/*public void Load( string filename ) {
* UnixCfg rd = new UnixCfg( filename );
* string line = rd.ReadUnixLine();
* char[] sep = new char[]{ ':' };
* string[] fields;
*
* while( line != null ) {
* PSSMposition pos;
* pos.order = uint.Parse( line.Replace("{","") );
* pos.entries = new List<PSSMentry>();
* line = rd.ReadUnixLine();
* while( line != null && !line.Contains("}") ) {
* PSSMentry entry;
* fields = line.Split( sep );
* entry.condition = fields[0].Trim();
* entry.score = double.Parse( fields[1] );
* pos.entries.Add( entry );
* line = rd.ReadUnixLine();
* }
* if( line != null )
* line = rd.ReadUnixLine();
* m_pssm.Add( pos );
* }
* rd.Close();
* }*/
public void Load(string filename)
{
UnixCfg rd = new UnixCfg(filename);
char[] sep = new char[] { ' ', '\t' };
string[] fields;
PSSMentry entry;
string line = rd.ReadUnixLine();
if (line == null)
{
rd.Close();
return;
}
fields = line.Split(sep);
PSSMposition[] pos = new PSSMposition[fields.Length - 1];
for (uint i = 0; i < pos.Length; i++)
{
pos[i].order = i;
pos[i].entries = new List <PSSMentry>();
}
do
{
fields = line.Split(sep);
entry.condition = fields[0].Trim();
for (uint i = 0; i < pos.Length; i++)
{
entry.score = double.Parse(fields[i + 1]);
pos[i].entries.Add(entry);
}
line = rd.ReadUnixLine();
} while(line != null);
rd.Close();
m_pssm.AddRange(pos);
}
private double GetScore( PSSMposition pos, AminoAcid aa )
{
foreach( PSSMentry entry in pos.entries ) {
if( entry.condition.Length == 1 ) {
if( entry.condition.CompareTo(aa.Letter.ToString())==0 )
return entry.score;
else
continue;
}
switch( entry.condition.ToLower() ) {
case "acidic":
if( aa.Acidic ) return entry.score;
break;
case "basic":
if( aa.Basic ) return entry.score;
break;
case "hydrophobic":
if( aa.Hydrophobic ) return entry.score;
break;
case "polar":
if( aa.Polar ) return entry.score;
break;
case "charge":
if( aa.Charge != 0 ) return entry.score;
break;
case "positive":
if( aa.Positive ) return entry.score;
break;
case "negative":
if( aa.Negative ) return entry.score;
break;
case "aromatic":
if( aa.Aromatic ) return entry.score;
break;
case "aliphatic":
if( aa.Aliphatic ) return entry.score;
break;
default:
throw new ApplicationException( "Undefined PSSM condition: " + entry.condition );
}
}
return 0.0;
}
private double GetScore(PSSMposition pos, AminoAcid aa)
{
foreach (PSSMentry entry in pos.entries)
{
if (entry.condition.Length == 1)
{
if (entry.condition.CompareTo(aa.Letter.ToString()) == 0)
{
return(entry.score);
}
else
{
continue;
}
}
switch (entry.condition.ToLower())
{
case "acidic":
if (aa.Acidic)
{
return(entry.score);
}
break;
case "basic":
if (aa.Basic)
{
return(entry.score);
}
break;
case "hydrophobic":
if (aa.Hydrophobic)
{
return(entry.score);
}
break;
case "polar":
if (aa.Polar)
{
return(entry.score);
}
break;
case "charge":
if (aa.Charge != 0)
{
return(entry.score);
}
break;
case "positive":
if (aa.Positive)
{
return(entry.score);
}
break;
case "negative":
if (aa.Negative)
{
return(entry.score);
}
break;
case "aromatic":
if (aa.Aromatic)
{
return(entry.score);
}
break;
case "aliphatic":
if (aa.Aliphatic)
{
return(entry.score);
}
break;
default:
throw new ApplicationException("Undefined PSSM condition: " + entry.condition);
}
}
return(0.0);
}
/*public void Load( string filename ) {
UnixCfg rd = new UnixCfg( filename );
string line = rd.ReadUnixLine();
char[] sep = new char[]{ ':' };
string[] fields;
while( line != null ) {
PSSMposition pos;
pos.order = uint.Parse( line.Replace("{","") );
pos.entries = new List<PSSMentry>();
line = rd.ReadUnixLine();
while( line != null && !line.Contains("}") ) {
PSSMentry entry;
fields = line.Split( sep );
entry.condition = fields[0].Trim();
entry.score = double.Parse( fields[1] );
pos.entries.Add( entry );
line = rd.ReadUnixLine();
}
if( line != null )
line = rd.ReadUnixLine();
m_pssm.Add( pos );
}
rd.Close();
}*/
public void Load( string filename )
{
UnixCfg rd = new UnixCfg( filename );
char[] sep = new char[]{ ' ', '\t' };
string[] fields;
PSSMentry entry;
string line = rd.ReadUnixLine();
if( line == null ) {
rd.Close();
return;
}
fields = line.Split( sep );
PSSMposition[] pos = new PSSMposition[fields.Length-1];
for( uint i = 0; i < pos.Length; i++ ) {
pos[i].order = i;
pos[i].entries = new List<PSSMentry>();
}
do {
fields = line.Split( sep );
entry.condition = fields[0].Trim();
for( uint i = 0; i < pos.Length; i++ ) {
entry.score = double.Parse( fields[i+1] );
pos[i].entries.Add( entry );
}
line = rd.ReadUnixLine();
} while( line != null );
rd.Close();
m_pssm.AddRange( pos );
}