GenExplorer-Use Cases-Version1

Use Case ID	GENEX01	Use Case Name	Highlighting Nucleotides
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		When clicked on a nucleotide base in DNA sequence, highlighting corresponding nucleotide in mRNA sequence and amino acid.
Preconditions		GenExplorer must be running
Post conditions		Highlighting parts show up
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		Actor Actions		*System Responses*
		1. User clicks once on DNA nucleotide base		2.Highlights the DNA base nucleotide and corresponding mRNA nucleotide and amino acid
Alternative Course		Actor Actions		System Responses
		1. User clicks once on DNA nucleotide base		2. Highlights DNA nucleotide only, as corresponding mRNA, amino acid are not present
Exceptions		Actor Actions		System Responses
		1. User clicks on promoter/terminator		2. Displays an alert message
Includes (another use case id)
Special requirements		DNA, mRNA and Amino acid sequences must be present
Assumptions
Notes and issues

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Use Case ID	GENEX02	Use Case Name	Highlighting
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		When clicked on a nucleotide base in RNA sequence, highlighting corresponding nucleotide in DNA sequence and amino acid.
Preconditions		GenExplorer must be running
Post conditions		Highlighting parts show up
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User clicks once on mRNA nucleotide base.		2.Highlights the mRNA nucleotide and corresponding DNA nucleotide and amino acid.
Alternative Course		Actor Actions		System Responses
		1. User clicks once on mRNA nucleotide base		2. Highlights mRNA and DNA nucleotide only, as corresponding amino acid is not present
Exceptions		*Actor Actions*		System Responses
		1. User clicks on start sequence & end sequence		2. Displays an alert message
Includes (another use case id)
Special requirements		DNA, mRNA and Amino acid sequences must be present
Assumptions
Notes and issues

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Use Case ID	GENEX03	Use Case Name	Highlighting
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		When clicked on an amino acid, corresponding nucleotides in DNA and mRNA are highlighted
Preconditions		GenExplorer must be running
Post conditions		Highlighting parts show up
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User clicks once on an amino acid		2.Highlights the corresponding DNA and mRNA nucleotides
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements		DNA, mRNA and Amino acid sequences must be present
Assumptions
Notes and issues

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Use Case ID	GENEX04	Use Case Name	Editing
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		Editing a DNA nucleotide base in the input sequence
Preconditions		GenExplorer must be running and a valid DNA sequence must be present
Post conditions		DNA nucleotide changed to the entered value
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User double-clicks on a DNA nucleotide 3. Enters new nucleotide		2. Requests for the new nucleotide base 4. If the nucleotide base matches with its pair, changes all DNA, mRNA and amino acid sequences, otherwise displays error message
Alternative Course		*Actor Actions*		System Responses
		1. User double-clicks on a DNA nucleotide 3. Enters new nucleotide		2. Requests for the new nucleotide base 4. If the value is not one of A, C, G, T displays an error message
Exceptions		*Actor Actions*		System Responses
		1. User double clicks on promoter/ terminator to edit		2. Displays error message
Includes (another use case id)
Special requirements		DNA, mRNA and Amino acid sequences must be present
Assumptions
Notes and issues

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Use Case ID	GENEX05	Use Case Name	Help
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		When the user requests for help on a subject, displays the help information
Preconditions		GenExplorer must be running
Post conditions		Help information presented
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User selects ‘Help’ option and enters/selects a help topic		2. Displays help window of corresponding subject
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX06	Use Case Name	Resetting DNA Sequence
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		Resets the DNA sequence to a default value or clears the screen
Preconditions		GenExplorer must be running and at least once sequence exists on the screen
Post conditions		Screen cleared or sequence set to a default value
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User selects ‘Reset DNA sequence’ option 3. Selects ‘Yes’ to confirm		2. Asks for user confirmation to reset 4. Resets the DNA sequence to a default value or clears the screen
Alternative Course		*Actor Actions*		System Responses
		1. User selects ‘Reset DNA sequence’ option 3. Selects ‘No’ to confirm		2. Asks for user confirmation to reset 4. No changes made
Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements		Any of the sequences must be present
Assumptions
Notes and issues

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Use Case ID	GENEX07	Use Case Name	Printer Friendly Version
Created by	Sumana	Last Updated by
Date Created	10/7/03	Date Last Updated
Actor		Student, Instructor, Tester
Description		To display a printer friendly version of all sequences.
Preconditions		GenExplorer must be running and at least once sequence exists on the screen
Post conditions		Printer friendly version of sequences displayed
Priority: (low/medium/high)		High
Frequency of Use		Low / Medium
Normal Course
		*Actor Actions*		*System Responses*
		1. User selects ‘Printer Friendly Version’ option		2. Displays printer friendly version of all sequences in a new window
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements		Any of the sequences must be present
Assumptions
Notes and issues

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Use Case ID	GENEX08	Use Case Name	Unit Testing
Created by	Prasoon	Last Updated by
Date Created	10/14/03	Date Last Updated
Actor		Developer.
Description		Used for testing the system and comparing the outputs with the help of a script.
Preconditions		GenExplorer must be running
Post conditions		All tests pass successfully.
Priority: (low/medium/high)		High
Frequency of Use		Very High
Normal Course
		*Actor Actions*		*System Responses*
		1. Runs the application in test mode		2. System reads the input file for input sequences and displays the result. 3. Gives a detailed report on system responses.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements		Input file must be present.
Assumptions
Notes and issues		This test should run every time there is a change in the system.

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Use Case ID	GENEX09	Use Case Name	Analysis of students work
Created by	Prasoon	Last Updated by
Date Created	10/14/03	Date Last Updated
Actor		Developer.
Description		The TA runs the application in a batch mode and gets the detailed report of students work
Preconditions		GenExplorer is running.
Post conditions		A detailed report of students work is generated.
Priority: (low/medium/high)		Low
Frequency of Use		Low
Normal Course
		*Actor Actions*		*System Responses*
		1. Runs the application in test mode		2. System starts reading on the saved files of students work and compares with the TA specifications. 3. Gives a detailed report on system responses.
Alternative Course		*Actor Actions*		System Responses
		1. If TA wants to retrieve the work of a particular student then it enter the student ID		2. System displays the student work saved in the files.
Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements		Input file must be present.
Assumptions
Notes and issues		This test should run every time there is a change in the system.

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Use Case ID	GENEX10	Use Case Name	Scanning for promoter and terminator
Created by	Prasoon	Last Updated by
Date Created	10/14/03	Date Last Updated
Actor		Developer.
Description		Checking for promoter and terminator in a sequence in normal mode.
Preconditions		GenExplorer is running.
Post conditions		The promoter and terminator are detected and displayed.
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User clicks on the “Express Gene” button		2. System scans the input string for the promoter and the terminator. 3. If found it displays the promoter and the terminator.
Alternative Course		*Actor Actions*		System Responses
		1. User clicks on the “Express Gene” button.		2. No promoter and terminator found.
Exceptions		*Actor Actions*		System Responses
		1. User clicks on the “Express Gene” button.		2. More than one promoter and terminator found??
Includes (another use case id)
Special requirements
Assumptions		Sequence consists of only A, T, C or G
Notes and issues

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Use Case ID	GENEX11	Use Case Name	Check input sequence
Created by	Chitra	Last Updated by
Date Created	10/09/03	Date Last Updated
Actor		User (Instructor, Student, T.A.)
Description		Check if the user entered the valid letter (T, A, G, C which represents the four types of Nucleotides) while entering the gene sequence.
Preconditions		The user types in the gene sequence without paying attention to the four letters (T, A, G, C) that are valid for the gene sequence.
Post conditions
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. User types in a letter		2a. if the length of gene on typing the letter doesn’t exceed the valid gene length then 2a1. if the letter typed is a T or A or G or C then return to the user and read in the next letter and check for the Valid input letter. 2a2. Else throw an error message. 2b. else throw error message.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX12	Use Case Name	Transcription
Created by	Chitra	Last Updated by
Date Created	10/09/03	Date Last Updated
Actor		System
Description		To transcribe a strand of DNA sequence into an mRNA.
Preconditions		The user has entered a valid promoter and terminator sequence of the gene.
Post conditions
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. The system provides a gene sequence that the user had input. 3. The resulting mRNA is displayed on the screen.		2. The sequence gets transcribed into a premature mRNA
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses
		1.There is no input from the system as the user did not input the right promoter or terminator sequence for the gene.		2. Error Message will be thrown.
Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX13	Use Case Name	Splicing
Created by	Chitra	Last Updated by
Date Created	10/09/03	Date Last Updated
Actor		System
Description		To separate the Introns and the Exons from the premature mRNA.
Preconditions		Valid promoter and terminator sequence of the gene exists.
Post conditions
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. The system provides a premature mRNA. 3. The resulting mature mRNA is displayed on the screen.		2. The system scans the mRNA and based on the promoter and the terminator sequence of the exons. Separates the exons from the introns such that all the exons combine to form mature mRNA.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses
		1. There is no input from the system as the user did not input the right promoter or terminator sequence for the gene.		2. Error Message will be thrown.
Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX14	Use Case Name	Translation
Created by	Chitra	Last Updated by
Date Created	10/09/03	Date Last Updated
Actor		System
Description		To translate the mature mRNA into a protein sequence.
Preconditions		Valid promoter and terminator sequence of the gene exists
Post conditions
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. The system provides a mature mRNA sequence. 3. The resulting protein sequence is displayed on the screen.		2. The system scans the mRNA and using the codon table finds the corresponding amino acid for each codon.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses
		1. There is no input from the system as the user did not input the right promoter or terminator sequence for the gene.		2. Error Message will be thrown.
Includes (another use case id)		GENEX15
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX15	Use Case Name	Codon Table
Created by	Chitra	Last Updated by
Date Created	10/09/03	Date Last Updated
Actor		System
Description		To translate the given sequence of codon into an amino acid.
Preconditions		Valid promoter and terminator sequence of the gene exists.
Post conditions
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. The system provides a codon sequence.		2. The system finds the corresponding amino acid and returns.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses
		1. There is no corresponding amino acid for the codon sequence.		2. Error Message will be thrown.
Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX16	Use Case Name	Running Non Strict Mode
Created by	Chitra	Last Updated by
Date Created	10/09/03	Date Last Updated
Actor		User (Instructor, Student, T.A.)
Description		To run the system in a non strict for the promoter and the terminator sequences of the gene.
Preconditions		The user has defined the user mode to be of the non strict mode type.
Post conditions
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. The user types in the gene sequence.		2. The system checks for a valid promoter and the valid terminator sequence with one variation in the provided promoter and terminator sequences.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX17	Use Case Name	Close
Created by	Ziping	Last Updated by
Date Created	10/08/03	Date Last Updated
Actor		Students
Description		To close a current opened file.
Preconditions		A file is opened.
Post conditions		The file is closed and disappeared from screen.
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. Users activate the close function. 3. User selected a skip option and confirm.		2. To display save, skip, or cancel options. 4. Closing the file and back to the previous file or blank.
Alternative Course		*Actor Actions*		System Responses
		1. User selects a save option and confirms 3. User input/choose a directory and a file name and confirm. 5.User selects a cancel option		2. Display a directory and files list. 4. File saved and disappeared from the screen.
Exceptions		*Actor Actions*		System Responses

Includes (another use case id)		UC-SaveAs, UC-Save
Special requirements
Assumptions
Notes and issues		Depends on if the client wants the students to save their work for later use

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Use Case ID	GENEX18	Use Case Name	Open
Created by	Ziping	Last Updated by
Date Created	10/08/03	Date Last Updated
Actor		Students
Description		To open an existed file in a computer.
Preconditions		There one file at least exists.
Post conditions		The file is open and shows up.
Priority: (low/medium/high)		Medium
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. Users activate the open function. 3. User selected a file and confirm		2. To display a directory option and a files list. 4. Selected file shows up.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses
		1. User cancels open		2. Back to the previous display
Includes (another use case id)		UC-SaveAs, UC-Save
Special requirements
Assumptions
Notes and issues		Depends on if the client wants the students to save their work for later use

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Use Case ID	GENEX19	Use Case Name	QuestionMark
Created by	Ziping	Last Updated by
Date Created	10/08/03	Date Last Updated
Actor		Students
Description		To help students retrieve in a easy way an explanation on a selected target
Preconditions
Post conditions		User-specified target related information shows up.
Priority: (low/medium/high)		Low
Frequency of Use		Low
Normal Course
		*Actor Actions*		*System Responses*
		1. Users activate the question mark. 3. Move the icon to the target and activate the target		2. Question mark function is highlighted and its icon shows up. 4. Target related information shows up.
Alternative Course		*Actor Actions*		System Responses

Exceptions		*Actor Actions*		System Responses

Includes (another use case id)		UC - Help
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX20	Use Case Name	Save
Created by	Ziping	Last Updated by
Date Created	10/08/03	Date Last Updated
Actor		Students
Description		To help students to save their practice or homework in a certain format file in a computer
Preconditions		Gene sequences exist
Post conditions		Files are created and saved in a certain directory on computers.
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. Executing a Save function. 3. Confirm		2. Display current directory and the file name 4. Save and back to the current display.
Alternative Course		*Actor Actions*		System Responses
		1. Choose another directory, file name 3. Cancel save function		2.Save and back to the current display 4. Cancel save and back to the current display
Exceptions		*Actor Actions*		System Responses
		1. Close the running application 3. Close the current working stage		2. Display alert information 4. Display alert information
Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX21	Use Case Name	SaveAs
Created by	Ziping	Last Updated by
Date Created	10/08/03	Date Last Updated
Actor		Students
Description		To help students to save their practice or homework in a certain format and a new file name in a computer
Preconditions		Gene sequences exist
Post conditions		User-specified files are created and saved in a certain directory on computers.
Priority: (low/medium/high)		High
Frequency of Use		High
Normal Course
		*Actor Actions*		*System Responses*
		1. Executing a SaveAs function. 3. Choose another directory, a file name, and confirm		2. Display current directory and the file name 4. Save and back to the current display.
Alternative Course		*Actor Actions*		System Responses
		1. Cancel save function 3. Choose a file name that already exists 5. Confirm save. 7. Confirm cancel		2. Cancel save and back to the current display. 4. Display alert information 6. Save and back to the current display 8. Cancel save and back to the current display
Exceptions		*Actor Actions*		System Responses
		1. Close the running application 3. Close the current working stage		2. Display alert information 4. Display alert information
Includes (another use case id)
Special requirements
Assumptions
Notes and issues

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Use Case ID	GENEX22	Use Case Name	ZoomInOut
Created by	Ziping	Last Updated by
Date Created	10/08/03	Date Last Updated
Actor		Students, Instructors
Description		To help users to see an enlarged gene sequence section in order to get specific detail of some parts of gene sequence
Preconditions		Gene sequences exist
Post conditions		A new enlarged specific sequence part shows up.
Priority: (low/medium/high)		Medium
Frequency of Use		Medium
Normal Course
		*Actor Actions*		*System Responses*
		1. Activates ZoomInOut feature. 3. Enlarge action on a target sequence segment.		2. Ready to execute ZoomInOut 4. Responds by a size changed target sequence.
Alternative Course		*Actor Actions*		System Responses
		1. Giving a specific size request 3. Giving a fraction of original size.		2. Shows up the required sequence. 4. Shows up the size-changed sequence.
Exceptions		*Actor Actions*		System Responses
		1. Continuously doing same action on a same target		2. Keeping size change until reach a preset size limit.
Includes (another use case id)		UC-help, UC-highlighting, UC-print
Special requirements		Do not use mouse right click for the reason of using Mac.
Assumptions
Notes and issues		UC id will be decided with other UCs together

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Analysis of students work

Scanning for promoter and terminator