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//
// TestBCSuffixArray.m
// BioCocoa
//
// Created by Scott Christley on 9/24/07.
// Copyright (c) 2003-2009 The BioCocoa Project.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// 3. The name of the author may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
// NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#import "TestBCSuffixArray.h"
@implementation TestBCSuffixArray
// test construct suffix array
#if 0
// disable for now as inMemory suffix array needs to be reworked
- (void)testMemoryConstructSuffixArray
{
NSBundle *aBundle = [NSBundle bundleForClass: [self class]];
NSString *fileName = [aBundle pathForResource: @"test" ofType: @"fa"];
BCSuffixArray *anArray = [[BCSuffixArray alloc] init];
// errors are concatenated
NSMutableString *error=[NSMutableString stringWithString:@""];
if (anArray == nil)
[error appendString: @"Suffix array is nil\n"];
else {
// construct the suffix array
if (![anArray constructFromSequenceFile: fileName strand: nil])
[error appendString: @"Error while constructing suffix array\n"];
if ([anArray numberOfSequences] != 2)
[error appendFormat: @"Number of sequence in array is incorrect, 2 != %d\n", [anArray numberOfSequences]];
else {
BCSequenceArray *sequenceArray = [anArray sequenceArray];
NSDictionary *metaDictionary = [anArray metaDictionary];
if (metaDictionary == nil)
[error appendString: @"Meta dictionary is nil\n"];
else {
if ([[metaDictionary objectForKey: @"length"] intValue] != 619)
[error appendFormat: @"Total length of sequences is incorrect, 619 != %@\n", [metaDictionary objectForKey: @"length"]];
BCSequence *aSeq = [sequenceArray sequenceAtIndex: 0];
if ([aSeq length] != 517)
[error appendFormat: @"Length of sequence is incorrect, 517 != %d\n", [aSeq length]];
}
}
}
// if error!=@"", the test failed
STAssertTrue ([error isEqualToString:@""], error);
}
#endif
// test construct suffix array
- (void)testFileConstructSuffixArray
{
NSBundle *aBundle = [NSBundle bundleForClass: [self class]];
NSString *fileName = [aBundle pathForResource: @"test" ofType: @"fa"];
// delete temporary files
NSFileManager *fileManager = [NSFileManager defaultManager];
NSString *s = [fileName stringByAppendingPathExtension: @"sa"];
if ([fileManager fileExistsAtPath: s]) [fileManager removeFileAtPath: s handler: nil];
s = [fileName stringByAppendingPathExtension: @"meta_sa"];
if ([fileManager fileExistsAtPath: s]) [fileManager removeFileAtPath: s handler: nil];
BCSuffixArray *anArray = [[BCSuffixArray alloc] init];
// errors are concatenated
NSMutableString *error=[NSMutableString stringWithString:@""];
if (anArray == nil)
[error appendString: @"Suffix array is nil\n"];
else {
// construct the suffix array
if (![anArray constructFromSequenceFile: fileName strand: nil])
[error appendString: @"Error while constructing suffix array\n"];
// write to disk
if (![anArray writeToFile: fileName withMasking: YES])
[error appendFormat: @"Error while writing suffix array to file: %@\n", fileName];
[anArray release];
// read from disk
anArray = [[BCSuffixArray alloc] initWithContentsOfFile: fileName inMemory: NO];
if (anArray == nil)
[error appendFormat: @"Could not read suffix array from file: %@\n", fileName];
else {
if ([anArray numberOfSequences] != 2)
[error appendFormat: @"Number of sequence in array is incorrect, 2 != %d\n", [anArray numberOfSequences]];
else {
BCSequenceArray *sequenceArray = [anArray sequenceArray];
NSDictionary *metaDictionary = [anArray metaDictionary];
if (metaDictionary == nil)
[error appendString: @"Meta-dictionary is nil\n"];
else {
if ([[metaDictionary objectForKey: @"length"] intValue] != 619)
[error appendFormat: @"Total length of sequences in meta-dictionary is incorrect, 619 != %@\n",
[metaDictionary objectForKey: @"length"]];
NSArray *seqs = [metaDictionary objectForKey: @"sequences"];
if (!seqs) [error appendString: @"Meta-dictionary missing sequences\n"];
NSDictionary *d = [seqs objectAtIndex: 0];
int aValue = [[d objectForKey: @"length"] intValue];
if (aValue != 517)
[error appendFormat: @"Length of sequence in meta-dictionary is incorrect, 517 != %d\n", aValue];
aValue = [[d objectForKey: @"number"] intValue];
if (aValue != 0)
[error appendFormat: @"Sequence number in meta-dictionary is incorrect, 0 != %d\n", aValue];
d = [seqs objectAtIndex: 1];
aValue = [[d objectForKey: @"length"] intValue];
if (aValue != 102)
[error appendFormat: @"Length of sequence in meta-dictionary is incorrect, 102 != %d\n", aValue];
aValue = [[d objectForKey: @"number"] intValue];
if (aValue != 1)
[error appendFormat: @"Sequence number in meta-dictionary is incorrect, 1 != %d\n", aValue];
BCSequence *aSeq = [sequenceArray sequenceAtIndex: 0];
if ([aSeq length] != 517)
[error appendFormat: @"Length of sequence is incorrect, 517 != %d\n", [aSeq length]];
aSeq = [sequenceArray sequenceAtIndex: 1];
if ([aSeq length] != 102)
[error appendFormat: @"Length of sequence is incorrect, 102 != %d\n", [aSeq length]];
}
}
}
}
// if error!=@"", the test failed
STAssertTrue ([error isEqualToString:@""], error);
}
@end
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