Scientific web programming Part 2

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Scientific web programmingPart 2

• (in which the saga continues)

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PHP functions

• We don't need PHP to do what we just did
• We can send output just as easily in HTML
• This is harder to do in HTML though

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From numbers to nucleotides
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ltifgt statement reformulated
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Many choices ltswitchgt statement
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Code re-use and functions
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Short-hand notation
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Intermezzo configuring PHP

• What if shorthand fails?
• Go to php.ini

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Further compartmentalization
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ltwhilegt loop
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ltforgt loop
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Help, Im lost! d

• What to do if you need help?
• Get to know your IDE
• Syntax highlighting, intellicode (Ctrlspace)
• Instant feedback on incorrect syntax
• Tag matching
• Should you buy a book on PHP?
• Should you go to the library?
• Another way go to http//www.php.net

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Parameterized functions
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Default values for arguments
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Multiple functions
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Built-in PHP fucntions

• Luckily, many functions already exist
• Functions that operate on text (strings)
• Strlen() gives you the size of a string
• Substr() lets you cut out a piece of a string
• http//us2.php.net/manual/en/ref.strings.php
• Mathematical functions
• Rand(), round(), abs(), sin(), cos(), atan(),
  exp()
• http//us2.php.net/manual/en/ref.math.php

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Pop quiz

• How many genes are there in
• Saccharomyces cerevisiae (bakers yeast)?
• Homo sapiens?
• Arabidopsis thaliana?
• How many forms of Ig are there?
• Light chain combinations?
• Heavy chain combinations?
• Think DNA, RNA, protein data

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Introducing arrays

• When a simple string doesnt suffice
• Use arrays
• Different genes in a genome
• Alternative splicing forms of a single gene
• Example
• http//us2.php.net/manual/en/function.array.php

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Where to from here?

• Exercises on covered material
• Tuesday HTML forms, text files
• Wednesday databases

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Questions

• http//lab.bcb.iastate.edu/training/webdev/nmsu