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//
// TestBCCachedSequenceFile.m
// BioCocoa
//
// Created by Scott Christley on 9/25/07.
// 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 "TestBCCachedSequenceFile.h"
@implementation TestBCCachedSequenceFile
// read fasta format, DNA
- (void)testReadDNAFastaFile
{
NSLog(@"-testReadDNAFastaFile");
NSBundle *aBundle = [NSBundle bundleForClass: [self class]];
NSString *fileName = [aBundle pathForResource: @"test" ofType: @"fa"];
// read as cache and read in memory, then compare
BCCachedSequenceFile *cacheFile = [BCCachedSequenceFile readCachedFileUsingPath: fileName];
BCSequenceReader *sequenceReader = [[[BCSequenceReader alloc] init] autorelease];
BCSequenceArray *sequenceArray = [sequenceReader readFileUsingPath: fileName format: BCFastaFileFormat];
// errors are concatenated
NSMutableString *error=[NSMutableString stringWithString:@""];
if (cacheFile == nil)
[error appendString: @"cache file is nil\n"];
else {
if (sequenceArray == nil)
[error appendString: @"Sequence array is nil\n"];
else {
if ([sequenceArray count] != 2)
[error appendFormat: @"Number of sequence in array is incorrect, 2 != %d\n", [sequenceArray count]];
else {
BCSequence *aSeq = [sequenceArray sequenceAtIndex: 0];
BCSequence *revSeq = [aSeq reverseComplement];
const unsigned char *seqData1 = [aSeq bytes];
int aLen = [aSeq length];
char seqData2[aLen];
if (aLen != 517)
[error appendFormat: @"Length of sequence is incorrect, 517 != %d\n", aLen];
// forward strand
int result = [cacheFile symbols: seqData2 atPosition: 0 ofLength: aLen forSequenceNumber: 0];
if (result != aLen)
[error appendFormat: @"Could not read full length of sequence, %d != %d\n", aLen, result];
int i;
for (i = 0; i < result; ++i) {
if (seqData1[i] != seqData2[i]) {
[error appendFormat: @"Sequence data does not match at position %d, %c != %c\n", i, seqData1[i], seqData2[i]];
break;
}
}
#if 0 // reverse complement in BCSequence not working right
NSLog(@"%@\n", [revSeq sequenceString]);
// reverse strand
seqData1 = [revSeq bytes];
result = [cacheFile symbols: seqData2 atPosition: aLen ofLength: aLen forSequenceNumber: 0];
for (i = 0; i < result; ++i) {
if (seqData1[i] != seqData2[i]) {
[error appendFormat: @"Sequence data does not match at position %d, %c != %c\n", i, seqData1[i], seqData2[i]];
break;
}
}
#endif
}
}
}
// if error!=@"", the test failed
STAssertTrue ([error isEqualToString:@""], error);
}
@end
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