graph LR
User_Interface_Entry_Points["User Interface & Entry Points"]
Data_Management_Utilities["Data Management & Utilities"]
Antibody_Analysis_Core["Antibody Analysis Core"]
Asynchronous_Task_Management["Asynchronous Task Management"]
Application_Monitoring_Metrics["Application Monitoring & Metrics"]
User_Interface_Entry_Points -- "invokes" --> Asynchronous_Task_Management
User_Interface_Entry_Points -- "invokes" --> Antibody_Analysis_Core
User_Interface_Entry_Points -- "uses" --> Data_Management_Utilities
User_Interface_Entry_Points -- "reports to" --> Application_Monitoring_Metrics
Data_Management_Utilities -- "provides input to" --> Antibody_Analysis_Core
Antibody_Analysis_Core -- "provides results to" --> Data_Management_Utilities
Data_Management_Utilities -- "used by" --> User_Interface_Entry_Points
Data_Management_Utilities -- "used by" --> Asynchronous_Task_Management
Data_Management_Utilities -- "reports to" --> Application_Monitoring_Metrics
Antibody_Analysis_Core -- "executed by" --> Asynchronous_Task_Management
Antibody_Analysis_Core -- "executed by" --> User_Interface_Entry_Points
Antibody_Analysis_Core -- "reports to" --> Application_Monitoring_Metrics
Asynchronous_Task_Management -- "schedules and invokes" --> Antibody_Analysis_Core
Asynchronous_Task_Management -- "receives requests from" --> User_Interface_Entry_Points
Asynchronous_Task_Management -- "uses" --> Data_Management_Utilities
Asynchronous_Task_Management -- "reports to" --> Application_Monitoring_Metrics
Application_Monitoring_Metrics -- "receives data from" --> User_Interface_Entry_Points
Application_Monitoring_Metrics -- "receives data from" --> Data_Management_Utilities
Application_Monitoring_Metrics -- "receives data from" --> Antibody_Analysis_Core
Application_Monitoring_Metrics -- "receives data from" --> Asynchronous_Task_Management
click User_Interface_Entry_Points href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/BioPhi/User_Interface_Entry_Points.md" "Details"
click Data_Management_Utilities href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/BioPhi/Data_Management_Utilities.md" "Details"
click Antibody_Analysis_Core href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/BioPhi/Antibody_Analysis_Core.md" "Details"
click Asynchronous_Task_Management href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/BioPhi/Asynchronous_Task_Management.md" "Details"
click Application_Monitoring_Metrics href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/BioPhi/Application_Monitoring_Metrics.md" "Details"
Abstract Components Overview
User Interface & Entry Points [Expand]
Serves as the primary interface for users, managing both command-line interactions and the web application. It handles initial user input and dispatches requests for processing or task initiation.
Related Classes/Methods:
biophi/common/cli/main.py(1:1)biophi/common/cli/web.py(1:1)biophi/common/web/views.py(1:1)biophi/humanization/web/views.py(1:1)
Data Management & Utilities [Expand]
Responsible for all aspects of data handling, including reading, parsing, validating, and formatting various biological sequence inputs and outputs. It also provides general utilities for sequence manipulation.
Related Classes/Methods:
Antibody Analysis Core [Expand]
Contains the fundamental algorithms and logic for antibody humanization (e.g., Sapiens humanization, CDR grafting) and humanness score calculations, including comparisons against germline sequences and statistical analysis.
Related Classes/Methods:
biophi/humanization/methods/humanization.py(1:1)biophi/humanization/methods/humanness.py(1:1)biophi/humanization/methods/stats.py(1:1)
Asynchronous Task Management [Expand]
Manages the scheduling, execution, and monitoring of long-running computational tasks (e.g., humanization, humanness analysis) to ensure the application remains responsive, especially in a web context.
Related Classes/Methods:
Application Monitoring & Metrics [Expand]
Collects and records various application events, such as user submissions, task statuses, and operational metrics. This data is crucial for system health monitoring, debugging, and usage pattern analysis.
Related Classes/Methods: