public void TestMissingDirectory()
{
string filepath = @"NoDirectoryHere\NoFileHere.fa";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.Fail("Should not get here!");
}
public void TestMissingFile()
{
string filepath = @"TestUtils\NoFileHere.fa";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.AreEqual(SequenceParsers.Fasta, foundParser);
}
public void TestMissingFile()
{
string filepath = @"TestUtils\NoFileHere.fa";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.Fail("Should not get here!");
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <returns>If found returns the parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByFile(string fileName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (Helper.IsGenBank(fileName))
{
parser = new GenBankParser();
}
else if (fileName.EndsWith(Resource.GFF_FILEEXTENSION, StringComparison.OrdinalIgnoreCase))
{
parser = new GffParser();
}
else if (Helper.IsFasta(fileName))
{
parser = new FastaParser();
}
else if (Helper.IsFastQ(fileName))
{
parser = new FastQParser();
}
else
{
parser = null;
}
}
return(parser);
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="parserName">Name of the parser to use.</param>
/// <returns>If found returns the open parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByName(string fileName, string parserName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName) && !string.IsNullOrEmpty(parserName))
{
if (parserName == Properties.Resource.FastAName)
{
parser = new FastAParser(fileName);
}
else if (parserName == Properties.Resource.FastQName)
{
parser = new FastQParser(fileName);
}
else if (parserName == Properties.Resource.GENBANK_NAME)
{
parser = new GenBankParser(fileName);
}
else
{
// Do a search through the known parsers to pick up custom parsers added through add-in.
parser = All.FirstOrDefault(p => p.Name == parserName);
// If we found a match based on extension, then open the file - this
// matches the above behavior where a specific parser was created for
// the passed filename - the parser is opened automatically in the constructor.
if (parser != null)
{
parser.Open(fileName);
}
}
}
return(parser);
}
public void TestMissingDirectory()
{
string filepath = @"NoDirectoryHere\NoFileHere.fa";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.AreEqual(SequenceParsers.Fasta, foundParser);
}
public void ReturnNoParser()
{
string dummyFileName = "dummy.abc";
ISequenceParser parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.AreEqual(parser, null);
}
/// <summary>
/// When implemented in a derived class, performs the execution of the activity.
/// </summary>
/// <param name="context">The execution context under which the activity executes.</param>
protected override IEnumerable <ISequence> Execute(CodeActivityContext context)
{
string filename = Filename.Get(context);
ISequenceParser parser = SequenceParsers.FindParserByFileName(filename);
if (parser == null)
{
throw new ArgumentException("Could not determine parser for " + filename);
}
string alphaName = DesiredAlphabet;
if (!string.IsNullOrEmpty(alphaName))
{
alphaName = alphaName.ToLowerInvariant();
IAlphabet alphabet = Alphabets.All.FirstOrDefault(a => a.Name.ToLowerInvariant() == alphaName);
if (alphabet == null)
{
throw new ArgumentException("Unknown alphabet name");
}
parser.Alphabet = alphabet;
}
if (LogOutput)
{
var tw = context.GetExtension <TextWriter>() ?? Console.Out;
tw.WriteLine("Reading sequences from " + filename);
}
return(parser.Parse());
}
/// <summary>
/// Alternative constructor for performing quality score-level QC when
/// read length max and count is not available and needs to be determined.
/// </summary>
/// <param name="sequences">Sequence parser</param>
/// <param name="format">FastQ Format Type.</param>
/// <param name="filename">the input filename</param>
public QualityScoreAnalyzer(ISequenceParser sequences, FastQFormatType format, string filename) : base(sequences, filename)
{
List <long> lengths = this.DetermineReadLengths();
this.Count = lengths.Count;
Initialize(format);
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="parserName">Name of the parser to use.</param>
/// <returns>If found returns the parser as IParser else returns null.</returns>
public static ISequenceParser FindParserByName(string fileName, string parserName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (parserName == Properties.Resource.FastAName)
{
parser = new FastAParser(fileName);
}
else if (parserName == Properties.Resource.FastQName)
{
parser = new FastQParser(fileName);
}
else if (parserName == Properties.Resource.GENBANK_NAME)
{
parser = new GenBankParser(fileName);
}
else if (parserName == Properties.Resource.GFF_NAME)
{
parser = new GffParser(fileName);
}
else
{
parser = null;
}
}
return(parser);
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="parserName">Name of the parser to use.</param>
/// <returns>If found returns the open parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByName(string fileName, string parserName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName) && !string.IsNullOrEmpty(parserName))
{
if (parserName == Properties.Resource.FastAName)
{
parser = fasta;
}
else if (parserName == Properties.Resource.FastQName)
{
parser = new SequenceParserDecorator <FastQParser, IQualitativeSequence>(fastq);
}
else if (parserName == Properties.Resource.GENBANK_NAME)
{
parser = genBank;
}
else if (parserName == Properties.Resource.GFF_NAME)
{
parser = gff;
}
else
{
// Do a search through the known parsers to pick up custom parsers added through add-in.
parser = All.FirstOrDefault(p => p.Name == parserName);
}
}
return(parser);
}
/// <summary>
/// Finds a suitable parser that supports the specified file, opens the file and returns the parser.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <returns>If found returns the parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByFileName(string fileName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (IsFasta(fileName))
{
parser = new FastAParser(fileName);
}
else if (IsFastQ(fileName))
{
parser = new FastQParser(fileName);
}
else if (IsGenBank(fileName))
{
parser = new GenBankParser(fileName);
}
else if (fileName.EndsWith(Properties.Resource.GFF_FILEEXTENSION, StringComparison.InvariantCultureIgnoreCase))
{
parser = new GffParser(fileName);
}
else
{
parser = null;
}
}
return(parser);
}
public void FindGenBankParser()
{
string dummyFileName = "dummy.gb";
ISequenceParser parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(GenBankParser), parser);
}
public void FindFastaParser()
{
string dummyFileName = "dummy.fasta";
ISequenceParser parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
dummyFileName = "dummy.fa";
parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
dummyFileName = "dummy.mpfa";
parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
dummyFileName = "dummy.fna";
parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
dummyFileName = "dummy.faa";
parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
dummyFileName = "dummy.fsa";
parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
dummyFileName = "dummy.fas";
parser = SequenceParsers.FindParserByFile(dummyFileName);
Assert.IsInstanceOf(typeof(FastaParser), parser);
}
/// <summary>
/// Finds a suitable parser that supports the specified file, opens the file and returns the parser.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <returns>If found returns the open parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByFileName(string fileName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (IsFasta(fileName))
{
parser = fasta;
}
else if (IsFastQ(fileName))
{
parser = new SequenceParserDecorator <FastQParser, IQualitativeSequence>(fastq);
}
else if (IsGenBank(fileName))
{
parser = genBank;
}
else if (fileName.EndsWith(Properties.Resource.GFF_FILEEXTENSION, StringComparison.OrdinalIgnoreCase))
{
parser = gff;
}
else
{
// Do a search through the known parsers to pick up custom parsers added through add-in.
string fileExtension = Path.GetExtension(fileName);
if (!string.IsNullOrEmpty(fileExtension))
{
parser = All.FirstOrDefault(p => p.SupportedFileTypes.Contains(fileExtension));
}
}
}
return(parser);
}
public void TestUnknownFileExtension()
{
string filepath = @"Test.ukn";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.IsNull(foundParser);
}
/// <summary>
/// Constructor when called from GUI. Used when read length max and count is not available and needs to be determined.
/// </summary>
/// <param name="sequences">Sequence parser</param>
/// <param name="format">FastQ Format Type.</param>
/// <param name="filename">the input filename</param>
/// <param name="worker">Background worker</param>
/// <param name="e">Background Worker event args</param>
public QualityScoreAnalyzer(ISequenceParser sequences, FastQFormatType format, string filename, BackgroundWorker worker, DoWorkEventArgs e)
: base(sequences, filename, worker, e)
{
List <long> lengths = this.DetermineReadLengths();
this.Count = lengths.Count;
Initialize(format);
}
/// <summary>
/// Constructor for discarding reads based on minimum length.
/// </summary>
/// <param name="parser">Input sequence parser</param>
/// <param name="filtered">Output sequence formatter</param>
/// <param name="discarded">Output discarded sequences formatter</param>
/// <param name="length">The minimum length that reads must satisfy in
/// order to not be discarded.</param>
public DiscardByLength(ISequenceParser parser, ISequenceFormatter filtered, ISequenceFormatter discarded, long length)
: base(parser, filtered, discarded)
{
if (length <= 0)
{
throw new ArgumentOutOfRangeException("Minimum length must be > 0.");
}
minLengthThreshold = length;
}
private void btnOK_Click(object sender, EventArgs e)
{
ISequenceParser foundParser = (ISequenceParser)cbParserList.SelectedItem;
if (foundParser != null)
{
SelectedParser = SequenceParsers.FindParserByName(FileName, foundParser.Name);
}
}
/// <summary>
/// Parses a file containing a sequence in .NET Bio supported formats.
/// </summary>
/// <param name="file">Path to a parsed file.</param>
/// <returns>Fragment sequence.</returns>
private ISequence ParseFile(String file)
{
parser = SequenceParsers.FindParserByFileName(file);
if (parser == null)
{
throw new FileFormatException("Parser for " + file + " not found.");
}
return(ParseFragment(parser, file));
}
public void TestTxtFileExtension()
{
string filepath = @"TestUtils\BLOSUM50.txt";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.IsNull(foundParser);
// Should not auto-locate FieldTextParser.
}
public void TestGffFileExtension()
{
string filepath = @"TestUtils\Simple_Gff_Dna.gff";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.IsNotNull(foundParser);
Assert.IsInstanceOf <GffParser>(foundParser);
}
public void TestSffFileExtension()
{
string filepath = @"TestUtils\dummy.sff";
ISequenceParser foundParser = SequenceParsers.FindParserByFileName(filepath);
Assert.IsNotNull(foundParser);
Assert.IsInstanceOf <SFFParser>(foundParser);
}
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
String inputFileName = InputFile;
ISequenceParser parser = SequenceParsers.FindParserByFile(inputFileName);
SequenceResult = parser.ParseOne(inputFileName);
return(ActivityExecutionStatus.Closed);
}
/// <summary>
/// Constructor for trimming sequences based on length or percentage
/// </summary>
/// <param name="parser">Input sequences parser</param>
/// <param name="filtered">Output sequences formatter</param>
/// <param name="discarded">Discarded sequences formatter</param>
/// <param name="newLength">If > 1, this is the minimum length (rounded to the nearest integer)
/// sequences will be trimmed at. If between 0 and 1, this will be treated as
/// a percentage and reads are trimmed based on this amount (i.e. if newLength = 0.5, 50%
/// of the read will be trimmed.</param>
/// <param name="fromStart">Trim from the start of the read</param>
public TrimByLength(ISequenceParser parser, ISequenceFormatter filtered, ISequenceFormatter discarded, double newLength, bool fromStart)
: base(parser, filtered, discarded, fromStart)
{
if (newLength <= 0)
{
throw new ArgumentOutOfRangeException("Trim length cannot be less than zero.");
}
this.TrimLength = newLength;
}
// Parses a sequence and adds it to the displayed list
private void ParseSequence(ISequenceParser parser, string filename)
{
IList <ISequence> parsed = parser.Parse(filename);
ListBox sequenceList = (ListBox)FindName("SequencesListBox");
foreach (ISequence seq in parsed)
{
sequenceList.Items.Add(seq);
}
}
/// <summary>
/// Constructor for processing the input file
/// </summary>
/// <param name="file">Input filename</param>
public InputSubmission(string file)
{
if (file == null)
{
throw new ArgumentNullException("file");
}
this.Filename = file;
this.Parser = SequenceParsers.FindParserByFileName(file);
}
/// <summary>
/// Helper method to parse the given filename into a set
/// of ISequence elements. This routine will load sequences from
/// any support sequence parser in .NET Bio.
/// </summary>
/// <param name="fileName">Filename to load data from</param>
/// <returns>Enumerable set of ISequence elements</returns>
protected static IEnumerable <ISequence> ParseFile(string fileName)
{
ISequenceParser parser = SequenceParsers.FindParserByFileName(fileName);
if (parser == null)
{
throw new Exception("Could not locate an appropriate sequence parser for " + fileName);
}
return(parser.Parse());
}
/// <summary>
/// Helper method to parse the given filename into a set
/// of ISequence elements. This routine will load sequences from
/// any support sequence parser in .NET Bio.
/// </summary>
/// <param name="fileName">Filename to load data from</param>
/// <returns>Enumerable set of ISequence elements</returns>
internal static IEnumerable <ISequence> ParseFile(string fileName)
{
ISequenceParser parser = SequenceParsers.FindParserByFileName(fileName);
if (parser == null)
{
parser = new FastAParser(fileName);
}
return(parser.Parse());
}
// Parses a sequence and adds it to the displayed list
private void ParseSequence(ISequenceParser parser, string filename)
{
parser.Open(filename);
IEnumerable <ISequence> parsed = parser.Parse();
ListBox sequenceList = (ListBox)FindName("SequencesListBox");
foreach (ISequence seq in parsed)
{
sequenceList.Items.Add(seq);
}
parser.Close();
}
public void ValidateParserExceptions(ISequenceParser parser)
{
try
{
var parserTypes = parser.GetType();
Assert.IsNotNull(parserTypes);
}
catch (NullReferenceException exception)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider) null,
"Sequence Parser P2 : Validated Exception {0} successfully",
exception.Message));
}
}
/// <summary>
/// This method is called when the user wants to import a Sequence file
/// into excel. The user chooses a particular Sequence file which will
/// be parsed by parsers available in our framework and is then imported
/// into a excel file.
/// </summary>
/// <param name="parser">SequenceParser instance.</param>
/// <param name="fileName">Name of the file</param>
/// <param name="currentRow">Current row of insertion</param>
private void ReadSequences(ISequenceParser parser, string fileName, ref int currentRow)
{
this.ScreenUpdate(false);
if (this.sequencesPerWorksheet == 1)
{
this.ImportSequencesOnePerSheet(parser, fileName);
}
else if (this.sequencesPerWorksheet <= 0)
{
this.ImportSequencesAllInOneSheet(parser, fileName, ref currentRow);
}
else if (this.sequencesPerWorksheet > 0)
{
this.ImportSequencesAcrossSheets(parser, fileName, ref currentRow);
}
this.ScreenUpdate(true);
}
/// <summary>
/// This method breaks the sequences across multiple worksheets.
/// </summary>
/// <param name="parser"></param>
/// <param name="fileName"></param>
/// <param name="currentRow"></param>
private void ImportSequencesAcrossSheets(ISequenceParser parser, string fileName, ref int currentRow)
{
Workbook workBook = Globals.ThisAddIn.Application.ActiveWorkbook;
int sequenceCount = 0;
Worksheet worksheet = null;
Globals.ThisAddIn.Application.EnableEvents = false;
try
{
foreach (ISequence sequence in parser.Parse())
{
if (worksheet == null || sequenceCount++ >= this.sequencesPerWorksheet)
{
if (worksheet != null)
{
worksheet.Cells[1, 1].EntireColumn.AutoFit(); // Autofit first column
}
currentRow = 1;
sequenceCount = 1;
worksheet =
workBook.Worksheets.Add(
Type.Missing,
workBook.Worksheets.Item[workBook.Worksheets.Count],
Type.Missing,
Type.Missing) as Worksheet;
if (worksheet == null)
{
return;
}
// Get a name for the worksheet.
string validName =
this.GetValidFileNames(
string.IsNullOrEmpty(sequence.ID)
? Path.GetFileNameWithoutExtension(fileName)
: sequence.ID);
worksheet.Name = validName;
((_Worksheet)worksheet).Activate();
Globals.ThisAddIn.Application.ActiveWindow.Zoom = ZoomLevel;
}
// If sequence ID cannot be used as a sheet name, update the sequence DisplayID with the string used as sheet name.
if (string.IsNullOrEmpty(sequence.ID))
{
sequence.ID = Path.GetFileNameWithoutExtension(fileName) + "_" + sequenceCount;
}
this.WriteOneSequenceToWorksheet(parser, ref currentRow, sequence, worksheet);
}
if (worksheet != null)
{
worksheet.Cells[1, 1].EntireColumn.AutoFit(); // Autofit first column
}
}
finally
{
this.EnableAllControls();
Globals.ThisAddIn.Application.EnableEvents = true;
}
}
public void openProject(String file)
{
Sequence sequence = null;
parser = SequenceParsers.GenBank;
parser.Open(file);
sequence = (Sequence)parser.Parse().ToList()[0];
parser.Close();
Fragment project = new Fragment(file, "project", sequence);
GenBankMetadata meta = sequence.Metadata["GenBank"] as GenBankMetadata;
FragmentDict = new Dictionary<string, Fragment>();
foreach (var feat in meta.Features.MiscFeatures)
{
String subseq = project.GetString().Substring(feat.Location.LocationStart-1, feat.Location.LocationEnd - feat.Location.LocationStart + 1);
FragmentDict.Add(feat.StandardName, new Fragment(file, feat.StandardName, new Sequence(Alphabets.AmbiguousDNA, subseq)));
}
}
/// <summary>
/// This method imports a set of sequences, one per worksheet.
/// </summary>
/// <param name="parser">SequenceParser instance.</param>
/// <param name="fileName">Name of the file</param>
private void ImportSequencesOnePerSheet(ISequenceParser parser, string fileName)
{
Workbook workBook = Globals.ThisAddIn.Application.ActiveWorkbook;
foreach (ISequence sequence in parser.Parse())
{
var worksheet =
workBook.Worksheets.Add(
Type.Missing,
workBook.Worksheets.Item[workBook.Worksheets.Count],
Type.Missing,
Type.Missing) as Worksheet;
if (worksheet == null)
{
return;
}
string validName =
this.GetValidFileNames(
string.IsNullOrEmpty(sequence.ID) ? Path.GetFileNameWithoutExtension(fileName) : sequence.ID);
// If sequence ID cannot be used as a sheet name, update the sequence DisplayID with the string used as sheet name.
if (string.IsNullOrEmpty(sequence.ID))
{
sequence.ID = validName;
}
worksheet.Name = validName;
((_Worksheet)worksheet).Activate();
Globals.ThisAddIn.Application.ActiveWindow.Zoom = ZoomLevel;
Globals.ThisAddIn.Application.EnableEvents = false;
try
{
int currentRow = 1;
this.WriteOneSequenceToWorksheet(parser, ref currentRow, sequence, worksheet);
this.currentFileNumber++;
}
finally
{
worksheet.Cells[1, 1].EntireColumn.AutoFit(); // Autofit first column
this.EnableAllControls();
Globals.ThisAddIn.Application.EnableEvents = true;
}
}
}
/// <summary>
/// Parses a fragment using an appropriate parser.
/// </summary>
/// <param name="parser">Open parser.</param>
/// <param name="fragmentName">Fragment name.</param>
/// <returns>Fragment sequence.</returns>
private ISequence ParseFragment(ISequenceParser parser, String fragmentName)
{
List<ISequence> sequences;
using (parser)
{
sequences = parser.Parse().ToList();
}
if (sequences.Count != 1)
{
throw new SequenceCountException(fragmentName + " contains " + sequences.Count + " well-formatted sequences. It should contain exactly one.");
}
if (sequences.First().Count < 150)
{
throw new SequenceLengthException("Sequence in " + fragmentName + " is shorter than 150nt. It should not be used as a fragment.", sequences.First());
}
return sequences.First();
}
/// <summary>
/// Parses a file containing a sequence in .NET Bio supported formats.
/// </summary>
/// <param name="file">Path to a parsed file.</param>
/// <returns>Fragment sequence.</returns>
private ISequence ParseFile(String file)
{
parser = SequenceParsers.FindParserByFileName(file);
if (parser == null)
{
throw new FileFormatException("Parser for " + file + " not found.");
}
return ParseFragment(parser, file);
}
/// <summary>
/// This method imports a set of sequences, one sequence per row.
/// </summary>
/// <param name="parser">SequenceParser instance.</param>
/// <param name="fileName">Name of the file</param>
/// <param name="currentRow">Next row of insertion</param>
private void ImportSequencesAllInOneSheet(ISequenceParser parser, string fileName, ref int currentRow)
{
Workbook workBook = Globals.ThisAddIn.Application.ActiveWorkbook;
var worksheet =
workBook.Worksheets.Add(
Type.Missing,
workBook.Worksheets.Item[workBook.Worksheets.Count],
Type.Missing,
Type.Missing) as Worksheet;
worksheet.Name = this.GetValidFileNames(Path.GetFileNameWithoutExtension(fileName));
((_Worksheet)worksheet).Activate();
Globals.ThisAddIn.Application.ActiveWindow.Zoom = ZoomLevel;
Globals.ThisAddIn.Application.EnableEvents = false;
try
{
int sequenceCount = 0;
foreach (ISequence sequence in parser.Parse())
{
sequenceCount++;
if (string.IsNullOrEmpty(sequence.ID))
{
sequence.ID = Path.GetFileNameWithoutExtension(fileName) + "_" + sequenceCount;
}
this.WriteOneSequenceToWorksheet(parser, ref currentRow, sequence, worksheet);
this.currentFileNumber++;
}
}
finally
{
worksheet.Cells[1, 1].EntireColumn.AutoFit(); // Autofit first column
this.EnableAllControls();
Globals.ThisAddIn.Application.EnableEvents = true;
}
}
/// <summary>
/// This writes out a single sequence with header, data, quality scores and metadata into the worksheet.
/// </summary>
/// <param name="parser"></param>
/// <param name="currentRow"></param>
/// <param name="sequence"></param>
/// <param name="worksheet"></param>
private void WriteOneSequenceToWorksheet(
ISequenceParser parser,
ref int currentRow,
ISequence sequence,
Worksheet worksheet)
{
// Write the header (sequence id)
if (!string.IsNullOrEmpty(sequence.ID))
{
string[,] formattedMetadata = ExcelImportFormatter.SequenceIDHeaderToRange(sequence);
Range range = this.WriteToSheet(worksheet, formattedMetadata, currentRow, 1);
if (range != null)
{
range.WrapText = false;
currentRow += range.Rows.Count;
}
}
// Write out the data
Range dataRange;
if (sequence.Count > 0)
{
currentRow = this.WriteSequence(worksheet, sequence, currentRow, out dataRange);
if (dataRange != null)
{
dataRange.Columns.AutoFit(); // Autofit columns with sequence data
}
}
// Write quality values if file is FastQ
if (sequence is QualitativeSequence)
{
currentRow++;
worksheet.Cells[currentRow, 1].Value2 = Resources.Sequence_QualityScores;
currentRow = this.WriteQualityValues(
sequence as QualitativeSequence,
worksheet,
currentRow,
3,
out dataRange);
if (dataRange != null)
{
dataRange.Columns.AutoFit(); // Autofit columns with quality scores
}
}
// Write out the metadata
Range metadataRange;
this.WriteMetadata(sequence, parser, worksheet, currentRow, out metadataRange);
if (metadataRange != null)
{
currentRow += metadataRange.Rows.Count;
}
currentRow++; // Add space row between sequences
}
/// <summary>
/// Formats the metadata depending on the sequence type and displays it.
/// </summary>
/// <param name="sequence">Sequence which is holding the metadata</param>
/// <param name="parserUsed">Parser used to read data</param>
/// <param name="worksheet">Sheet on to which the metadata should be written.</param>
/// <param name="startingRow">Row we are on</param>
/// <param name="metadataRange">Will have the range to which the metadata was written</param>
private void WriteMetadata(
ISequence sequence,
ISequenceParser parserUsed,
Worksheet worksheet,
int startingRow,
out Range metadataRange)
{
if (parserUsed is GenBankParser)
{
if (sequence.Metadata.ContainsKey(GenbankMetadataKey))
{
string[,] formattedMetadata =
ExcelImportFormatter.GenBankMetadataToRange(
sequence.Metadata[GenbankMetadataKey] as GenBankMetadata);
metadataRange = this.WriteToSheet(worksheet, formattedMetadata, startingRow, 1);
if (metadataRange != null)
{
// Turn off wrapping for metadata values.
metadataRange.WrapText = false;
}
}
else
{
metadataRange = null;
}
}
else if (parserUsed is GffParser)
{
string[,] formattedMetadata = ExcelImportFormatter.GffMetaDataToRange(sequence);
metadataRange = this.WriteToSheet(worksheet, formattedMetadata, startingRow, 1);
if (metadataRange != null)
{
metadataRange.Columns.VerticalAlignment = XlVAlign.xlVAlignTop;
metadataRange.WrapText = false;
// Now wrap data columns
metadataRange.Columns[2].AutoFit();
metadataRange.Columns[2].WrapText = true;
metadataRange.Columns[2].AutoFit();
}
}
else
{
metadataRange = null;
// No error on this.
//MessageBox.Show(Resources.MetadataFormatError, Resources.CAPTION, MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
}
}
