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hamming

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# Getting Started
These exercises lean on Test-Driven Development (TDD), but they're not an
exact match.
## Setup
You'll need access to a mounted Oracle DB. If you don't have one already
installed, here are a few options:
* download VirtualBox from Oracle and run one of the freely
available images; at the time of writing, the easiest to get started with
at the time of writing might be _Database App Development VM_. The
image is quite large...
* download and install the a version of the Oracle DB itself. Developer licenses
are free.
* get a free workspace at https://apex.oracle.com
**Note**: if you're using the online version of APEX, compilation errors will
not be indicated very clearly when working in _SQL Commands_ - you will simply
get "Error at line XX: PL/SQL: Statement ignored"... More insight can be
found using the _Object Browser_ and navigating to the object you created
(select either _Packages_ or _Procedures_ in the dropdown menu showing _Tables_,
depending on what you created for the exercise). Also, when you run statements,
"run" each individual `create` statement individually by selecting its text.
APEX does not seem to like doing too much work at once...
To work on individual problems, a nice and free way is to use SQL Developer. If
you don't want to use yet another IDE, you can simply copy and paste your code
into a terminal / command prompt connected to the database. The files are
prepared in a way that will simply overwrite the previously compiled version.
#Exercise
## Step 1
Compile the test suite. You can easily do that by copy / pasting (let's call
that _installing_ for simplicity) into your terminal connected to a mounted
Oracle database.
This will fail, complaining that there is no package called `HAMMING#`.
To fix the error create the package by installing the prepared solution stub.
Note that you will have to re-install the package body of `UT_HAMMING#`.
A few words about naming: the `#` at the end of the name signifies that this
is a package. `UT` means _unit test_. _PL/SQL_ has a maximum identifier length
of 30 characters, which is why you will find that many words are abbreviated.
If you've worked with PL/SQL before, you might wonder why the template is a
package and not simply a standalone function. That would of course also be a
possibility, but in practice standalone procedures or functions are rarely used.
## Step 2
Try to run the test. You will notice that you are missing the function's
implementation. Create it (see the test package for examples).
Note that functions have to return a value, so for now just `return null;`.
## Step 3
Run the test again. It should now execute, but the test will fail.
That's where you get to actually implement the function!
## Wash, Rinse, Repeat
Only the first test is enabled at first, the others are commented out. To enable
them, simply delete the `--` in front of the procedure call and they'll run
when you next install the test package!
## Submit
When everything is passing, you can submit your code with the following
command:
$ exercism submit hamming#.plsql

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# Hamming
Write a program that can calculate the Hamming difference between two DNA strands.
A mutation is simply a mistake that occurs during the creation or
copying of a nucleic acid, in particular DNA. Because nucleic acids are
vital to cellular functions, mutations tend to cause a ripple effect
throughout the cell. Although mutations are technically mistakes, a very
rare mutation may equip the cell with a beneficial attribute. In fact,
the macro effects of evolution are attributable by the accumulated
result of beneficial microscopic mutations over many generations.
The simplest and most common type of nucleic acid mutation is a point
mutation, which replaces one base with another at a single nucleotide.
By counting the number of differences between two homologous DNA strands
taken from different genomes with a common ancestor, we get a measure of
the minimum number of point mutations that could have occurred on the
evolutionary path between the two strands.
This is called the 'Hamming distance'.
It is found by comparing two DNA strands and counting how many of the
nucleotides are different from their equivalent in the other string.
GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^ ^ ^ ^^
The Hamming distance between these two DNA strands is 7.
# Implementation notes
The Hamming distance is only defined for sequences of equal length. This means
that based on the definition, each language could deal with getting sequences
of equal length differently.
## Setup
Go through the setup instructions for PL/SQL to get ready to code:
http://help.exercism.io/getting-started-with-plsql.html
## Running the Tests
Execute the tests by calling the `run` method in the respective `ut_<exercise>#` package.
The necessary code should be contained at the end of the test package.
As an example, the test for the _hamming_ exercise would be run using
```
begin
ut_hamming#.run;
end;
/
```
## Source
The Calculating Point Mutations problem at Rosalind [view source](http://rosalind.info/problems/hamm/)

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create or replace package hamming#
is
--+--------------------------------------------------------------------------+
-- Computes the Hamming distance between two starnds.
--
-- @param i_first sequence to compare
-- @param i_second sequence to compare
--
-- @return Hamming distance between i_first and i_second
--+--------------------------------------------------------------------------+
function distance (
i_first varchar2
,i_second varchar2
) return pls_integer;
end hamming#;
/
create or replace package body hamming#
is
end hamming#;
/

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create or replace package ut_hamming#
is
procedure run;
end ut_hamming#;
/
create or replace package body ut_hamming#
is
procedure test (
i_descn varchar2
,i_exp pls_integer
,i_act pls_integer
)
is
begin
if i_exp = i_act then
dbms_output.put_line('SUCCESS: ' || i_descn);
else
dbms_output.put_line(
'FAILURE: ' || i_descn
|| ': expected ' || nvl('' || i_exp, 'null')
|| ', but got ' || nvl('' || i_act, 'null')
|| '!'
);
end if;
end test;
procedure run
is
begin
test('test_no_difference_between_identical_strands' , 0, hamming#.distance(i_first => 'A' , i_second => 'A' ));
--test('test_complete_hamming_distance_of_for_single_nucleotide_strand', 1, hamming#.distance(i_first => 'A' , i_second => 'G' ));
--test('test_complete_hamming_distance_of_for_small_strand' , 2, hamming#.distance(i_first => 'AG' , i_second => 'CT' ));
--test('test_small_hamming_distance' , 1, hamming#.distance(i_first => 'AG' , i_second => 'AT' ));
--test('test_small_hamming_distance_in_longer_strand' , 1, hamming#.distance(i_first => 'GGACG' , i_second => 'GGTCG' ));
--test('test_nonunique_characters_within_first_strand' , 1, hamming#.distance(i_first => 'AGA' , i_second => 'AGG' ));
--test('test_nonunique_characters_within_second_strand' , 1, hamming#.distance(i_first => 'AGG' , i_second => 'AGA' ));
--test('test_large_hamming_distance' , 4, hamming#.distance(i_first => 'GATACA' , i_second => 'GCATAA' ));
--test('test_hamming_distance_in_very_long_strand' , 9, hamming#.distance(i_first => 'GGACGGATTCTG', i_second => 'AGGACGGATTCT'));
exception
when others then
dbms_output.put_line('Test execution failed.');
dbms_output.put_line(sqlerrm);
end run;
end ut_hamming#;
/
begin
ut_hamming#.run;
end;
/