public void ValidateDerivedSequenceConvertToString()
{
string seqLargeStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeStr);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualLargeString = DeriveSeqLarge.ToString();
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpectedNode);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(expectedLargeString, ActualLargeString);
// Get input and expected values from xml
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
ISequence seq = new Sequence(alphabet, expectedSequence);
var derSequence = new DerivedSequence(seq, false, false);
Assert.AreEqual(expectedSequence.Substring(2, 5), derSequence.ConvertToString(2, 5));
}
public void ValidateDnaDerivedSequenceIndexOfNonGap()
{
// Get input and expected values from xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence);
try
{
derSequence.IndexOfNonGap();
Assert.Fail("The method is now implemented");
}
catch (NotImplementedException)
{
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of IndexOfNonGap() method of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of IndexOfNonGap() method of derived sequence completed successfully");
}
}
public void ValidateDnaDerivedSequenceGetSubSequence()
{
// Get input and expected values from xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.AlphabetNameNode);
string rangeObj = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.Range);
string expSubSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.RangeSequence);
string derivedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.DerivedSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence);
string[] ranges = rangeObj.Split(',');
// Validate IndexOf() derived Sequence.
Assert.AreEqual(derivedSequence, new string(derSequence.Select(a => (char)a).ToArray()));
Assert.AreEqual(expSubSequence, new string(derSequence.GetSubSequence(long.Parse(ranges[0],
(IFormatProvider)null), long.Parse(ranges[1], (IFormatProvider)null)).Select(a => (char)a).ToArray()));
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetSubSequence() method of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetSubSequence() method of derived sequence completed successfully");
}
public void InValidateReplaceDerivedSequenceItems()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.DNA, "AAGGTT");
DerivedSequence deriSeqObj = new DerivedSequence(seqObj);
// Pass invalid index value and get the exception required
try
{
deriSeqObj.Replace(-1, deriSeqObj[0]);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for ReplaceRange() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for ReplaceRange() method");
}
// Pass invalid sequence and get the exception required
try
{
deriSeqObj.Replace(1, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for ReplaceRange() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for ReplaceRange() method");
}
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Validates expected items are present in derived sequence using Contains() method.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceContains(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DerivedSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence, addSequence, removeRange);
// Validate Contains() derived Sequence.
Assert.AreEqual(derivedSequence, derSequence.ToString());
Sequence sequence = new Sequence(alphabet, addSequence);
foreach (ISequenceItem item in sequence)
{
Assert.IsTrue(derSequence.Contains(item));
}
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Contains() method of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Contains() method of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Clear the derived sequence changes and validated that it matches against oroginal sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceClear(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence, addSequence, removeRange);
// clear the changes.
derSequence.Clear();
// Validate derived Sequence changes are cleared
// It matches now with source sequence.
Assert.AreEqual(expectedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Clear() method of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Clear() method of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after removing few items using RemoveAt() from original sequence.
/// Validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceRemoveAt(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange1);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveDerivedSequence2);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence.
Sequence seq = new Sequence(alphabet, expectedSequence);
DerivedSequence derSequence = new DerivedSequence(seq);
string[] removals = removeRange.Split(',');
int position = int.Parse(removals[0], null);
int length = int.Parse(removals[1], null);
// Remove items
for (int index = position; index <= length; index++)
{
derSequence.RemoveAt(index);
}
// Validate Derived Sequence
Assert.AreEqual(derivedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of RemoveAt() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of RemoveAt() of derived sequence completed successfully");
}
public void ValidateCopyTo()
{
// Get input and expected values from xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence seqObj = CreateDerivedSequence(
alphabet, expectedSequence);
byte[] array = new byte[expectedSequence.Length];
seqObj.CopyTo(array, 0, expectedSequence.Length);
StringBuilder builder = new StringBuilder();
for (int i = 0; i < expectedSequence.Length; i++)
{
builder.Append((char)array[i]);
}
string actualValue = builder.ToString();
Assert.AreEqual(expectedSequence, actualValue);
//check with a part of the expected seq only
seqObj.CopyTo(array, 0, 5);
builder = new StringBuilder();
for (int i = 0; i < 5; i++)
{
builder.Append((char)array[i]);
}
actualValue = builder.ToString();
Assert.AreEqual(expectedSequence.Substring(0, 5), actualValue);
}
/// <summary>
/// Creates a dna derived sequence after inserting few items using Insert(pos,item) from original sequence.
/// Validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceInsertWithSequenceItem(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.InsertDerivedSequence);
string insertSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence.
Sequence seq = new Sequence(alphabet, expectedSequence);
DerivedSequence derSequence = new DerivedSequence(seq);
int position = 1;
// Insert sequence item
Sequence insertSeq = new Sequence(alphabet, insertSequence);
foreach (ISequenceItem item in insertSeq)
{
derSequence.Insert(position, item);
}
// Validate Derived Sequence
Assert.AreEqual(derivedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Insert() by passing item of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Insert() by passing item of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding few items using Add() from original sequence.
/// Validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceAdd(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddDerivedSequence);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence.
Sequence seq = new Sequence(alphabet, expectedSequence);
DerivedSequence derSequence = new DerivedSequence(seq);
// Add sequence item
Sequence addSeq = new Sequence(alphabet, addSequence);
foreach (ISequenceItem item in addSeq)
{
derSequence.Add(item);
}
// Validate Derived Sequence
Assert.AreEqual(derivedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Add() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Add() of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Create a copy of derived sequence and validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceClone(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DerivedSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence, addSequence, removeRange);
DerivedSequence derSequenceCopy = derSequence.Clone();
// Validate copy of derived Sequence.
Assert.AreEqual(derSequence.ToString(), derSequenceCopy.ToString());
Assert.AreEqual(derivedSequence, derSequenceCopy.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Clone() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Clone() of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Replace few items by passing char using Replace() and validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceReplaceWithChar(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = Utility._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string derivedSequence = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ReplaceSequence);
string replaceSequence = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ReplaceRangeSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence.
Sequence seq = new Sequence(alphabet, expectedSequence);
DerivedSequence derSequence = new DerivedSequence(seq);
int position = 0;
// Replace sequence with char.
Sequence replaceSeq = new Sequence(alphabet, replaceSequence);
foreach (ISequenceItem item in replaceSeq)
{
derSequence.Replace(position, item.Symbol);
position++;
}
// Validate Derived Sequence
Assert.AreEqual(derivedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Replace() by passing char of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Replace() by passing char of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Get a sub sequence using Range() and validates it against expected sequence.
/// </summary>
/// <param name="nodeName"></param>
private void ValidateDerivedSequenceRange(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
string rangeSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RangeSequence);
string range = _utilityObj._xmlUtil.GetTextValue(nodeName, Constants.Range);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence, addSequence, removeRange);
string[] ranges = range.Split(',');
int position = int.Parse(ranges[0], null);
int length = int.Parse(ranges[1], null);
ISequence sequence = derSequence.Range(position, length);
// Validate range Sequence.
Assert.AreEqual(rangeSequence, sequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Range() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of Range() of derived sequence completed successfully");
}
public void ValidateDnaDerivedSequenceGetComplemented()
{
// Get input and expected values from xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.AlphabetNameNode);
string complementObj = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.Complement);
string derivedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.DerivedSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence);
// Validate IndexOf() derived Sequence.
Assert.AreEqual(derivedSequence, new string(derSequence.Select(a => (char)a).ToArray()));
Assert.AreEqual(complementObj, new string(derSequence.GetComplementedSequence().Select(a => (char)a).ToArray()));
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetComplementedSequence() method of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetComplementedSequence() method of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Validates items of derived sequence using GeEnumerator()
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceGetEnumerator(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DerivedSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence, addSequence, removeRange);
// Validate GetEnumerator() derived Sequence.
Assert.AreEqual(derivedSequence, derSequence.ToString());
IEnumerator <ISequenceItem> list = derSequence.GetEnumerator();
int index = 0;
while (list.MoveNext())
{
Assert.AreEqual(list.Current.Symbol, derivedSequence[index]);
index++;
}
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetEnumerator() method of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetEnumerator() method of derived sequence completed successfully");
}
public void ValidateDnaDerivedSequenceProperties()
{
// Get input and expected values from xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.AlphabetNameNode);
string derivedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.DnaDerivedSequenceNode, Constants.DerivedSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence);
// Validate properties of derived Sequence.
Assert.AreEqual(derivedSequence, new string(derSequence.Select(a => (char)a).ToArray()));
Assert.AreEqual(alphabet, derSequence.Alphabet);
Assert.IsNotNull(derSequence.Metadata);
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of properties of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of properties of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Replace few items using ReplaceRange() and validates it against expected sequence.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceReplaceRange(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ReplaceSequence);
string replaceSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ReplaceRangeSequence);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence.
Sequence seq = new Sequence(alphabet, expectedSequence);
DerivedSequence derSequence = new DerivedSequence(seq);
int position = 0;
// Replace range of sequence.
derSequence.ReplaceRange(position, replaceSequence);
// Validate Derived Sequence
Assert.AreEqual(derivedSequence, derSequence.ToString());
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of ReplaceRange() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of ReplaceRange() of derived sequence completed successfully");
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// </summary>
/// <param name="alphabet">Alphabet</param>
/// <param name="source">source sequence</param>
private static DerivedSequence CreateDerivedSequence(
IAlphabet alphabet, string source)
{
ISequence seq = new Sequence(alphabet, source);
DerivedSequence derSequence = new DerivedSequence(seq, false, false);
return(derSequence);
}
public void TestDerivedSequenceConvertToString()
{
Sequence baseSeq = new Sequence(Alphabets.DNA, "ATCGATCGGATCGATCGGCTACTAATATCGATCGGCTACGATCGGCTAATCGATCGATCGGCTAATCGATCGATCGGCTAGCTA");
DerivedSequence seq = new DerivedSequence(baseSeq, false, false);
const string expectedValue = "TCGATCGGCT";
string actualValue = seq.ConvertToString(10, 10);
Assert.AreEqual(expectedValue, actualValue);
}
public void TestGetReverseComplementedSequence()
{
const string sequence = "ATGCC";
const string expectedSequence = "GGCAT";
ISequence orignalSequence = new Sequence(Alphabets.DNA, sequence);
DerivedSequence deriveSequence = new DerivedSequence(orignalSequence, false, false);
string actualSequence = new string(deriveSequence.GetReverseComplementedSequence().Select(a => (char)a).ToArray());
Assert.AreEqual(expectedSequence, actualSequence);
}
public void TestDerivedSequenceConvertToString()
{
Sequence baseSeq = new Sequence(Alphabets.DNA, "ATCGATCGGATCGATCGGCTACTAATATCGATCGGCTACGATCGGCTAATCGATCGATCGGCTAATCGATCGATCGGCTAGCTA");
DerivedSequence seq = new DerivedSequence(baseSeq, false, false);
const string expectedValue = "TCGATCGGCT";
string actualValue = seq.ConvertToString(10, 10);
Assert.AreEqual(expectedValue, actualValue);
}
public void TestGetReverseComplementedSequence()
{
const string sequence = "ATGCC";
const string expectedSequence = "GGCAT";
ISequence orignalSequence = new Sequence(Alphabets.DNA, sequence);
DerivedSequence deriveSequence = new DerivedSequence(orignalSequence, false, false);
string actualSequence = new string(deriveSequence.GetReverseComplementedSequence().Select(a => (char)a).ToArray());
Assert.AreEqual(expectedSequence, actualSequence);
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// Validates its updated items against expected updated items.
/// </summary>
/// <param name="nodeName">alphabet xml node.</param>
private void ValidateDerivedSequenceGetUpdatedItems(string nodeName)
{
// Get input and expected values from xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string removeRange = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.RemoveRange);
string addSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AddSequence);
string derivedSequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DerivedSequence);
string updatedItems = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.UpdatedItemList);
string updatedIndices = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.UpdatedItemsIndex);
string updatedTypes = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.UpdatedTypeList);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
DerivedSequence derSequence = CreateDerivedSequence(
alphabet, expectedSequence, addSequence, removeRange);
string[] updatedIndexList = updatedIndices.Split(',');
string[] updatedTypesList = updatedTypes.Split(',');
Assert.AreEqual(updatedTypesList.Length, updatedIndexList.Length);
// Validate derived Sequence.
Assert.AreEqual(derivedSequence, derSequence.ToString());
// Validate GetUpdatedItems
IList <IndexedItem <UpdatedSequenceItem> > actualUpdatedItemList =
derSequence.GetUpdatedItems();
Assert.AreEqual(updatedIndexList.Length, actualUpdatedItemList.Count);
for (int index = 0; index < actualUpdatedItemList.Count; index++)
{
Assert.AreEqual(updatedIndexList[index],
actualUpdatedItemList[index].Index.ToString((IFormatProvider)null));
Assert.AreEqual(updatedItems[index].ToString(),
actualUpdatedItemList[index].Item.SequenceItem.Symbol.ToString((IFormatProvider)null));
Assert.AreEqual(updatedTypesList[index],
actualUpdatedItemList[index].Item.Type.ToString());
}
Console.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetUpdatedItems() of derived sequence completed successfully");
ApplicationLog.WriteLine(
"DerivedSequenceBvtTestCases:Validation of GetUpdatedItems() of derived sequence completed successfully");
}
public void TestDeriveSequenceCopyTo()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATCG");
DerivedSequence derSeq = new DerivedSequence(seq, false, true);
byte[] array = new byte[2];
derSeq.CopyTo(array, 1, 2);
string expectedValue = "AG";
StringBuilder b = new StringBuilder();
b.Append((char)array[0]);
b.Append((char)array[1]);
string actualValue = b.ToString();
Assert.AreEqual(expectedValue, actualValue);
}
public void ValidateDerivedContainsNullSeqItem()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.Protein, "EEE");
DerivedSequence deriSeq = new DerivedSequence(seqObj);
// Validate null sequence item in the derived sequence object
Assert.IsFalse(deriSeq.Contains(null));
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the Contains method for null sequence item");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the Contains method for null sequence item");
}
public void ValidateDerivedIndexOfNull()
{
Sequence seqObj = new Sequence(Alphabets.Protein, "KIE");
// Valid index of validation
DerivedSequence deriSeq = new DerivedSequence(seqObj);
Assert.AreEqual(-1, deriSeq.IndexOf(null));
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated IndexOf() method with null values");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the IndexOf() method with null values");
}
public void ValidateDerivedInvalidRemove()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.DNA, "AAGGTT");
DerivedSequence deriSeqObj = new DerivedSequence(seqObj);
ISequence tempSeq = new Sequence(Alphabets.DNA, "C");
Assert.IsFalse(deriSeqObj.Remove(tempSeq[0]));
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveAt() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveAt() method");
}
public void TestDerivedSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
ISequence seqLarge = new Sequence(Alphabets.DNA, "ATCGGGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTTTTT");
ISequence DeriveSeqSmall = new DerivedSequence(seqSmall, false, true);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualSmallString = DeriveSeqSmall.ToString();
string ActualLargeString = DeriveSeqLarge.ToString();
string ExpectedSmallString = "TAGC";
string expectedLargeString = string.Format(CultureInfo.CurrentCulture, "TAGCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCAAAAA... +[{0}]", (seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
}
public void ValidateDerivedSeqInvalidRange()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.DNA, "AAGGTT");
DerivedSequence deriSeqObj = new DerivedSequence(seqObj);
// Pass invalid index value and get the exception required
try
{
deriSeqObj.Range(-1, -1);
Assert.IsTrue(false);
}
catch (ArgumentOutOfRangeException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for Range() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for Range() method");
}
// Pass length value lesser than zero.
try
{
deriSeqObj.Range(1, -21);
Assert.IsTrue(false);
}
catch (ArgumentOutOfRangeException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for Range() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for Range() method");
}
// Pass invalid length and startPos value.
try
{
deriSeqObj.Range(2, 6);
Assert.IsTrue(false);
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for Range() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for Range() method");
}
}
public void ValidateDerivedInvalidRemoveRange()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.DNA, "AAGGTT");
DerivedSequence deriSeqObj = new DerivedSequence(seqObj);
// Pass invalid index value and get the exception required
try
{
deriSeqObj.RemoveRange(-1, 0);
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveRange() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveRange() method");
}
// Pass invalid length value and get the exception required
try
{
deriSeqObj.RemoveRange(3, -1);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveRange() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveRange() method");
}
// Pass invalid length, index value and get the exception required
try
{
deriSeqObj.RemoveRange(1, 10);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveRange() method");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the exception for RemoveRange() method");
}
}
public void ValidateDerivedContainsDnaRnaSeqItem()
{
// Pass protein sequences
ISequence seqObj = new Sequence(Alphabets.DNA, "GCT");
ISequence tempObj = new Sequence(Alphabets.RNA, "UUU");
ISequenceItem seqItemObj = tempObj[0];
DerivedSequence deriSeq = new DerivedSequence(seqObj);
// Validate in valid sequence item in the derived sequence object
Assert.IsFalse(deriSeq.Contains(seqItemObj));
ApplicationLog.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the Contains method for Rna sequence item");
Console.WriteLine(
"DerivedSequenceP2TestCases : Successfully validated the Contains method for Rna sequence item");
}
public void TestDeriveSequenceCopyTo()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATCG");
DerivedSequence derSeq = new DerivedSequence(seq, false, true);
byte[] array = new byte[2];
derSeq.CopyTo(array, 1, 2);
string expectedValue = "AG";
StringBuilder b = new StringBuilder();
b.Append((char)array[0]);
b.Append((char)array[1]);
string actualValue = b.ToString();
Assert.AreEqual(expectedValue, actualValue);
}
public void ValidateDerivedSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
string seqLargeStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeStr);
ISequence DeriveSeqSmall = new DerivedSequence(seqSmall, false, true);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualSmallString = DeriveSeqSmall.ToString();
string ActualLargeString = DeriveSeqLarge.ToString();
string ExpectedSmallString = "TAGC";
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpectedNode);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
//read sequences from file
// Get input and expected values from xml
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
ISequence seq = new Sequence(alphabet, expectedSequence);
var derSequence = new DerivedSequence(seq, false, false);
string actualDerivedSeqStr = derSequence.ToString();
if (actualDerivedSeqStr.Length > Helper.AlphabetsToShowInToString)
{
//check if the whole sequence string contains the string retrieved from ToString
Assert.IsTrue(
expectedSequence.Contains(derSequence.ToString().Substring(0, Helper.AlphabetsToShowInToString)));
Assert.IsTrue(derSequence.ToString().Contains("... +["));
}
else
{
Assert.AreEqual(expectedSequence, derSequence.ToString());
}
}
public void ValidateDerivedSequenceConvertToString()
{
string seqLargeStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeStr);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualLargeString = DeriveSeqLarge.ToString();
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpectedNode);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(expectedLargeString, ActualLargeString);
// Get input and expected values from xml
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
ISequence seq = new Sequence(alphabet, expectedSequence);
var derSequence = new DerivedSequence(seq, false, false);
Assert.AreEqual(expectedSequence.Substring(2, 5), derSequence.ConvertToString(2, 5));
}
public void InvalidateDerivedSequenceConvertToString()
{
try
{
//check with blank sequene
var baseSeq = new Sequence(Alphabets.DNA, "");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with length greater than actual length
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 30);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with length < 0
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, -30);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with start index < 0
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(-10, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with start index greater than actual length
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(30, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with null sequence
Sequence baseSeq = null;
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 3);
Assert.Fail();
}
catch (NullReferenceException nre)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + nre.Message);
}
}
public void ValidateDerivedSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
string seqLargeStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeStr);
ISequence DeriveSeqSmall = new DerivedSequence(seqSmall, false, true);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualSmallString = DeriveSeqSmall.ToString();
string ActualLargeString = DeriveSeqLarge.ToString();
string ExpectedSmallString = "TAGC";
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpectedNode);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
//read sequences from file
// Get input and expected values from xml
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
ISequence seq = new Sequence(alphabet, expectedSequence);
var derSequence = new DerivedSequence(seq, false, false);
string actualDerivedSeqStr = derSequence.ToString();
if (actualDerivedSeqStr.Length > Helper.AlphabetsToShowInToString)
{
//check if the whole sequence string contains the string retrieved from ToString
Assert.IsTrue(
expectedSequence.Contains(derSequence.ToString().Substring(0, Helper.AlphabetsToShowInToString)));
Assert.IsTrue(derSequence.ToString().Contains("... +["));
}
else
{
Assert.AreEqual(expectedSequence, derSequence.ToString());
}
}
/// <summary>
/// Creates a dna derived sequence after adding and removing few items from original sequence.
/// </summary>
/// <param name="alphabet">Alphabet</param>
/// <param name="source">source sequence</param>
private static DerivedSequence CreateDerivedSequence(
IAlphabet alphabet, string source)
{
ISequence seq = new Sequence(alphabet, source);
DerivedSequence derSequence = new DerivedSequence(seq, false, false);
return derSequence;
}
public void TestDerivedSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
ISequence seqLarge = new Sequence(Alphabets.DNA, "ATCGGGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTTTTT");
ISequence DeriveSeqSmall = new DerivedSequence(seqSmall, false, true);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualSmallString = DeriveSeqSmall.ToString();
string ActualLargeString = DeriveSeqLarge.ToString();
string ExpectedSmallString = "TAGC";
string expectedLargeString = string.Format(CultureInfo.CurrentCulture, "TAGCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCAAAAA... +[{0}]", (seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
}
/// <summary>
/// Returns a sequence which contains bases from the specified sequence as specified by the location.
/// If the location contains accession then the sequence from the referredSequences which matches the
/// accession of the location will be considered.
///
/// For example,
/// if location is "join(100..200, J00089.1:10..50, J00090.2:30..40)"
/// then bases from 100 to 200 will be considered from the sequence parameter and referredSequences will
/// be searched for the J00089.1 and J00090.2 accession if found then those sequences will be considered
/// for constructing the output sequence.
/// If the referred sequence is not found in the referredSequences then an exception will occur.
/// </summary>
/// <param name="location">Location instance.</param>
/// <param name="sequence">Sequence instance from which the sub sequence has to be returned.</param>
/// <param name="referredSequences">A dictionary containing Accession numbers as keys and Sequences as values, this will be used when
/// the location or sub-locations contains accession.</param>
public ISequence GetSubSequence(ILocation location, ISequence sequence, Dictionary<string, ISequence> referredSequences)
{
if (location == null)
{
throw new ArgumentNullException(Properties.Resource.ParameterNameLocation);
}
if (sequence == null)
{
throw new ArgumentNullException(Properties.Resource.ParameterNameSequence);
}
DerivedSequence basicDerSeq;
if (location.Operator == LocationOperator.Complement)
{
if (location.SubLocations.Count > 1)
{
throw new ArgumentException(Properties.Resource.ComplementWithMorethanOneSubLocs);
}
if (location.SubLocations.Count > 0)
{
basicDerSeq = new DerivedSequence(location.SubLocations[0].GetSubSequence(sequence, referredSequences), false, true);
}
else
{
basicDerSeq = new DerivedSequence(GetSubSequence(location.LocationStart, location.LocationEnd, location.Accession, location.Separator, sequence, referredSequences), false, true);
}
byte[] tempSeqData = new byte[basicDerSeq.Count];
for (int i = 0; i < basicDerSeq.Count; i++)
{
tempSeqData[i] = basicDerSeq[i];
}
return new Sequence(sequence.Alphabet, tempSeqData);
}
if (location.Operator == LocationOperator.Order)
{
List<ISequence> subSequences = new List<ISequence>();
if (location.SubLocations.Count > 0)
{
foreach (ILocation loc in location.SubLocations)
{
subSequences.Add(loc.GetSubSequence(sequence, referredSequences));
}
}
else
{
basicDerSeq = new DerivedSequence(GetSubSequence(location.LocationStart, location.LocationEnd, location.Accession, location.Separator, sequence, referredSequences), false, false);
byte[] seqData = new byte[basicDerSeq.Count];
for (long i = 0; i < basicDerSeq.Count; i++)
{
seqData[i] = basicDerSeq[i];
}
subSequences.Add(new Sequence(sequence.Alphabet, seqData));
}
long totalSubSequenceLength = 0;
long j = 0;
foreach (ISequence seq in subSequences)
{
totalSubSequenceLength += seq.Count;
}
byte[] tempSeqData = new byte[totalSubSequenceLength];
totalSubSequenceLength = 0;
IAlphabet alphabet = null;
int m = 0;
foreach (ISequence seq in subSequences)
{
totalSubSequenceLength += seq.Count;
while (j < totalSubSequenceLength)
{
tempSeqData[j] = seq[m];
j++;
m++;
}
m = 0;
alphabet = seq.Alphabet;
}
//return Segmented sequence.
return new Sequence(alphabet, tempSeqData);
}
if (location.Operator == LocationOperator.Join || location.Operator == LocationOperator.Bond)
{
if (location.SubLocations.Count > 0)
{
List<ISequence> subSequences = new List<ISequence>();
foreach (ILocation loc in location.SubLocations)
{
subSequences.Add(loc.GetSubSequence(sequence, referredSequences));
}
long i = 0;
long subSeqLength = 0;
foreach (ISequence subSeq in subSequences)
{
subSeqLength += subSeq.Count;
}
byte[] seqData = new byte[subSeqLength];
subSeqLength = 0;
int m = 0;
foreach (ISequence subSeq in subSequences)
{
subSeqLength += subSeq.Count;
while (i < subSeqLength)
{
seqData[i] = subSeq[m];
i++;
m++;
}
m = 0;
}
Sequence seq = new Sequence(sequence.Alphabet,seqData);
return seq;
}
else
{
return GetSubSequence(location.LocationStart, location.LocationEnd, location.Accession, location.Separator, sequence, referredSequences);
}
}
if (location.SubLocations.Count > 0)
{
throw new ArgumentException(Properties.Resource.NoneWithSubLocs);
}
return GetSubSequence(location.LocationStart, location.LocationEnd, location.Accession, location.Separator, sequence, referredSequences);
}
