/** Tests the calc. of increments */
public void TestGetIncrement () {
Sequence seq = new Sequence( AlphabetType.DNA, "aggtccagtccagcgt" );
Profile profile = new ProfileAll();
profile.Add( new RegularExp( "regex1", "ag" ) );
profile.Add( -1, 1, new RegularExp( "regex2", "gt" ) );
FeatureList matches = seq.Search( 0, 0, profile );
Assert.AreEqual( 3, matches.Count );
Assert.AreEqual( "aggt", matches[0].Letters() );
Assert.AreEqual( "agt", matches[1].Letters() );
Assert.AreEqual( "agcgt", matches[2].Letters() );
}
/** Tests the match method of a sequence of patterns */
public void TestMatch1 () {
Sequence seq = new Sequence( AlphabetType.DNA, "baaacc" );
ProfileAll pf = new ProfileAll();
Motif motif;
ProfileElement element;
FeatureList matches;
motif = new Motif( "motif1", AlphabetType.DNA, "aa", 0.5 );
element = pf.Add( motif );
matches = seq.Search( 1, seq.Length, pf );
Assert.AreEqual( 4, matches.Count );
Assert.AreEqual( "ba", matches[ 0 ].Letters() );
Assert.AreEqual( 1, matches[ 0 ].Start );
Assert.AreEqual( "aa", matches[ 1 ].Letters() );
Assert.AreEqual( 2, matches[ 1 ].Start );
Assert.AreEqual( "aa", matches[ 2 ].Letters() );
Assert.AreEqual( 3, matches[ 2 ].Start );
Assert.AreEqual( "ac", matches[ 3 ].Letters() );
Assert.AreEqual( 4, matches[ 3 ].Start );
motif = new Motif( "motif2", AlphabetType.DNA, "acc", 0.5 );
element = pf.Add( element, ProfileElement.AlignmentType.END, 0, 1, motif );
matches = seq.Search( 1, seq.Length, pf );
Assert.AreEqual( 3, matches.Count );
Assert.AreEqual( "baaac", matches[ 0 ].Letters() );
Assert.AreEqual( 1, matches[ 0 ].Start );
Assert.AreEqual( "baaacc", matches[ 1 ].Letters() );
Assert.AreEqual( 1, matches[ 1 ].Start );
Assert.AreEqual( "aaacc", matches[ 2 ].Letters() );
Assert.AreEqual( 2, matches[ 2 ].Start );
motif = new Motif( "motif3", AlphabetType.DNA, "cc", 1.0 );
element = pf.Add( element, ProfileElement.AlignmentType.END, -2, 1, motif );
matches = seq.Search( 1, seq.Length, pf );
Assert.AreEqual( 3, matches.Count );
Assert.AreEqual( "baaacc", matches[ 0 ].Letters() );
Assert.AreEqual( 1, matches[ 0 ].Start );
Assert.AreEqual( "baaacc", matches[ 1 ].Letters() );
Assert.AreEqual( 1, matches[ 1 ].Start );
Assert.AreEqual( "aaacc", matches[ 2 ].Letters() );
Assert.AreEqual( 2, matches[ 2 ].Start );
}
/** Tests the match method for a pattern which matches all the time */
public void TestMatch5 () {
Sequence seq = new Sequence( AlphabetType.DNA, "bacgt" );
ProfileAll pf = new ProfileAll();
Motif motif;
FeatureList matches;
motif = new Motif( "motif1", AlphabetType.DNA, "aa", 0.0 );
pf.Add( motif );
matches = seq.Search( 1, seq.Length, pf );
Assert.AreEqual( 4, matches.Count );
Assert.AreEqual( "ba", matches[ 0 ].Letters() );
Assert.AreEqual( 1, matches[ 0 ].Start );
Assert.AreEqual( "ac", matches[ 1 ].Letters() );
Assert.AreEqual( 2, matches[ 1 ].Start );
}
/** Tests the match method for a hierarchical pattern */
public void TestMatch3 () {
Sequence seq = new Sequence( AlphabetType.DNA, "baaacc" );
ProfileAll pf1 = new ProfileAll();
ProfileAll pf2 = new ProfileAll();
Motif motif;
ProfileElement element;
FeatureList matches;
motif = new Motif( "motif1", AlphabetType.DNA, "aa", 1.0 );
element = pf1.Add( motif );
motif = new Motif( "motif2", AlphabetType.DNA, "aa", 1.0 );
element = pf1.Add( element, ProfileElement.AlignmentType.START, 0, 1, motif );
matches = seq.Search( 1, seq.Length, pf1 );
Assert.AreEqual( 3, matches.Count );
Assert.AreEqual( "aa", matches[ 0 ].Letters() );
Assert.AreEqual( "aaa", matches[ 1 ].Letters() );
Assert.AreEqual( "aa", matches[ 2 ].Letters() );
motif = new Motif( "motif3", AlphabetType.DNA, "aa", 1.0 );
element = pf2.Add( motif );
motif = new Motif( "motif4", AlphabetType.DNA, "cc", 1.0 );
element = pf2.Add( element, ProfileElement.AlignmentType.CENTER, 0, 2, motif );
matches = seq.Search( 1, seq.Length, pf2 );
Assert.AreEqual( 2, matches.Count );
Assert.AreEqual( "aaacc", matches[ 0 ].Letters() );
Assert.AreEqual( "aacc", matches[ 1 ].Letters() );
pf1.Add( pf1[0], ProfileElement.AlignmentType.END, -1, 0, pf2 );
pf2.Threshold = ( 1.0 );
matches = seq.Search( 1, seq.Length, pf1 );
Assert.AreEqual( 2, matches.Count );
Assert.AreEqual( "aaacc", matches[ 0 ].Letters() );
Assert.AreEqual( "aaacc", matches[ 1 ].Letters() );
}