Chapter 10. Incorporating Third-party Applications

Table of Contents

10.1. Benefits to Incorporating Applications into EMBOSS
10.2. Wrappers and Ports
10.3. Pros and Cons
10.3.1. Development Cost
10.3.2. Flexibility
10.3.3. Limitations
10.3.4. Maintenance Cost
10.3.5. Support Cost
10.3.6. Perceived Risk
10.3.7. Summary
10.4. How To Wrap Third Party Applications
10.4.1. Planning and Design
10.4.2. ACD File Development
10.4.3. C Source Code Development
10.4.4. Quality Assurance Testing
10.4.5. Documentation
10.4.6. Integration
10.5. HMMER Wrapper: Overview
10.6. HMMER Wrapper: hmmbuild
10.6.1. HMMER Wrapper: ehmmbuild.acd Application Definition and Inputs Required Section Advanced Section Output Section
10.6.2. HMMER Wrapper: ehmmbuild.c Header Documentation main() Function Processing the ACD File Housekeeping and File Format Handling Building the Command line Invoking the Application
10.7. HMMER Wrapper: hmmalign
10.7.1. HMMER Wrapper: hmmalign.acd Input Section Output Section
10.7.2. HMMER Wrapper: ehmmalign.c Documentation Header main() Function, Housekeeping and ACD File Processing File Format Handling Building the Command line Invoking the Application
10.8. Reducing The Length Of The Command Line
10.9. How To Port Third Party Applications
10.10. HMMER port
10.10.1. HMMER Port: ohmmalign.acd
10.10.2. HMMER Port: ohmmalign.c Heading Code main() Function Variable Declarations ACD File Processing Handling Input Data Exiting Cleanly
10.11. Summary