private void WriteProteinList( TextWriter w, Tag tr, Protein.EvidenceType evidence )
{
Tag a = new Tag( evidence == Protein.EvidenceType.Filtered ? null : "a", "href" );
Tag td = new Tag( "td" );
Tag tdr = new Tag( "td", "rowspan" );
Tag tdc = new Tag( "td", "colspan" );
foreach( Protein p in Proteins ) {
if( p.Evidence != evidence )
continue;
if( p.Subset.Count == 0 ) {
w.Write( tr.Render(
td.Render(a.Render("#"+p.Accession,p.EntryEx))+
td.Render(p.Evidence.ToString())+
tdc.Render("2",Peptides2Html(p))+
td.Render(p.Desc) ));
continue;
}
w.WriteLine( tr.Render(
tdr.Render(p.Subset.Count.ToString(),p.Entry)+
tdr.Render(p.Subset.Count.ToString(),p.Evidence.ToString())+
td.Render(a.Render("#"+p.Subset[0].Accession,p.Subset[0].EntryEx)+": ")+
td.Render(Peptides2Html(p.Subset[0]))+
td.Render(p.Subset[0].Desc) ));
tr.Hold = true;
for( int i = 1; i < p.Subset.Count; i++ )
w.WriteLine( tr.Render(
td.Render(a.Render("#"+p.Subset[i].Accession,p.Subset[i].EntryEx)+": ")+
td.Render(Peptides2Html(p.Subset[i]))+
td.Render(p.Subset[i].Desc) ));
tr.Hold = false;
}
}
private void WriteProteinDetails( TextWriter w, Protein p )
{
Tag tr = new Tag( "tr", true );
Tag td = new Tag( "td", "colspan" );
Tag th = new Tag( "th", "rowspan" );
Tag a = new Tag( "a", "href" );
int i;
w.WriteLine( "<table>\n<caption><a name=\""+p.Accession+"\"/>Protein "+p.Accession+"</caption>" );
//w.WriteLine( "<col width=\"10%\"/><col width=\"5%\"/><col width=\"10%\"/><col width=\"75%\"/>" );
w.WriteLine( tr.Render(th.Render("Name")+td.Render("3",p.EntryEx)) );
w.WriteLine( tr.Render(th.Render("Description")+td.Render("3",p.Desc)) );
w.WriteLine( tr.Render(th.Render("Sequence")+td.Render("3","<pre>"+p.ParseSeq(10)+"</pre>")) );
w.WriteLine( tr.Render(th.Render("Evidence")+td.Render("3",p.Evidence.ToString())) );
w.Write( tr+th.Render("Peptide list")+"<td colspan=\"3\">" );
if( p.Peptides.Count > 0 ) {
for( i = 0; i < p.Peptides.Count-1; i++ )
w.Write( a.Render("#"+p.Accession+"__"+p.Peptides[i].ID,p.Peptides[i].ToString()) + ", " );
w.Write( a.Render("#"+p.Accession+"__"+p.Peptides[i].ID,p.Peptides[i].ToString()) );
}
w.WriteLine( "</td>"+tr );
if( p.Peptides.Count == 0 ) {
w.WriteLine( "</table><br/>" );
return;
}
int rows = 8;
if( Spectra.Count != 0 )
rows++;
w.Write( tr+th.Render((p.Peptides.Count*rows).ToString(),"Peptides") );
bool first = true;
foreach( Peptide f in p.Peptides ) {
if( first )
first = false;
else
w.Write( tr.ToString() );
w.Write( th.Render(rows.ToString(),f.ToString()) );
w.WriteLine( th.Render("<a name=\""+p.Accession+"__"+f.ID+"\"/>Confidence")+td.Render(f.Confidence.ToString())+tr );
tr.Hold = true;
w.WriteLine( tr.Render(th.Render("Decoy")+td.Render(f.Decoy.ToString())) );
w.Write( tr+th.Render("Runs")+td );
for( i = 0; i < f.Runs.Count-1; i++ )
w.Write( f.Runs[i].ToString() + ", " );
w.WriteLine( f.Runs[i].ToString()+td+tr );
w.WriteLine( tr.Render(th.Render("Relation")+td.Render(f.Relation.ToString())) );
w.Write( tr+th.Render("Proteins")+td );
for( i = 0; i < f.Proteins.Count-1; i++ )
w.Write( a.Render("#"+f.Proteins[i].Accession,f.Proteins[i].EntryEx) + ", " );
w.WriteLine( a.Render("#"+f.Proteins[i].Accession,f.Proteins[i].EntryEx)+td.ToString()+tr );
w.WriteLine( tr.Render(th.Render("Sequence")+td.Render("<pre>"+f.Sequence+"</pre>")) );
w.WriteLine( tr.Render(th.Render("Position")+td.Render(f.GetPositions(p))) );
w.Write( tr+th.Render("PTMs")+td );
if( f.Variants.Count == 1 )
w.Write( Peptide.Variant2Str(f.LastVariant) );
else {
i = 1;
foreach( List<PTM> v in f.Variants )
w.Write( "Variant #"+(i++)+": "+Peptide.Variant2Str(v)+"<br/>" );
}
w.WriteLine( td.ToString()+tr );
if( Spectra.Count != 0 ) {
w.Write( tr+th.Render("PSMs")+td );
if( f.Psm != null ) {
for( i = 0; i < f.Psm.Count-1; i++ )
w.Write( a.Render("#PSM"+f.Psm[i].ID,f.Psm[i].ID.ToString()) + ", " );
w.WriteLine( a.Render("#PSM"+f.Psm[i].ID,f.Psm[i].ID.ToString()) );
}
w.WriteLine( td.ToString()+tr );
}
tr.Hold = false;
}
w.WriteLine( "</table><br/>" );
}
private string Peptides2Html( Protein p )
{
if( p.Peptides.Count == 0 )
return "";
int i;
Tag a = new Tag( "a", "href" );
string str = "";
for( i = 0; i < p.Peptides.Count-1; i++ )
str += a.Render("#"+p.Accession+"__"+p.Peptides[i].ID,p.Peptides[i].ToString()) + ", ";
str += a.Render("#"+p.Accession+"__"+p.Peptides[i].ID,p.Peptides[i].ToString());
return str;
}
/// <summary>
/// Saves results to a HTML file.
/// </summary>
public void SaveHtml( string fpath, string name )
{
TextWriter w = new StreamWriter(fpath);
string title = "PAnalyzer: Protein identification report for " + name;
Tag tr = new Tag( "tr", true );
Tag td = new Tag( "td" );
Tag th = new Tag( "th" );
Tag a = new Tag( "a", "href" );
#region Head
w.WriteLine( "<html>\n<head>" );
w.WriteLine( "<title>" + title + "</title>" );
w.WriteLine( "<style>" );
w.WriteLine( "body { padding: 0px; margin: 20px; }" );
w.WriteLine( "caption, .caption { font-size: 120%; color: darkgreen; text-align: left; }" );
w.WriteLine( "th, td { padding-left: 2px; padding-right: 2px; }" );
w.WriteLine( "th { text-align: left; }" );
w.WriteLine( "tr.odd { background-color: #e0e0e0; }" );
w.WriteLine( "tr.even { background-color: #fefefe; }" );
w.WriteLine( "table { border: 2px black solid; border-collapse: collapse; }" );
//w.WriteLine( "table { table-layout: fixed; }" );
w.WriteLine( "</style>" );
w.WriteLine( "<body>" );
w.WriteLine( "<a name=\"top\"/><h2>" + title + "</h2><hr/>" );
#endregion
#region Index
w.WriteLine( "<div class=\"caption\"><a name=\"index\"/>Content:</div>" );
w.WriteLine( "<ol>" );
w.WriteLine( "<li><a class=\"caption\" href=\"#config\">Analysis Configuration</a>" );
w.WriteLine( "<li><a class=\"caption\" href=\"#summary\">Protein Summary</a>" );
w.WriteLine( "<li><a class=\"caption\" href=\"#proteins\">Protein List</a>" );
w.WriteLine( "<li><a class=\"caption\" href=\"#details\">Protein Details</a>" );
if( Spectra.Count != 0 )
w.WriteLine( "<li><a class=\"caption\" href=\"#spectra\">Spectra Details</a>" );
w.WriteLine( "</ol><br/>" );
#endregion
#region Configuration
w.WriteLine( "<table>\n<caption><a name=\"config\"/>Analysis Configuration</caption>" );
//w.WriteLine( "<col width=\"150px\"/><col width=\"300px\"/>" );
w.WriteLine( tr.Render(th.Render("Software")+td.Render(a.Render(m_Software.Url,m_Software.ToString()))) );
w.WriteLine( tr+"\n"+th.Render("Analysis type") );
if( m_InputFiles.Count == 1 ) {
w.Write( td.Render("Single run analysis")+tr );
w.WriteLine( tr.Render(th.Render("Input file")+td.Render(m_InputFiles[0])) );
}
else {
w.WriteLine( td.Render("Multirun analysis")+tr );
w.WriteLine( tr.Render(th.Render("Number of runs")+td.Render(m_InputFiles.Count.ToString())) );
w.WriteLine( tr.Render(th.Render("Runs threshold")+td.Render(RunsThreshold.ToString())) );
w.WriteLine( tr+th.Render("Input files")+"\n<td>" );
foreach( string f in m_InputFiles )
w.WriteLine( f+"<br/>" );
w.WriteLine( "</td>"+tr );
}
w.WriteLine( tr.Render(th.Render("Input file type")+td.Render(ParserName)) );
if( Type == SourceType.Plgs )
w.WriteLine( tr.Render(th.Render("PLGS peptide threshold")+td.Render(PlgsThreshold.ToString())) );
else {
w.WriteLine( tr.Render(th.Render("SpectrumIdentificationItem passThreshold")+td.Render(RequirePassTh.ToString())) );
w.WriteLine( tr.Render(th.Render("SpectrumIdentificationItem rank threshold")+td.Render(RankThreshold.ToString())) );
w.WriteLine( tr.Render(th.Render("PeptideEvidence isDecoy")+td.Render(FilterDecoys?"Filter":"Ignore")) );
if( Type >= SourceType.mzIdentML110 && Type <= SourceType.mzIdentML120 ) {
if( SeqThreshold != Peptide.ConfidenceType.NoThreshold )
w.WriteLine( tr.Render(th.Render("ProteomeDiscoverer/SEQUEST xcorr PSM threshold")+td.Render(SeqThreshold.ToString())) );
}
}
w.WriteLine( "</table><br/>" );
#endregion
#region Summary
w.WriteLine( "<table>\n<caption><a name=\"summary\"/>Protein Summary</caption>" );
//w.WriteLine( "<col width=\"150px\"/><col width=\"300px\"/>" );
w.WriteLine( tr.Render(th.Render("Maximum")+td.Render(Stats.MaxProteins.ToString())) );
w.WriteLine( tr.Render(th.Render("Conclusive")+td.Render(Stats.Conclusive.ToString())) );
w.WriteLine( tr.Render(th.Render("Indistinguishable")+
td.Render(Stats.Indistinguisable==0?"0":Stats.Indistinguisable.ToString()+" in "+Stats.IGroups+
(Stats.IGroups==1?" group":" groups"))) );
w.WriteLine( tr.Render(th.Render("Ambiguous groups")+
td.Render(Stats.Grouped==0?"0":Stats.Grouped.ToString()+" in "+Stats.Groups+
(Stats.Groups==1?" group":" groups"))) );
w.WriteLine( tr.Render(th.Render("Non conclusive")+td.Render(Stats.NonConclusive.ToString())) );
w.WriteLine( tr.Render(th.Render("Filtered")+td.Render(Stats.Filtered.ToString())) );
w.WriteLine( "</table><br/>" );
#endregion
#region Protein List
tr.Reset();
w.WriteLine( "<table>\n<caption><a name=\"proteins\"/>Protein List</caption>" );
//w.WriteLine( "<col width=\"10%\"/><col width=\"10%\"/><col width=\"10%\"/><col width=\"20%\"/><col width=\"50%\"/>" );
w.WriteLine( tr.Render("<th>Name</th><th>Evidence</th><th colspan=\"2\" width=\"40%\">"+
"Peptide list (unique, discriminating*, non-discriminating**)</th><th>Description</th>") );
WriteProteinList( w, tr, Protein.EvidenceType.Conclusive );
WriteProteinList( w, tr, Protein.EvidenceType.Indistinguishable );
WriteProteinList( w, tr, Protein.EvidenceType.Group );
WriteProteinList( w, tr, Protein.EvidenceType.NonConclusive );
WriteProteinList( w, tr, Protein.EvidenceType.Filtered );
w.WriteLine( "</table><br/>" );
#endregion
#region Details
w.WriteLine( "<hr/><a name=\"details\"/>" );
WriteProteinDetails( w, Protein.EvidenceType.Conclusive );
WriteProteinDetails( w, Protein.EvidenceType.Indistinguishable );
WriteProteinDetails( w, Protein.EvidenceType.Group );
WriteProteinDetails( w, Protein.EvidenceType.NonConclusive );
//WriteProteinDetails( w, Protein.EvidenceType.Filtered );
#endregion
#region Details
if( Spectra.Count != 0 ) {
w.WriteLine( "<hr/><a name=\"spectra\"/>" );
WriteSpectraDetails( w );
}
#endregion
w.WriteLine( "</body>\n</html>" );
w.Close();
Notify( "Saved to " + fpath );
}
private void WriteSpectraDetails( TextWriter w, Spectrum s )
{
Tag tr = new Tag( "tr", true );
Tag td = new Tag( "td", "colspan" );
Tag th = new Tag( "th", "rowspan" );
Tag a = new Tag( "a", "href" );
int i;
w.WriteLine( "<table>\n<caption><a name=\"Spectrum"+s.ID+"\"/>Spectrum "+s.SpectrumID+"</caption>" );
w.WriteLine( tr.Render(th.Render("ID")+td.Render("3",s.SpectrumID)) );
w.WriteLine( tr.Render(th.Render("Location")+td.Render("3",s.File)) );
w.Write( tr+th.Render("PSM list")+"<td colspan=\"3\">" );
if( s.Psm.Count > 0 ) {
for( i = 0; i < s.Psm.Count-1; i++ )
w.Write( a.Render("#PSM"+s.Psm[i].ID,s.Psm[i].ID.ToString()) + ", " );
w.Write( a.Render("#PSM"+s.Psm[i].ID,s.Psm[i].ID.ToString()) );
}
w.WriteLine( "</td>"+tr );
if( s.Psm.Count == 0 ) {
w.WriteLine( "</table><br/>" );
return;
}
w.Write( tr+th.Render((s.Psm.Count*8).ToString(),"PSMs") );
bool first = true;
foreach( PSM psm in s.Psm ) {
if( first )
first = false;
else
w.Write( tr.ToString() );
w.Write( th.Render("8",psm.ID.ToString()) );
w.WriteLine( th.Render("<a name=\"PSM"+psm.ID+"\"/>Charge")+td.Render(psm.Charge.ToString())+tr );
tr.Hold = true;
w.WriteLine( tr+th.Render("M/Z")+td.Render(psm.Mz.ToString())+tr );
w.WriteLine( tr+th.Render("Rank")+td.Render(psm.Rank.ToString())+tr );
w.WriteLine( tr+th.Render("Score")+td.Render(psm.Score<0.0?"N/A":psm.Score.ToString())+tr );
w.WriteLine( tr+th.Render("Score type")+td.Render(psm.ScoreType)+tr );
w.WriteLine( tr+th.Render("Confidence")+td.Render(psm.Confidence.ToString())+tr );
w.WriteLine( tr+th.Render("PassThreshold")+td.Render(psm.passThreshold.ToString())+tr );
w.Write( tr+th.Render("Peptide")+td );
if( psm.Peptide != null ) {
w.Write( psm.Peptide.ToString() );
if( psm.Peptide.Proteins.Count > 0 ) {
w.Write( " (" );
for( i = 0; i < psm.Peptide.Proteins.Count - 1; i++ )
w.Write( a.Render("#"+psm.Peptide.Proteins[i].Accession+"__"+psm.Peptide.ID,psm.Peptide.Proteins[i].EntryEx) + ", " );
w.Write( a.Render("#"+psm.Peptide.Proteins[i].Accession+"__"+psm.Peptide.ID,psm.Peptide.Proteins[i].EntryEx) + ")" );
}
} else
w.Write( "N/A (ProCon duplicate?)" );
w.WriteLine( td.ToString()+tr);
tr.Hold = false;
}
w.WriteLine( "</table><br/>" );
w.Flush();
}
/// <summary>
/// Reset the odd/even state to the one of the specified tag.
/// </summary>
/// <param name='tag'>
/// Tag.
/// </param>
public void Reset( Tag tag )
{
mOdd = !tag.mOdd;
}