| public Set ( IBaseObject item, int index ) : void | ||
| item | IBaseObject | /// Element to set. /// |
| index | int | /// Position in sequence. /// |
| return | void | |
/// <summary>
/// Initializes a new instance of the <see cref="TestObject"/> class.
/// </summary>
public TestObject()
{
chain = new BaseChain(10);
chain2 = new BaseChain(5);
alpha.Add((ValueString)'a');
alpha.Add((ValueString)'b');
alpha.Add((ValueString)'c');
pm1 = new ValuePhantom { alpha[2], alpha[1] };
pm2 = new ValuePhantom { alpha[0] };
chain.Set(PhantomMessageBc, 0);
chain.Set(PhantomMessageA, 1);
chain.Set(PhantomMessageA, 2);
chain.Set(PhantomMessageBc, 3);
chain.Set(PhantomMessageA, 4);
chain.Set(PhantomMessageBc, 5);
chain.Set(PhantomMessageA, 6);
chain.Set(PhantomMessageBc, 7);
chain.Set(PhantomMessageA, 8);
chain.Set(PhantomMessageA, 9);
chain2.Set(alpha[1], 0);
chain2.Set(PhantomMessageA, 1);
chain2.Set(PhantomMessageBc, 2);
chain2.Set(alpha[0], 3);
chain2.Set(PhantomMessageBc, 4);
}
public void ContentTest()
{
var m1 = new ValuePhantom { new ValueString('1'), new ValueString('2'), new ValueString('3') };
var m2 = new ValuePhantom { new ValueString('4'), new ValueString('3') };
var test = new BaseChain(3);
test.Set(m1, 0);
test.Set(m2, 1);
test.Set(m2, 2);
var table = new PhantomTable(test);
Assert.AreEqual(m1, table[1].Content);
Assert.AreEqual(m2, table[2].Content);
Assert.AreEqual(m2, table[3].Content);
}
public void FirstTest()
{
var resultChain = new BaseChain(10);
resultChain.Set(mother.PhantomMessageBc[1], 0);
resultChain.Set(mother.PhantomMessageA[0], 1);
resultChain.Set(mother.PhantomMessageA[0], 2);
resultChain.Set(mother.PhantomMessageBc[1], 3);
resultChain.Set(mother.PhantomMessageA[0], 4);
resultChain.Set(mother.PhantomMessageBc[1], 5);
resultChain.Set(mother.PhantomMessageA[0], 6);
resultChain.Set(mother.PhantomMessageBc[1], 7);
resultChain.Set(mother.PhantomMessageA[0], 8);
resultChain.Set(mother.PhantomMessageA[0], 9);
var gen = new PhantomChainGenerator(mother.SourceChain, new MockGenerator());
List<BaseChain> res = gen.Generate(1);
Assert.AreEqual(res.Count, 1);
Assert.AreEqual(resultChain, res[0]);
}
public void VolumeTest()
{
var m3 = new ValuePhantom { new ValueString('a') };
var m1 = new ValuePhantom { new ValueString('1'), new ValueString('2'), new ValueString('3') };
var m2 = new ValuePhantom { new ValueString('4'), new ValueString('3') };
var test = new BaseChain(4);
test.Set(m1, 0);
test.Set(m2, 1);
test.Set(m2, 2);
test.Set(m3, 3);
var table = new PhantomTable(test);
Assert.AreEqual(12, table[0].Volume);
Assert.AreEqual(4, table[1].Volume);
Assert.AreEqual(2, table[2].Volume);
Assert.AreEqual(1, table[3].Volume);
Assert.AreEqual(1, table[4].Volume);
}
public void AddLengthMoreThanChainRankTest()
{
alphabet.Add(a);
alphabet.Add(b);
alphabet.Add(c);
alphabet.Add(d);
baseChain = new BaseChain(3);
baseChain.Set(a, 0);
baseChain.Set(b, 1);
baseChain.Set(b, 2);
matrix = new Matrix(alphabet.Cardinality, 2);
var arrayCh = new int[baseChain.GetLength()];
arrayCh[0] = alphabet.IndexOf(baseChain[0]);
arrayCh[1] = alphabet.IndexOf(baseChain[1]);
arrayCh[2] = alphabet.IndexOf(baseChain[2]);
Assert.Throws<ArgumentException>(() => matrix.Add(arrayCh));
}
/// <summary>
/// Addes chain to alphabet.
/// </summary>
/// <param name="item">
/// The item.
/// </param>
/// <returns>
/// <see cref="int"/>.
/// </returns>
public override int Add(IBaseObject item)
{
var temp = item as BaseChain;
if (temp == null)
{
temp = new BaseChain(1);
temp.Set(item, 0);
}
return base.Add(temp);
}
/// <summary>
/// Reorganizes <see cref="AbstractChain"/> into <see cref="AbstractChain"/>.
/// </summary>
/// <param name="source">
/// Source chain.
/// </param>
/// <returns>
/// The <see cref="AbstractChain"/>.
/// </returns>
public override AbstractChain Reorganize(AbstractChain source)
{
var resent = new BaseChain();
resent.ClearAndSetNewLength(source.GetLength());
for (int i = 0; i < source.GetLength(); i++)
{
var phantom = source[i] as ValuePhantom;
resent.Set(phantom != null ? phantom[0] : source[i], i);
}
return resent;
}
public void TreeVolumeTest()
{
var m1 = new ValuePhantom { new ValueString('1'), new ValueString('2'), new ValueString('3') };
var m2 = new ValuePhantom { new ValueString('4'), new ValueString('3') };
var m3 = new ValuePhantom { new ValueString('a') };
var test = new BaseChain(4);
test.Set(m1, 0);
test.Set(m2, 1);
test.Set(m2, 2);
test.Set(m3, 3);
IGenerator gen = new SimpleGenerator();
var tree = new TreeTop(test, gen);
Assert.AreEqual(12, tree.Volume);
var ch1 = tree.GetChild(0);
Assert.AreEqual(4, ch1.Volume);
var ch2 = tree.GetChild(1);
Assert.AreEqual(4, ch2.Volume);
var ch3 = tree.GetChild(2);
Assert.AreEqual(4, ch3.Volume);
}
public void SortListTest()
{
var temp = new ChainsAlphabet();
var a = new BaseChain(2);
for (int i = 0; i < a.GetLength(); i++)
{
a.Set((ValueInt)i, i);
}
temp.Add(a);
var b = new BaseChain(1);
for (int i = 0; i < b.GetLength(); i++)
{
b.Set((ValueInt)i, i);
}
temp.Add(b);
var c = new BaseChain(5);
for (int i = 0; i < c.GetLength(); i++)
{
c.Set((ValueInt)i, i);
}
temp.Add(c);
var d = new BaseChain(2);
for (int i = 0; i < d.GetLength(); i++)
{
d.Set((ValueInt)(i + 1), i);
}
temp.Add(d);
ArrayList list = temp.GetLengthList();
Assert.AreEqual(5, list[2]);
Assert.AreEqual(2, list[1]);
Assert.AreEqual(1, list[0]);
}
/// <summary>
/// Creates literature sequence in database.
/// </summary>
/// <param name="commonSequence">
/// The common sequence.
/// </param>
/// <param name="sequenceStream">
/// The sequence stream.
/// </param>
/// <param name="languageId">
/// The language id.
/// </param>
/// <param name="original">
/// The original.
/// </param>
/// <param name="translatorId">
/// The translator id.
/// </param>
public void Create(CommonSequence commonSequence, Stream sequenceStream, int languageId, bool original, int? translatorId)
{
var stringSequence = FileHelper.ReadSequenceFromStream(sequenceStream);
string[] text = stringSequence.Split('\n');
for (int l = 0; l < text.Length - 1; l++)
{
// removing "\r"
text[l] = text[l].Substring(0, text[l].Length - 1);
}
var chain = new BaseChain(text.Length - 1);
// file always contains empty string at the end
// TODO: rewrite this, add empty string check at the end or write a normal trim
for (int i = 0; i < text.Length - 1; i++)
{
chain.Set(new ValueString(text[i]), i);
}
MatterRepository.CreateMatterFromSequence(commonSequence);
var alphabet = ElementRepository.ToDbElements(chain.Alphabet, commonSequence.NotationId, true);
Create(commonSequence, original, languageId, translatorId, alphabet, chain.Building);
}
public void SecondTest()
{
var resultChain = new BaseChain(5);
resultChain.Set(mother.PhantomMessageBc[1], 0);
resultChain.Set(mother.PhantomMessageA[0], 1);
resultChain.Set(mother.PhantomMessageBc[1], 2);
resultChain.Set(mother.PhantomMessageA[0], 3);
resultChain.Set(mother.PhantomMessageBc[0], 4);
var gen = new PhantomChainGenerator(mother.UnnormalChain, new MockGenerator());
List<BaseChain> res = gen.Generate(1);
Assert.AreEqual(1, res.Count);
Assert.AreEqual(resultChain, res[0]);
}
public void SixthTest()
{
var sourceChain = new BaseChain(3);
sourceChain.Set(new ValueString("X"), 0);
sourceChain.Set(new ValueString("S"), 1);
sourceChain.Set(new ValueString("C"), 2);
BaseChain forBuild = DnaTransformer.Decode(sourceChain);
var gen = new PhantomChainGenerator(forBuild, new SimpleGenerator());
List<BaseChain> res = gen.Generate(1);
Assert.AreEqual(9, res[0].GetLength());
}
public void LargerNTest()
{
alphabet.Add(a);
alphabet.Add(b);
alphabet.Add(c);
alphabet.Add(d);
baseChain = new BaseChain(2);
baseChain.Set(f, 0);
baseChain.Set(c, 1);
matrix = new Matrix(alphabet.Cardinality, 2);
var array = new int[baseChain.GetLength()];
array[0] = alphabet.IndexOf(baseChain[0]);
array[1] = alphabet.IndexOf(baseChain[1]);
Assert.Throws<ArgumentOutOfRangeException>(() => matrix.FrequencyFromObject(array));
}
public void Initialize()
{
alphabet = new Alphabet();
a = new ValueString('a');
b = new ValueString('b');
c = new ValueString('c');
d = new ValueString('d');
f = new ValueString('f');
testChain = new Chain(12);
testChain.Set((ValueString)"a", 0);
testChain.Set((ValueString)"d", 1);
testChain.Set((ValueString)"b", 2);
testChain.Set((ValueString)"a", 3);
testChain.Set((ValueString)"a", 4);
testChain.Set((ValueString)"c", 5);
testChain.Set((ValueString)"b", 6);
testChain.Set((ValueString)"b", 7);
testChain.Set((ValueString)"a", 8);
testChain.Set((ValueString)"a", 9);
testChain.Set((ValueString)"c", 10);
testChain.Set((ValueString)"a", 11);
}
public void GetWithIndexesTest()
{
alphabet.Add(a); // 0 => a
alphabet.Add(b); // 1 => b
alphabet.Add(c); // 2 => c
alphabet.Add(d); // 3 => d
baseChain = new BaseChain(2);
var ch1 = new BaseChain(2);
var ch2 = new BaseChain(2);
var ch3 = new BaseChain(2);
var ch4 = new BaseChain(2);
var ch5 = new BaseChain(1);
var ch6 = new BaseChain(1);
var ch7 = new BaseChain(1);
baseChain.Set(a, 0);
baseChain.Set(b, 1);
ch1.Set(c, 0);
ch1.Set(b, 1);
ch2.Set(b, 0);
ch2.Set(a, 1);
ch3.Set(b, 0);
ch3.Set(c, 1);
matrix = new Matrix(alphabet.Cardinality, 2);
var arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch1[0]);
arrayToTeach[1] = alphabet.IndexOf(ch1[1]);
matrix.Add(arrayToTeach);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch2[0]);
arrayToTeach[1] = alphabet.IndexOf(ch2[1]);
matrix.Add(arrayToTeach);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(baseChain[0]);
arrayToTeach[1] = alphabet.IndexOf(baseChain[1]);
matrix.Add(arrayToTeach);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch3[0]);
arrayToTeach[1] = alphabet.IndexOf(ch3[1]);
matrix.Add(arrayToTeach);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch1[0]);
arrayToTeach[1] = alphabet.IndexOf(ch1[1]);
matrix.Add(arrayToTeach);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch3[0]);
arrayToTeach[1] = alphabet.IndexOf(ch3[1]);
matrix.Add(arrayToTeach);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch1[0]);
arrayToTeach[1] = alphabet.IndexOf(ch1[1]);
Assert.AreEqual(2, matrix.FrequencyFromObject(arrayToTeach));
ch4.Set(a, 0);
ch4.Set(c, 1);
arrayToTeach = new int[2];
arrayToTeach[0] = alphabet.IndexOf(ch4[0]);
arrayToTeach[1] = alphabet.IndexOf(ch4[1]);
Assert.AreEqual(0, matrix.FrequencyFromObject(arrayToTeach));
ch5.Set(b, 0);
arrayToTeach = new int[1];
arrayToTeach[0] = alphabet.IndexOf(ch5[0]);
Assert.AreEqual(3, matrix.FrequencyFromObject(arrayToTeach));
ch6.Set(a, 0);
arrayToTeach = new int[1];
arrayToTeach[0] = alphabet.IndexOf(ch6[0]);
Assert.AreEqual(1, matrix.FrequencyFromObject(arrayToTeach));
ch7.Set(c, 0);
arrayToTeach = new int[1];
arrayToTeach[0] = alphabet.IndexOf(ch7[0]);
Assert.AreEqual(2, matrix.FrequencyFromObject(arrayToTeach));
}
