Finding Multiple Genes

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Do curso por Duke University

Java Programming: Solving Problems with Software

2085 classificações

Duke University

Java Programming: Solving Problems with Software

2085 classificações

Curso 1 de 4 em Specialization Object Oriented Programming in Java

Building upon Duke’s “Programming and the Web for Beginners” course, you will grow in your ability to be a problem-solver and programmer by writing Java programs. We are excited that you've chosen to learn Java with us! You will soon be able to solve problems that you find interesting and useful by practicing a design process you will learn in this course. Java concepts presented in this course include basic control flow; object-oriented concepts including classes and methods; custom, open-source classes; and a design-implement-debug process that you can continue to leverage as you build your experience and knowledge of programming principles. The custom, open-source classes will provide a consistent application programming interface (API) so that you can write programs that access and transform images, websites, comma separated value (CSV) files and other data files using simple and accessible coding idioms built on the Java Iterable interface. You will learn to design, test, and debug programs and to find and read Java documentation that can serve as the basis for continued study of Java and programming. After completing this course you will be able to: 1. Edit, compile, and run a Java program; 2. Use conditionals and for loops appropriately in a Java program; 3. Use Java API documentation in writing programs. 4. Debug a Java program using the scientific method; 5. Develop a Java method to solve a specific problem; 6. Develop a set of test cases as part of developing a program; 7. Create a class with multiple methods that work together to solve a problem; and 8. Use divide-and-conquer design techniques for a program that uses more than one method.

Na lição

Strings in Java

This module begins with a short presentation from Raluca Gordân, an assistant professor in Duke University’s Center for Genomic and Computational Biology, about an important problem genomics scientists encounter regularly: how to identify genes in a strand of DNA. To tackle this problem, you will need to understand strings: series of characters such as letters, digits, punctuation, etc. After learning about Java methods that work with strings, you will be able to find genes within a DNA string as well as tackle other string related problems, such as finding all of the links in a web page. By the end of this module, you will be able to: (1) Use important methods for the Java String class; (2) Use conditionals, for loops, and while loops appropriately in a Java program; (3) Find patterns in the data represented by strings to help develop the algorithm for your program; (4) Understand the importance of designing programs that keep different data processing steps separate; (5) Use the StorageResource iterable for this course to store some data for further processing; and (6) Rely on Java documentation to better understand how to use different Java packages and classes.

Introduction0:48

Conceptual Understanding4:01

While Loops9:30

While Loop Syntax and Semantics3:06

Coding While Loops6:45

Three Stop Codons5:03

Coding Three Stop Codons - Part I7:45

Coding Three Stop Codons - Part II4:35

Logical And / Or8:01

Coding And / Or6:52

Finding Multiple Genes5:16

Translating to Code8:00

Conheça os instrutores

Owen Astrachan
Professor of the Practice
Computer Science
Robert Duvall
Lecturer
Computer Science
Andrew D. Hilton
Associate Professor of the Practice
Electrical and Computer Engineering
Susan H. Rodger
Professor of the Practice
Computer Science

Hi, so far you've written a method to find a gene and gradually improved it.

It's gotten much more sophisticated than when you first started.

Although it's still a bit of a simplication of what you'd actually do.

Rather than continuing to refine this method,

let's ponder a different facet of searching for genes.

So far, you've only been looking for the first gene in the string.

However, strings may have many genes.

What if you wanted to find them all, and print them all out?

You can already find one.

Although you might want to make some slight adjustments to the methods so

you can start looking midway through the string.

Since you can find one and

you want to find many, you want to repeat steps using a loop.

Loops should be getting pretty familiar by now.

Since you might want to repeat things, as long as there are more genes,

you can make use of the while loop that you recently learned about.

However, there's a bit of a difficulty here.

We wont know if there are more genes until we start searching for them.

This may make it seem hard to write a loop condition.

There are many ways to deal with this situation in code.

But, the one we're going to teach you about is how to use a break statement

to leave the middle of the body of a loop.

We'll work through a slightly shorter example than we normally walk through

in developing the algorithm to print all genes.

If you don't understand this completely when we finish, pause the video and

work through steps 1, 2, and 3 yourself.

We're going to show you how it operates on this DNA string as we write it.

First, we're going to set startIndex to 0.

StartIndex will represent where we start looking for the next gene.

Then we're going to repeat some steps,

as long as there are more genes after startIndex.

We want to find the next gene after startIndex.

We want to print that gene out.

And then set startIndex to just past the end of the gene we found.

To show you how the algorithm would continue working on the string,

we then go back to Step 2 and

keep repeating these steps, as there are more genes after startIndex.

Notice, this is the difficulty we alluded to before.

We need to know if we will find more genes or not, but we haven't looked for

them yet.

We'd find the next gene, print it out, update startIndex,

and then realize we should stop repeating steps because there are no more genes.

However, we have this difficulty.

We need to know if we have more genes in Step 2, but we don't look for

a gene until Step 3, which makes the algorithm a bit awkward to implement.

Really, we'd like to make a decision about whether to keep going or

to stop right here, between Steps 3 and 4.

Here's a slightly modified version of the algorithm which does exactly that.

Notice that our repetition instructions no longer have any condition,

they just say repeat these steps.

We'll figure out later when to stop.

Likewise, we now have another step in the middle of the loop that says,

leave the loop if we did not find any genes.

This would be much easier to implement,

once we learn how to translate these kind of steps into code.

For step two, repeating steps without checking any particular condition,

you can simply write, while true.

If the condition of a while loop is simply true, the code will always enter the loop

body when we reach the top, because true always evaluates to true.

The other new piece of Java syntax we'll need is the break statement.

This is how you say, leave this loop.

In this example, we've translated if no gene was found,

into an if statement that says, if gene.isEmpty.

The isEmpty method for

a string returns true if the string is the empty string and false otherwise.

Remember, our gene finding method returns the empty string

whenever it can't find a gene.

Inside the if statement, we've seen leave this loop,

translated into a break statement.

A break statement which is written in Java simply with the keyword break,

followed by a semi-colon, causes Java to leave the current loop.

Regardless of whether it's a while loop or a for loop or

any kind of loop you might yet learn about, like a do while loop.

Basically, Java jumps past the close right curly brace that ends the loop.

Now we know how to implement these steps.

Let's turn the algorithm into code and try it out.

We'll find every kind of gene there is.

Have fun.

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