-node-id---an integer
+
sibling-node-id---an integer
+
+
The generic function insert-node inserts a new node as the sibling of the specified node in the phylogenetic tree. + It creates a parent node for the specified nodes and inserts it in the appropriate place. The function takes three parameters, + clarity-handle, which identifies the clarity database; new-node, which is the integer id of the new node in the tree table + of the database and sibling-node-id, which is the id of the node to which the new node is most similar and the node + which will be its sibling in the phylogenetic tree.
+ + ++
+
+ insert-node (cl-handle clarity-handle) (new-node-id integer) (sibling-node-id integer) ++ + +
cl-prompt: (clarity:insert-node cl-handle 7 9)+ +
None.
+ +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ insert clarity-handle filename filedate ++ + +
clarity handle---a clarity-handle
+
filename--- a string or path
+
filedate--- a string
+
+
+
The generic function insert inserts a datafile into the database. It calls the functions ganttify, store-gantt-charts as well as store-numerical-data. + The function then pops up a confirmer, where a user may select to add the data to the tree. + It takes three parameters, clarity handle, to preserve one's session, filename + the location of the data to be inserted and filedate the creation date of the file.
+ + ++
+
+ insert (clarity-handle-object clarity-handle) (filename string) (filedate string) ++ + + +
cl-prompt: (clarity:insert myclarityhandle "C:/Files/myfile.txt" "MO/DAY/YR")+ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ lastid cl-handle table ++ + +
cl-handle---a cl-handle
+
table---a string
+
+
The generic function lastid returns the value of the more recently created id number for a table. + It takes two parameters, cl-handle, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and table a string that identifies the table.
+ + ++
+
+ lastid (cl-handle clarity-handle) (table string) ++ + +
cl-prompt: (clarity:lastid cl-handle :table "timecourse_data") ++ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ needleman-wunsch string-1 string-2 ++ + +
string-1---a string
+
string-2---a string
+
+
The generic function needleman-wunsch uses the Needleman Wunsch algorithm to align two strings and then returns their + alignment score. It takes two parameters string-1 and string-2, the strings to be aligned.
+ + ++
+
+ needleman-wunsch (string-1 string) (string-2 string) ++ + +
cl-prompt: (clarity:needleman-wunsch "UDUUID" "UUDDID") + cl-prompt: -2+ +
None.
+ +SCORE-PAIR
+ SCORE-PAIR-CONSENSUS
+ ALIGN-CHARTS
+ ALIGN-TO-CONSENSUS
None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ score-pair-consensus cl-handle timecourse-id consensus-id ++ + +
cl-handle---a cl-handle
+
timecourse-id---an integer
+
consensus-id---an integer
+
+
Given a time course id and a consensus id (note that the consensus id is equivalent to a tree id), + score-pair-consensus computes their alignment and returns the score. + It takes three parameters, cl-handle, which preserves the session; timecourse-id which identifies the timecourse + dataset and consensus id which identifies the consensus sequence in the database.
+ + ++
+
+ score-pair-consensus (cl-handle clarity-handle) (timecourse-id integer) (consensus-id integer) ++ + +
cl-prompt: (clarity:score-pair-consensus cl-handle 6 8) + cl-prompt: 12+ +
None.
+ +None.
+ +ALIGN-CHARTS
+ SCORE-PAIR
+ ALIGN-TO-CONSENSUS
+ STRING-ALIGNMENT
None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ score-pair cl-handle timecourse-id-1 timecourse-id-2 ++ + +
cl-handle---a cl-handle
+
timecourse-id-1---an integer
+
timecourse-id-2---an integer
+
+
Given two timecourse data ids, score-pair computes their alignment and returns the score. + It takes three parameters, cl-handle, which preserves the session; and timecourse-id-1 and timecourse-id-2, + which are the numerical ids identifying the timecourse datasets in the database.
+ + ++
+
+ score-pair (cl-handle clarity-handle) (timecourse-id-1 integer) (timecourse-id-2 integer) ++ + +
cl-prompt: (clarity:score-pair cl-handle 6 8) + cl-prompt: 12+ +
None.
+ +None.
+ +ALIGN-CHARTS
+ SCORE-PAIR-CONSENSUS
+ ALIGN-TO-CONSENSUS
+ STRING-ALIGNMENT
None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ score char1 char2 ++ + +
char-1---a character
+
char-2---a character
+
+
The generic function score is used to compute the score of two characters during alignment using the string-alignment + function. It takes two parameters char-1 and char-2, the characters being scored.
+ + ++
+
+ score (char-1 character) (char-2 character) ++ + +
cl-prompt: (clarity:score #\D #\I) +cl-prompt: -1+ +
None.
+ +None.
+ +This is the function that should be edited if you would like to alter the scoring.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ store-consensus-sequence cl-handle node-id term-name sequence ++ + +
cl-handle---a clarity-handle
+
node-id---an integer
+
term-name---a string
+
sequence---a string
+
+
+
The generic function store-consensus-sequence stores a consensus sequence and its identifying information + in the database. It takes four parameters, clarity-handle, which identifies the clarity database; node-id, the + integer id of the tree node the consensus sequence belongs to; term name, and sequence which is a gantt chart + sequence.
+ + ++
+
+ store-consensus-sequence (cl-handle clarity-handle) (node-id integer) (term-name string) + (sequence string) ++ + +
cl-prompt: (clarity:store-consensus-sequence cl-handle 7 "apoptosis" "UDDIDN")+ +
None.
+ +None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ store-gantt-chart cl-handle data-id file ++ + +
cl-handle---a cl-handle
+
data-id---an integer
+
chart---a list
+
+
The generic function store-gantt-chart stores a single gantt chart and term associated with a dataset in the database. + It takes three parameters, cl-handle, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and a list of the term and its associated gantt chart.
+ + ++
+
+ store-gantt-chart (cl-handle clarity-handle) (data-id integer) (chart list) ++ + +
cl-prompt: (clarity:store-gantt-chart cl-handle 6 '("apoptosis" "UUDDUUNN"))
+
+
+ None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ store-gantt-charts cl-handle data-id chart-list ++ + +
cl-handle---a cl-handle
+
data-id---an integer
+
chart-list---a list
+
+
The generic function store-gantt-charts takes a list of gantt charts and stores them in the database. + It takes three parameters, cl-handle, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and a list of gantt charts created with the ganttify function.
+ + ++
+
+ store-gantt-charts (cl-handle clarity-handle) (data-id integer) (chart-list list) ++ + +
cl-prompt: (clarity:store-gantt-charts cl-handle 6 '(("cell cycle" "UDUDU") ("apoptosis" "DDUUU")))
+
+
+ None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ store-numerical-data cl-handle data-id file ++ + +
cl-handle---a cl-handle
+
data-id---an integer
+
file---a path to a file
+
+
The generic function store-numerical-data takes a file containing a numerical timecourse dataset and stores it in the database. + It takes three parameters, cl-handle, which preserves the session; data-id, which is the numerical id + identifying the timecourse dataset in the database; and a path to the file to insert.
+ + ++
+
+ store-numerical-data (cl-handle clarity-handle) (data-id integer) (file path) ++ + +
cl-prompt: (clarity:store-numerical-data cl-handle 6 "C:/data/dataset.txt") ++ +
None.
+ +None.
+ +None
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ string-alignment string-1 string-2 ++ + +
string-1---a string
+
string-2---a string
+
+
The generic function string-alignment uses a variant of the Needleman-Wunsch and Smith-Waterman algorithms to align two strings and then returns their + alignment score. It takes two parameters string-1 and string-2, the strings to be aligned.
+ + ++
+
+ string-alignment (string-1 string) (string-2 string) ++ + +
cl-prompt: (clarity:string-alignment "UDUUID" "UUDDID") + cl-prompt: -2+ +
None.
+ +SCORE-PAIR
+ SCORE-PAIR-CONSENSUS
+ ALIGN-CHARTS
+ ALIGN-TO-CONSENSUS
None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ tree-insert-recursive cl-handle new-node current-node ++ + +
cl-handle---a clarity-handle
+
new-node---an integer
+
current-node---an integer
+
+
The generic function tree-insert-recursive inserts new data into the phylogenetic tree. It takes three parameters, + clarity-handle, which identifies the clarity database; new-node, which is the integer id of the new node in the tree table + of the database and current-node, which is the id of the current node to which the new node is being aligned. It returns two + values, the number of the node to which the alignment score was highest, as well as that score.
+ + ++
+
+ tree-insert-recursive (cl-handle clarity-handle) (new-node integer) (current-node integer) ++ + +
cl-prompt: (clarity:tree-insert-recursive cl-handle 7 9) + cl-prompt: 7 42+ +
None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ +CLARITY
+
+ tree-insert cl-handle timecourse-data-id ++ + +
cl-handle---a clarity-handle
+
timecourse-data-id---an integer
+
+
The generic function tree-insert inserts new data into the phylogenetic tree. It takes two parameters, + clarity-handle, which identifies the clarity database; and timecourse-data-id, the id of the new data to be inserted. + It calls the recursive function tree-insert-recursive after creating a new tree node for the data.
+ + ++
+
+ tree-insert (cl-handle clarity-handle) (timecourse-data-id integer) ++ + +
cl-prompt: (clarity:tree-insert cl-handle 7)+ +
None.
+ +None.
+ +None.
+ + + +News in chronological order, most recent on top. +
+ ++ DISCLAIMER: The code associated to these documents is not + completely tested and it is bound to contain errors and omissions. + This documentation may contain errors and omissions as well.
+ +The file COPYING contains an LGPL license. You + are advised to use the code at your own risk. No warranty + whatsoever is provided, the author will not be held responsible for + any effect generated by your use of the library, and you can put + here the scarier extra disclaimer you can think of. +
+ +The CVS repository is here. + You can download a tarball directly from there.
+ + + + + + +Questions? Queries? Suggestions? Comments? Please direct them + at me. +
+ +News in chronological order, most recent on top. +
+ +The CLARITY GUI allows users to insert data into the databse, browse the database, and view the phylogenetic-like tree. + Users may view similarities between datasets at various levels of resolution. +
+CL-GODB Screenshot
+
The area below the "Phylogeny" tab is where the tree of data is displayed. A 0 indicates an internal node, which contains a collection of + consensus terms. Nodes with numerical values are labelled with the id number of the dataset with which they are associated. Clicking on an + internal node will display information in regions 2 and 3 of the above diagram. Clicking on a leaf node will display information in the leaf + node tab, which can be selected by clicking.
+These panels, displayed as tree views, contain the terms that are either not in the intersection of the two children of the selected node, + or those which are regulated differently. Clicking on each term in these panels will expand the tree and display a number of windows with colored + icons. The icons represent the terms overall regulation, or activity, in that window of time. Green denotes a term which is down regulated, + red denotes up regulation, and yellow denotes neither. If there is a plus sign next to the window's icon, it means that probe, or gene, information + was provided with the data. Clicking on these icons displays the list of genes.
+Selecting an internal node fills this list panel. It contains the highly similarly regulated terms of the selected node's two + immediate children.
+ + + +Questions? Queries? Suggestions? Comments? Please direct them + at me. +
+ + +News in chronological order, most recent on top. +
+ +CLARITY is a tool and method for the storage and comparison of data with numeric and + set membership components. It is specifically geared toward timecourse microarray data, which is used to + study the activity of genes across time. By using data that has been redescribed into Gene Ontology (GO) terms, and summarizing the regulation + of these terms across time using characters (together forming sequences) we are able to use standard DNA alignment techniques with + these sequences. Due to the prevalence and size of microarray experiments, finding a way to analyze new experiments as well as consider their relation + to prior work is a significant contribution. CLARITY aims to help researchers update their prior findings as new data becomes available, and + to automate this process. Contained in the software is a novel method of comparison, based on Gantt charts, which allows us to reason about + numerical data in a way that we do DNA sequences. I.e. Rather than just looking at the numbers describing one gene across time as compared to another, + we can consider insertions, deletions, mutations in these sequences of numbers. This is done efficiently using a global alignment + with an affine (linear) gap score, a variant of the Needleman-Wunsch and Smith-Waterman algorithms + + +
+ The Gene Ontology (GO), is a controlled vocabulary used to aid the description of genes and gene product attributes in a variety of + organisms. There are three different ontologies that describe molecular functions, biological processes, and cellular components.
+ +CLARITY provides novel methods for computing and visualizing the relationship among large amounts of data. The graphical + interface allows the user to browse the database contents in text form as well as see the data arranged into a phylogenetic tree. + + There is more information on this interface here +
+
The CLARITY
+ dictionary contains all the definitions comprising the library.
+
+
+
This project was sponsored by the Google Summer of Code + program. The Lisp NYC group + provided moral guidance and support. The NYU Courant + Bioinformatics Group provided all the rest.
+ + +None yet.
+ + + +Questions? Queries? Suggestions? Comments? Please direct them + at me. +
+ + +News in chronological order, most recent on top. +
+ +-MySQL
+ -Lispworks
+ -Common SQL
+
+
If you don't have mySQL installed, go to the MySQL Downloads
+ page and follow their instructions. (Note: you probably want the "Community Edition - Generally Available (GA) Release")
+
+
+
+
Open the mysql command line interface (this can be done in Cygwin). Enter the root password +that was created during mysql installation. Replace the uppercase +"DATABASE" with the name of your choice, after entering the comand you will have created a database +named clarity with the tables needed for the library.
+mysql> \. C:/Path-to-clarity/utilities/clarity.sql;+
Alternatively, you may enter your password and run the creation script in one step:
+Prompt: mysql -u root -p < C:/Path-to-clarity/utilities/clarity.sql;+
+The clarity database is now set up and currently empty. +
+You may close the command line now. Open Microsoft ODBC
+Administrator (may be called "Data Sources (ODBC)" in shorcuts).
+Click add and then create a new data source using the MySQL ODBC
+driver. Choose a name for your Data Source (note: you will be using
+this name later
+when you connect with clarity), then input the User/Password you
+will be using to connect to the database. If the database is on your
+computer, you
+you can type in "localhost" or leave the server field blank. Now you
+should be able to select the database you created earlier in the drop
+down menu.
+
+
+
+ Get the CLARITY tarball from the downloads page and unpack it + into a directory where Lispworks will be able to see it. +
++You can either use mk:defsystem or compile and load the files in the +following order: clarity-package, decimal-number, database-functions, alignment-functions. In order to +use the gui, go into +gui/impl-dependent/lwcapi and then compile and load the insert-data-interface, clarity-interface, +clarity-interface-functions, clarity-database-setup-interface, and start-gui.
+If you don't already have it, you can download it from the CLOCC Sourceforge page + You can load it as below at the lisp prompt, or you can add that line to your Lisp startup file.
+cl-prompt: (load "path/to/defsystem.lisp") +; Loading text file Z:\lisp\defsystem-3.x\defsystem.lisp +#P"Z:/lisp/defsystem-3.x/defsystem.lisp"+ +
+If you're not working in the directory where you put the CLARITY +library, you will need to add that path to your registry. Otherwise, +you should +be able to start from "find-system" +
+cl-prompt: (mk:add-registry-location "/path/to/clarity/") +cl-prompt: (mk:find-system :clarity) +System CLARITY not loaded. Shall I try loading it? y + +; Loading text file Z:\clarity\clarity.system +#<DEFSYSTEM: CLARITY> ++
+Now just compile and load the system.
+cl-prompt: (mk:compile-system :clarity) + +cl-prompt: (mk:load-system :clarity)+ +
+ In the Lispworks Listener, start by creating a handle.
+
cl-prompt: (clarity:make-clarity-handle)+ Now connect to your database.
cl-prompt: (clarity:connect clarity::*current-clarity-handle* "DataSourceName/username/password")+ +
From here you can call any function in the library, or you can load the GUI with the following command.
+cl-prompt: (clarity::start-clarity-gui)+ +
To save your database information for future sessions, Open the clarity-database-setup-interface file and + change the three variables clarity-db-name, clarity-db-user, and clarity-db-password to reflect your setup.
+ + + +In the future the CLARITY may be ported to clsql
+Questions? Queries? Suggestions? Comments? Please direct them + at me. +
+ +News in chronological order, most recent on top. +
+ +The relevant links for the CLARITY project are: +
Questions? Queries? Suggestions? Comments? Please direct them + at me. +
+