private static void fill_reference(CitationReference reference, long id)
{
Reference refe = new Reference(reference, id);
MySqlCommand cmmd13 = new MySqlCommand(refe.get_query(), conn);
MySqlDataReader reader13 = cmmd13.ExecuteReader();
reader13.Close();
}
public static string CreateReferenceURL(CitationReference r)
{
if (r.PubMed != null)
{
return("http://www.ncbi.nlm.nih.gov/pubmed/" + r.PubMed);
}
else
{
return("http://academic.research.microsoft.com/Search.aspx?query=" + System.Web.HttpUtility.UrlEncode(r.Title));
}
}
public Reference(CitationReference reference, long id)
{
if (id < 1)
{
UpdaterException.check_data_exception(true);
}
this.id = 0;
this.prokaryote_id = id;
this.authors = reference.Authors;
this.consortium = reference.Consortiums;
this.journal = reference.Journal;
this.location = reference.Location;
this.medline = reference.Medline;
this.pub_med = reference.PubMed;
this.remark = reference.Remarks;
this.title = reference.Title;
}
public void GenBankMetadataClone()
{
LocationBuilder locBuilder = new LocationBuilder();
GenBankMetadata metadata = new GenBankMetadata();
metadata.Accession = new GenBankAccession();
metadata.Accession.Primary = "PAccession";
metadata.Accession.Secondary.Add("SAccession1");
metadata.Accession.Secondary.Add("SAccession2");
metadata.BaseCount = "a 1 c 2";
metadata.Comments.Add("Comment1");
metadata.Comments.Add("Comment2");
metadata.Contig = "Contig Info";
metadata.DBLink = new CrossReferenceLink();
metadata.DBLink.Type = CrossReferenceType.Project;
metadata.DBLink.Numbers.Add("100");
metadata.DBLink.Numbers.Add("200");
metadata.DBSource = "DbSourceInfo";
metadata.Definition = "Defination info";
metadata.Features = new SequenceFeatures();
FeatureItem feature = new FeatureItem("feature1", "1");
List <string> qualifierValues = new List <string>();
qualifierValues.Add("qualifier1value1");
qualifierValues.Add("qualifier1value2");
feature.Qualifiers.Add("qualifier1", qualifierValues);
metadata.Features.All.Add(feature);
feature = new FeatureItem("feature2", "2");
qualifierValues = new List <string>();
qualifierValues.Add("qualifier2value1");
qualifierValues.Add("qualifier2value2");
feature.Qualifiers.Add("qualifier2", qualifierValues);
metadata.Features.All.Add(feature);
feature = new FeatureItem("feature2", "2");
qualifierValues = new List <string>();
qualifierValues.Add("qualifier2value1");
qualifierValues.Add("qualifier2value2");
feature.Qualifiers.Add("qualifier2", qualifierValues);
metadata.Features.All.Add(feature);
metadata.Keywords = "keywords data";
metadata.Locus = new GenBankLocusInfo();
metadata.Locus.Date = DateTime.Now;
metadata.Locus.DivisionCode = SequenceDivisionCode.CON;
metadata.Locus.MoleculeType = MoleculeType.DNA;
metadata.Locus.Name = "LocusName";
metadata.Locus.SequenceLength = 100;
metadata.Locus.SequenceType = "bp";
metadata.Locus.Strand = SequenceStrandType.Double;
metadata.Locus.StrandTopology = SequenceStrandTopology.Linear;
metadata.Origin = "origin info";
metadata.Primary = "Primary info";
metadata.Project = new ProjectIdentifier();
metadata.Project.Name = "Project1";
metadata.Project.Numbers.Add("101");
metadata.Project.Numbers.Add("201");
CitationReference reference = new CitationReference();
reference.Authors = "Authors";
reference.Consortiums = "Consortiums";
reference.Journal = "Journal";
reference.Location = "3";
reference.Medline = "Medline info";
reference.Number = 1;
reference.PubMed = "pubmid";
reference.Remarks = "remarks";
reference.Title = "Title of the book";
metadata.References.Add(reference);
reference = new CitationReference();
reference.Authors = "Authors";
reference.Consortiums = "Consortiums";
reference.Journal = "Journal";
reference.Location = "4";
reference.Medline = "Medline info";
reference.Number = 2;
reference.PubMed = "pubmid";
reference.Remarks = "remarks";
reference.Title = "Title of the book";
metadata.References.Add(reference);
metadata.Segment = new SequenceSegment();
metadata.Segment.Count = 2;
metadata.Segment.Current = 1;
metadata.Source = new SequenceSource();
metadata.Source.CommonName = "ABC Xyz";
metadata.Source.Organism.Genus = "ABC";
metadata.Source.Organism.Species = "Xyz";
metadata.Source.Organism.ClassLevels = "123 123";
metadata.Version = new GenBankVersion();
metadata.Version.Accession = "PAccession";
metadata.Version.Version = "1";
metadata.Version.GINumber = "12345";
GenBankMetadata clonemetadta = metadata.Clone();
Assert.AreEqual(clonemetadta.Accession.Primary, metadata.Accession.Primary);
for (int i = 0; i < clonemetadta.Accession.Secondary.Count; i++)
{
Assert.AreEqual(clonemetadta.Accession.Secondary[i], metadata.Accession.Secondary[i]);
}
Assert.AreEqual(clonemetadta.BaseCount, metadata.BaseCount);
for (int i = 0; i < clonemetadta.Comments.Count; i++)
{
Assert.AreEqual(clonemetadta.Comments[i], metadata.Comments[i]);
}
Assert.AreEqual(clonemetadta.Contig, metadata.Contig);
Assert.AreEqual(clonemetadta.DBLink.Type, metadata.DBLink.Type);
for (int i = 0; i < clonemetadta.DBLink.Numbers.Count; i++)
{
Assert.AreEqual(clonemetadta.DBLink.Numbers[i], metadata.DBLink.Numbers[i]);
}
Assert.AreEqual(clonemetadta.DBSource, metadata.DBSource);
Assert.AreEqual(clonemetadta.Definition, metadata.Definition);
for (int i = 0; i < clonemetadta.Features.All.Count; i++)
{
Assert.AreEqual(clonemetadta.Features.All[i].Key, metadata.Features.All[i].Key);
Assert.AreEqual(locBuilder.GetLocationString(clonemetadta.Features.All[i].Location), locBuilder.GetLocationString(metadata.Features.All[i].Location));
foreach (KeyValuePair <string, List <string> > kvp in clonemetadta.Features.All[i].Qualifiers)
{
if (metadata.Features.All[i].Qualifiers.ContainsKey(kvp.Key))
{
if (kvp.Value == null)
{
Assert.IsNull(metadata.Features.All[i].Qualifiers[kvp.Key]);
}
else
{
for (int j = 0; j < kvp.Value.Count; j++)
{
Assert.AreEqual(kvp.Value[j], metadata.Features.All[i].Qualifiers[kvp.Key][j]);
}
}
}
else
{
Assert.Fail();
}
}
}
Assert.AreEqual(clonemetadta.Keywords, metadata.Keywords);
Assert.AreEqual(clonemetadta.Locus.Date, metadata.Locus.Date);
Assert.AreEqual(clonemetadta.Locus.DivisionCode, metadata.Locus.DivisionCode);
Assert.AreEqual(clonemetadta.Locus.MoleculeType, metadata.Locus.MoleculeType);
Assert.AreEqual(clonemetadta.Locus.Name, metadata.Locus.Name);
Assert.AreEqual(clonemetadta.Locus.SequenceLength, metadata.Locus.SequenceLength);
Assert.AreEqual(clonemetadta.Locus.SequenceType, metadata.Locus.SequenceType);
Assert.AreEqual(clonemetadta.Locus.Strand, metadata.Locus.Strand);
Assert.AreEqual(clonemetadta.Locus.StrandTopology, metadata.Locus.StrandTopology);
Assert.AreEqual(clonemetadta.Origin, clonemetadta.Origin);
Assert.AreEqual(clonemetadta.Primary, metadata.Primary);
Assert.AreEqual(clonemetadta.Project.Name, metadata.Project.Name);
for (int i = 0; i < clonemetadta.Project.Numbers.Count; i++)
{
Assert.AreEqual(clonemetadta.Project.Numbers[i], metadata.Project.Numbers[i]);
}
for (int i = 0; i < clonemetadta.References.Count; i++)
{
Assert.AreEqual(clonemetadta.References[i].Authors, metadata.References[i].Authors);
Assert.AreEqual(clonemetadta.References[i].Consortiums, metadata.References[i].Consortiums);
Assert.AreEqual(clonemetadta.References[i].Journal, metadata.References[i].Journal);
Assert.AreEqual(clonemetadta.References[i].Location, metadata.References[i].Location);
Assert.AreEqual(clonemetadta.References[i].Medline, metadata.References[i].Medline);
Assert.AreEqual(clonemetadta.References[i].Number, metadata.References[i].Number);
Assert.AreEqual(clonemetadta.References[i].PubMed, metadata.References[i].PubMed);
Assert.AreEqual(clonemetadta.References[i].Remarks, metadata.References[i].Remarks);
Assert.AreEqual(clonemetadta.References[i].Title, metadata.References[i].Title);
}
Assert.AreEqual(clonemetadta.Segment.Current, metadata.Segment.Current);
Assert.AreEqual(clonemetadta.Segment.Count, metadata.Segment.Count);
Assert.AreEqual(clonemetadta.Source.CommonName, metadata.Source.CommonName);
Assert.AreEqual(clonemetadta.Source.Organism.ClassLevels, metadata.Source.Organism.ClassLevels);
Assert.AreEqual(clonemetadta.Source.Organism.Genus, metadata.Source.Organism.Genus);
Assert.AreEqual(clonemetadta.Source.Organism.Species, metadata.Source.Organism.Species);
Assert.AreEqual(clonemetadta.Version.Accession, metadata.Version.Accession);
Assert.AreEqual(clonemetadta.Version.CompoundAccession, metadata.Version.CompoundAccession);
Assert.AreEqual(clonemetadta.Version.GINumber, metadata.Version.GINumber);
Assert.AreEqual(clonemetadta.Version.Version, metadata.Version.Version);
}
/// <summary>
/// Add GenBank metadata
/// </summary>
/// <param name="metadata">GenBank Metadata</param>
/// <returns>GenBank Metadat</returns>
private static GenBankMetadata AddGenBankMetadata(GenBankMetadata metadata)
{
metadata.Accession = new GenBankAccession();
metadata.Accession.Primary = "PAccession";
metadata.Accession.Secondary.Add("SAccession1");
metadata.Accession.Secondary.Add("SAccession2");
metadata.BaseCount = "a 1 c 2";
metadata.Comments.Add("Comment1");
metadata.Comments.Add("Comment2");
metadata.Contig = "Contig Info";
metadata.DBLink = new CrossReferenceLink();
metadata.DBLink.Type = CrossReferenceType.Project;
metadata.DBLink.Numbers.Add("100");
metadata.DBLink.Numbers.Add("200");
metadata.DBSource = "DbSourceInfo";
metadata.Definition = "Defination info";
metadata.Features = new SequenceFeatures();
FeatureItem feature = new FeatureItem("feature1", "1");
List <string> qualifierValues = new List <string>();
qualifierValues.Add("qualifier1value1");
qualifierValues.Add("qualifier1value2");
feature.Qualifiers.Add("qualifier1", qualifierValues);
metadata.Features.All.Add(feature);
feature = new FeatureItem("feature2", "2");
qualifierValues = new List <string>();
qualifierValues.Add("qualifier2value1");
qualifierValues.Add("qualifier2value2");
feature.Qualifiers.Add("qualifier2", qualifierValues);
metadata.Features.All.Add(feature);
feature = new FeatureItem("feature2", "2");
qualifierValues = new List <string>();
qualifierValues.Add("qualifier2value1");
qualifierValues.Add("qualifier2value2");
feature.Qualifiers.Add("qualifier2", qualifierValues);
metadata.Features.All.Add(feature);
metadata.Keywords = "keywords data";
metadata.Locus = new GenBankLocusInfo();
metadata.Locus.Date = DateTime.Now;
metadata.Locus.DivisionCode = SequenceDivisionCode.CON;
metadata.Locus.MoleculeType = MoleculeType.DNA;
metadata.Locus.Name = "LocusName";
metadata.Locus.SequenceLength = 100;
metadata.Locus.SequenceType = "bp";
metadata.Locus.Strand = SequenceStrandType.Double;
metadata.Locus.StrandTopology = SequenceStrandTopology.Linear;
metadata.Origin = "origin info";
metadata.Primary = "Primary info";
metadata.Project = new ProjectIdentifier();
metadata.Project.Name = "Project1";
metadata.Project.Numbers.Add("101");
metadata.Project.Numbers.Add("201");
CitationReference reference = new CitationReference();
reference.Authors = "Authors";
reference.Consortiums = "Consortiums";
reference.Journal = "Journal";
reference.Location = "3";
reference.Medline = "Medline info";
reference.Number = 1;
reference.PubMed = "pubmid";
reference.Remarks = "remarks";
reference.Title = "Title of the book";
metadata.References.Add(reference);
reference = new CitationReference();
reference.Authors = "Authors";
reference.Consortiums = "Consortiums";
reference.Journal = "Journal";
reference.Location = "4";
reference.Medline = "Medline info";
reference.Number = 2;
reference.PubMed = "pubmid";
reference.Remarks = "remarks";
reference.Title = "Title of the book";
metadata.References.Add(reference);
metadata.Segment = new SequenceSegment();
metadata.Segment.Count = 2;
metadata.Segment.Current = 1;
metadata.Source = new SequenceSource();
metadata.Source.CommonName = "ABC Xyz";
metadata.Source.Organism.Genus = "ABC";
metadata.Source.Organism.Species = "Xyz";
metadata.Source.Organism.ClassLevels = "123 123";
metadata.Version = new GenBankVersion();
metadata.Version.Accession = "PAccession";
metadata.Version.Version = "1";
metadata.Version.GINumber = "12345";
return(metadata);
}
public static string CreateReferenceURL(CitationReference r)
{
if (r.PubMed != null)
{
return "http://www.ncbi.nlm.nih.gov/pubmed/" + r.PubMed;
}
else
{
return "http://academic.research.microsoft.com/Search.aspx?query=" + System.Web.HttpUtility.UrlEncode(r.Title);
}
}
