public void MotifTestMatchAlternatives ()
{
Sequence seq = new Sequence(AlphabetType.DNA, "atgc");
Motif motif = new Motif("test", AlphabetType.DNA,"[ga]tg[c]", 0.0);
Match match = motif.Match(seq, 1);
Assert.AreEqual(1.0, match.Similarity, 1e-2);
}
public void TestMatch() {
Sequence seq = new Sequence(AlphabetType.DNA,"tttaagaacaagttt");
Motif motif = new Motif("motif", AlphabetType.DNA,"aag", 0.5);
Iteration iteration;
Match match;
iteration = new Iteration("test",motif,1,3,0.0);
match = iteration.Match(seq, 4);
Assert.AreEqual(4, match.Start);
Assert.AreEqual(9, match.Length);
Assert.AreEqual(1, match.Strand);
Assert.AreEqual("aagaacaag", match.Letters());
Assert.AreEqual(seq, match.BaseSequence);
Assert.AreEqual(0.888, match.Similarity, 1e-3);
iteration = new Iteration("test",motif,1,1,0.0);
match = iteration.Match(seq, 4);
Assert.AreEqual("aag", match.Letters());
Assert.AreEqual(1.0, match.Similarity, 1e-3);
iteration = new Iteration("test",motif,1,2,0.0);
match = iteration.Match(seq, 4);
Assert.AreEqual("aagaac", match.Letters());
Assert.AreEqual(0.833, match.Similarity, 1e-3);
iteration = new Iteration("test",motif,4,5,0.0);
Assert.AreEqual(null, iteration.Match(seq, 4));
}
public void Setup()
{
series = new SeriesBest("series", 0.0);
motif = new Motif("motif", AlphabetType.DNA, "accg", 1.0);
gap = new Gap("gap", 3, 3);
gap.Impact = 0.0;
series.Add(motif);
series.Add(gap);
}
/** Tests the getter of patterns */
public void TestGet () {
ProfileProxy pf = new ProfileProxy();
Motif pat1 = new Motif( "motif1", AlphabetType.DNA, "ac", 0 );
Motif pat2 = new Motif( "motif2", AlphabetType.DNA, "ag", 0 );
pf.Add( pat1 );
pf.Add( pat2 );
Assert.AreEqual( pat1, pf.Pattern( 0 ) );
Assert.AreEqual( pat2, pf.Pattern( 1 ) );
}
public void TestAddGetPattern () {
SetBest set = new SetBest();
Assert.AreEqual( 0, set.Count );
Motif motif = new Motif( "motif1", AlphabetType.DNA, "ACTG", 0.7 );
set.Add( motif );
Assert.AreEqual( 1, set.Count );
Assert.AreEqual( motif, set[0] );
}
public void TestConstructor()
{
Motif motif = new Motif("motif", AlphabetType.DNA, "tgn", 0.0);
Iteration iteration = new Iteration("test", motif, 3, 4, 0.0);
Assert.AreEqual("test", iteration.Name);
Assert.AreEqual(motif, iteration.Pattern);
Assert.AreEqual(3, iteration.Minimum);
Assert.AreEqual(4, iteration.Maximum);
}
public void MotifTestMatchAtStart () {
Sequence seq = new Sequence( AlphabetType.DNA, "aTtgattaca" );
Motif motif = new Motif( "test", AlphabetType.DNA, "attg", 0.0 );
Match match = motif.Match( seq, 1 );
Assert.AreEqual( 1, match.Start );
Assert.AreEqual( 4, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 1.0, match.Similarity, 1e-2 );
Assert.AreEqual( "attg", match.Letters() );
}
public void MotifTestMatch () {
Sequence seq = new Sequence( AlphabetType.DNA, "aTtga" );
Motif motif = new Motif( "test", AlphabetType.DNA, "tgn", 0.0 );
Match match = motif.Match( seq, 3 );
Assert.AreEqual( 3, match.Start );
Assert.AreEqual( 3, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 1.0, match.Similarity, 1e-2 );
match = motif.Match( seq, 2 );
Assert.AreEqual( 2, match.Start );
Assert.AreEqual( 3, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 0.66, match.Similarity, 1e-2 );
}
/** 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 adding of patterns to a profile */
public void TestAdd () {
IPattern pattern1, pattern2;
ProfileElement element1, element2;
ProfileProxy pf = new ProfileProxy();
Assert.AreEqual( 0, pf.Count );
pattern1 = new Motif( "motif1", AlphabetType.DNA, "ac", 0 );
element1 = pf.Add( null, ProfileElement.AlignmentType.NONE, 0, 0, pattern1 );
Assert.AreEqual( 1, pf.Count );
Assert.AreEqual( pattern1, element1.Pattern );
pattern2 = new Motif( "motif2", AlphabetType.DNA, "tg", 0 );
element2 = pf.Add( element1, ProfileElement.AlignmentType.START, -2, -1, pattern2 );
Assert.AreEqual( 2, pf.Count );
Assert.AreEqual( ProfileElement.AlignmentType.START, element2.Alignment );
Assert.AreEqual( -2, element2.MinGap );
Assert.AreEqual( -1, element2.MaxGap );
Assert.AreEqual( ProfileElement.AlignmentType.START, element2.Alignment );
Assert.AreEqual( element1, element2.RefElement );
}
/** 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() );
}
public void SetUp () {
seq = new Sequence( AlphabetType.DNA, "atgcatgc" );
series = new SeriesBest( "series", 1.0 );
motif1 = new Motif( "motif1", AlphabetType.DNA, "tgc", 1.0 );
motif2 = new Motif( "motif2", AlphabetType.DNA, "gca", 1.0 );
}
public void MotifTestMatchSimiliarity ()
{
Sequence seq = new Sequence(AlphabetType.DNA, "aCtG", true);
Assert.AreEqual(2, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 1).Length);
Assert.AreEqual(3, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 3).Start);
Assert.AreEqual(0.0, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 1).Similarity);
Assert.AreEqual(0.5, (new Motif("test", AlphabetType.DNA, "cc", 0)).Match(seq, 1).Similarity, 1e-3);
Assert.AreEqual(1.0, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 2).Similarity, 1e-3);
Assert.AreEqual(0.0, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 3).Similarity, 1e-3);
Assert.AreEqual(1.0, (new Motif("test", AlphabetType.DNA, "ctga", 0)).Match(seq, 2).Similarity, 1e-3);
Motif seq1 = new Motif("test", AlphabetType.DNA, "cc", 0.6);
Assert.AreEqual(null, seq1.Match(seq, 1));
}
/// <summary>
///
/// Reads a pattern from a starting specified node. This method
/// recursivly calls the reading methods of the different patterns.
/// </summary>
/// <param name="node">Node of the pattern the reading starts with.</param>
/// <param name="definition">Pattern definition which pattern list will be extended
/// with the pattern and all its sub-patterns read.
/// </param>
/// <returns>The read pattern or null if there is no pattern to read.</returns>
/// <exception cref="System.SystemException">Thrown when unknown pattern was found</exception>
public static IPattern ReadPattern
(XmlNode node, Definition definition)
{
while (node != null
&& node.NodeType != XmlNodeType.Element)
node = node.NextSibling; //Iterate thru the list of nodes until it is an element
IPattern pattern = null;
String mode = XMLHelper.GetAttrValueString(node, "mode");
switch (node.Name)
{
case "Any":
pattern = new Any();
break;
case "Alignment":
pattern = new Alignment();
break;
case "Composition" :
pattern = new Composition();
break;
case "Constraint":
pattern = new Constraint();
break;
case "Iteration":
pattern = new Iteration();
break;
case "Logic":
pattern = new Logic();
break;
case "Motif":
pattern = new Motif();
break;
case "PWM":
pattern = new PWM();
break;
case "Regex":
pattern = new RegularExp();
break;
case "Prosite":
pattern = new Prosite();
break;
case "Block":
pattern = new Block();
break;
case "Gap":
pattern = new Gap();
break;
case "Repeat":
pattern = new Repeat();
break;
case "Series":
pattern = mode.Equals("ALL") ?
pattern = new SeriesAll() : pattern = new SeriesBest();
break;
case "Set":
pattern = mode.Equals("ALL") ?
pattern = new SetAll() : pattern = new SetBest();
break;
case "Void":
pattern = new VoidPattern();
break;
case "Use":
pattern = new Use();
break;
throw new SystemException
("Unknown pattern found: " + node.Name);
}
pattern.ReadNode(node, definition); // read the node data and initialize the pattern
definition.Patterns.Add
(0, pattern); //Always adding the element to last index
return pattern;
}
public void TestSearch () {
Sequence seq = new Sequence( AlphabetType.DNA, "acttacttagttaac" );
Motif motif = new Motif( "motif1", AlphabetType.DNA, "act", 0.5 );
FeatureList list = seq.Search( 0, 0, motif );
Assert.AreEqual( 3, list.Count() );
Assert.AreEqual( 1, list[ 0 ].Start );
Assert.AreEqual( 1.0, ( (Match) list[ 0 ] ).Similarity, 1e-1 );
Assert.AreEqual( 5, list[ 1 ].Start );
Assert.AreEqual( 1.0, ( (Match) list[ 1 ] ).Similarity, 1e-1 );
Assert.AreEqual( 9, list[ 2 ].Start );
Assert.AreEqual( 0.6, ( (Match) list[ 2 ] ).Similarity, 1e-1 );
list = seq.Search( 11, seq.Length + 1, motif );
Assert.AreEqual( 1, list.Count() );
Assert.AreEqual( 14, list[ 0 ].Start );
Assert.AreEqual( 0.6, ( (Match) list[ 0 ] ).Similarity, 1e-1 );
}
/** Test for best match searching within a sequence */
public void TestSearchBest () {
Sequence seq = new Sequence( AlphabetType.DNA, "acttacttagttaatt" );
Motif motif = new Motif( "motif1", AlphabetType.DNA, "taga", 0.0 );
Match match = seq.SearchBest( 1, -1, motif );
Assert.AreEqual( "tagt", match.Letters() );
Assert.AreEqual( 8, match.Start );
Assert.AreEqual( 4, match.Length );
Assert.AreEqual( 0.75, match.Similarity, 1e-3 );
motif = new Motif( "motif2", AlphabetType.DNA, "aatt", 0.0 );
match = seq.SearchBest( 1, -1, motif );
Assert.AreEqual( 13, match.Start );
match = seq.SearchBest( 1, seq.Length, motif );
Assert.AreEqual( 13, match.Start );
match = seq.SearchBest( 1, seq.Length - 1, motif );
Assert.AreEqual( 1, match.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 );
}
public void TestMatchSubMatches()
{
Sequence seq = new Sequence(AlphabetType.DNA, "tttaagaacaagttt");
Motif motif = new Motif("motif", AlphabetType.DNA, "aag", 0.5);
Iteration iteration = new Iteration("test", motif, 1, 3, 0.0);
Match match = seq.SearchBest(0, 0, iteration);
Assert.AreEqual("aag", match.Letters());
Assert.AreEqual(10, match.Start);
Assert.AreEqual(1.0, match.Similarity);
Assert.AreEqual("aag", match.SubMatches[0].Letters()); //sub match to properties?
FeatureList matches = seq.Search(0, 0, iteration);
Assert.AreEqual(3, matches.Count);
Assert.AreEqual("aagaacaag", matches[0].Letters());
Assert.AreEqual(0.88, ((Match)matches[0]).Similarity, 1e-2);
Assert.AreEqual("aacaag", matches[1].Letters());
Assert.AreEqual(0.83, ((Match)matches[1]).Similarity, 1e-2);
Assert.AreEqual("aag", matches[2].Letters());
Assert.AreEqual(1.00, ((Match)matches[2]).Similarity, 1e-2);
}
public void MotifTestLetters ()
{
Motif motif = new Motif("test", AlphabetType.DNA, "tgn[at]C[TG]", 0.0);
Assert.AreEqual("tg[atcg][at]c[tg]", motif.Letters);
}