int IComparable.CompareTo(Object obj)
{
PSM temp = (PSM)obj;
if (string.Compare(this.Title, temp.Title) < 0)
{
return(-1);
}
else if (string.Compare(this.Title, temp.Title) > 0)
{
return(1);
}
return(0);
//int scan_number = int.Parse(this.Title.Split('.')[1]);
//int scan_number2 = int.Parse(temp.Title.Split('.')[1]);
//if (scan_number < scan_number2)
// return -1;
//else if (scan_number > scan_number2)
// return 1;
//int pParse_number = int.Parse(this.Title.Split('.')[4]);
//int pParse_number2 = int.Parse(temp.Title.Split('.')[4]);
//if (pParse_number < pParse_number2)
// return -1;
//else if (pParse_number > pParse_number2)
// return 1;
//return 0;
}
public static PSM getPSM_BySpectra(Spectra spec)
{
PSM psm = new PSM(0, spec.Title, "", "", 0.0, spec.Pepmass, 0.0, 0.0, 0.0, 0.0, ' ', "0", true, "", 0);
psm.Charge = spec.Charge;
psm.Spectra_mass = spec.Pepmass * spec.Charge - Config_Help.massZI * (spec.Charge - 1);
return(psm);
}
public ObservableCollection <PSM> filter_bySQ(PSM psm, ObservableCollection <PSM> all_psms)
{
ObservableCollection <PSM> psms = new ObservableCollection <PSM>();
string ss = psm.Sq;
for (int i = 0; i < all_psms.Count; ++i)
{
if (ss == all_psms[i].Sq)
{
psms.Add(all_psms[i]);
}
}
return(psms);
}
public ObservableCollection <PSM> filter_byPeptide(PSM psm, ObservableCollection <PSM> all_psms)
{
ObservableCollection <PSM> psms = new ObservableCollection <PSM>();
string ss = psm.Sq + "@" + psm.Mod_sites;
for (int i = 0; i < all_psms.Count; ++i)
{
string tmp_ss = all_psms[i].Sq + "@" + all_psms[i].Mod_sites;
if (ss == tmp_ss)
{
psms.Add(all_psms[i]);
}
}
return(psms);
}
private void display_btn(object sender, RoutedEventArgs e)
{
ObservableCollection <PSM> all_psms = this.mainW.display_psms;
filter_btn(null, null);
ObservableCollection <PSM> new_psms = this.mainW.display_psms;
this.mainW.display_psms = all_psms;
this.mainW.data.ItemsSource = all_psms;
this.mainW.display_size.Text = all_psms.Count.ToString();
if (new_psms.Count == 0)
{
return;
}
PSM selected_psm = new_psms[0];
this.mainW.data.SelectedItem = selected_psm;
object item = this.mainW.data.SelectedItem;
if (item != null)
{
this.mainW.data.ScrollIntoView(item);
}
}
public static void update_MS2_ratio(ObservableCollection <Protein> proteins, ObservableCollection <PSM> psms)
{
for (int i = 0; i < proteins.Count; ++i)
{
List <double> ratios = new List <double>();
List <double> a1_ratios = new List <double>();
System.Collections.Hashtable sq_hash = new System.Collections.Hashtable();
System.Collections.Hashtable sq_hash_a1 = new System.Collections.Hashtable();
List <int> psm_index = proteins[i].psm_index;
for (int j = 0; j < psm_index.Count; ++j)
{
int index = psm_index[j];
PSM one_psm = psms[index];
if (sq_hash[one_psm.Sq] == null)
{
List <double> rr = new List <double>();
if (one_psm.Ms2_ratio != 0.0)
{
rr.Add(Math.Log10(one_psm.Ms2_ratio) / Math.Log10(2.0));
}
sq_hash[one_psm.Sq] = rr;
rr = new List <double>();
if (one_psm.Ms2_ratio_a1 != 0.0)
{
rr.Add(Math.Log10(one_psm.Ms2_ratio_a1) / Math.Log10(2.0));
}
sq_hash_a1[one_psm.Sq] = rr;
}
else
{
if (one_psm.Ms2_ratio != 0.0)
{
List <double> rr = sq_hash[one_psm.Sq] as List <double>;
rr.Add(Math.Log10(one_psm.Ms2_ratio) / Math.Log10(2.0));
sq_hash[one_psm.Sq] = rr;
}
if (one_psm.Ms2_ratio_a1 != 0.0)
{
List <double> rr = sq_hash_a1[one_psm.Sq] as List <double>;
rr.Add(Math.Log10(one_psm.Ms2_ratio_a1) / Math.Log10(2.0));
sq_hash_a1[one_psm.Sq] = rr;
}
}
}
foreach (string key in sq_hash.Keys)
{
List <double> rr = sq_hash[key] as List <double>;
if (rr.Count > 0)
{
rr.Sort();
if (rr.Count % 2 != 0)
{
ratios.Add(rr[rr.Count / 2]);
}
else
{
ratios.Add((rr[rr.Count / 2] + rr[rr.Count / 2 - 1]) / 2);
}
}
}
foreach (string key in sq_hash_a1.Keys)
{
List <double> rr = sq_hash_a1[key] as List <double>;
if (rr.Count > 0)
{
rr.Sort();
if (rr.Count % 2 != 0)
{
a1_ratios.Add(rr[rr.Count / 2]);
}
else
{
a1_ratios.Add((rr[rr.Count / 2] + rr[rr.Count / 2 - 1]) / 2);
}
}
}
if (ratios.Count > 0)
{
ratios.Sort();
if (ratios.Count % 2 != 0)
{
proteins[i].MS2_Ratio = Math.Pow(2.0, ratios[ratios.Count / 2]);
}
else
{
proteins[i].MS2_Ratio = Math.Pow(2.0, (ratios[ratios.Count / 2] + ratios[ratios.Count / 2 - 1]) / 2);
}
}
if (a1_ratios.Count > 0)
{
a1_ratios.Sort();
if (a1_ratios.Count % 2 != 0)
{
proteins[i].MS2_Ratio_a1 = Math.Pow(2.0, a1_ratios[a1_ratios.Count / 2]);
}
else
{
proteins[i].MS2_Ratio_a1 = Math.Pow(2.0, (a1_ratios[a1_ratios.Count / 2] + a1_ratios[a1_ratios.Count / 2 - 1]) / 2);
}
}
}
}
public int Compare(object x, object y)
{
PSM psm1 = x as PSM;
PSM psm2 = y as PSM;
//sort int
if (header_name == "#")
{
int psm1_ID = psm1.Id;
int psm2_ID = psm2.Id;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_ID > psm2_ID)
{
return(1);
}
else if (psm1_ID < psm2_ID)
{
return(-1);
}
return(0);
}
else
{
if (psm1_ID > psm2_ID)
{
return(-1);
}
else if (psm1_ID < psm2_ID)
{
return(1);
}
return(0);
}
}
else if (header_name == "Spectrum")
{
string psm1_title = psm1.Title;
string psm2_title = psm2.Title;
if (this.direction == ListSortDirection.Ascending)
{
if (string.Compare(psm1_title, psm2_title) > 0)
{
return(1);
}
else if (string.Compare(psm1_title, psm2_title) < 0)
{
return(-1);
}
return(0);
}
else
{
if (string.Compare(psm1_title, psm2_title) > 0)
{
return(-1);
}
else if (string.Compare(psm1_title, psm2_title) < 0)
{
return(1);
}
return(0);
}
}
else if (header_name == "Charge")
{
int psm1_charge = psm1.Charge;
int psm2_charge = psm2.Charge;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_charge > psm2_charge)
{
return(1);
}
else if (psm1_charge < psm2_charge)
{
return(-1);
}
return(0);
}
else
{
if (psm1_charge > psm2_charge)
{
return(-1);
}
else if (psm1_charge < psm2_charge)
{
return(1);
}
return(0);
}
}
else if (header_name == "Spectrum mass")
{
double psm1_mass = psm1.Spectra_mass;
double psm2_mass = psm2.Spectra_mass;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_mass > psm2_mass)
{
return(1);
}
else if (psm1_mass < psm2_mass)
{
return(-1);
}
return(0);
}
else
{
if (psm1_mass > psm2_mass)
{
return(-1);
}
else if (psm1_mass < psm2_mass)
{
return(1);
}
return(0);
}
}
else if (header_name == "Sequence")
{
string psm1_sq = psm1.Sq;
string psm2_sq = psm2.Sq;
if (this.direction == ListSortDirection.Ascending)
{
if (string.Compare(psm1_sq, psm2_sq) > 0)
{
return(1);
}
else if (string.Compare(psm1_sq, psm2_sq) < 0)
{
return(-1);
}
return(0);
}
else
{
if (string.Compare(psm1_sq, psm2_sq) > 0)
{
return(-1);
}
else if (string.Compare(psm1_sq, psm2_sq) < 0)
{
return(1);
}
return(0);
}
}
else if (header_name == "Mod_Sites")
{
string psm1_modsites = psm1.Mod_sites;
string psm2_modsites = psm2.Mod_sites;
if (this.direction == ListSortDirection.Ascending)
{
if (string.Compare(psm1_modsites, psm2_modsites) > 0)
{
return(1);
}
else if (string.Compare(psm1_modsites, psm2_modsites) < 0)
{
return(-1);
}
return(0);
}
else
{
if (string.Compare(psm1_modsites, psm2_modsites) > 0)
{
return(-1);
}
else if (string.Compare(psm1_modsites, psm2_modsites) < 0)
{
return(1);
}
return(0);
}
}
else if (header_name == "Specific")
{
char psm1_specific_flag = psm1.Specific_flag;
char psm2_specific_flag = psm2.Specific_flag;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_specific_flag > psm2_specific_flag)
{
return(1);
}
else if (psm1_specific_flag < psm2_specific_flag)
{
return(-1);
}
return(0);
}
else
{
if (psm1_specific_flag > psm2_specific_flag)
{
return(-1);
}
else if (psm1_specific_flag < psm2_specific_flag)
{
return(1);
}
return(0);
}
}
else if (header_name == "Missed_Cleavage")
{
int psm1_missed_number = psm1.Missed_cleavage_number;
int psm2_missed_number = psm2.Missed_cleavage_number;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_missed_number > psm2_missed_number)
{
return(1);
}
else if (psm1_missed_number < psm2_missed_number)
{
return(-1);
}
return(0);
}
else
{
if (psm1_missed_number > psm2_missed_number)
{
return(-1);
}
else if (psm1_missed_number < psm2_missed_number)
{
return(1);
}
return(0);
}
}
else if (header_name == "Score")
{
double psm1_score = psm1.Score;
double psm2_score = psm2.Score;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_score > psm2_score)
{
return(1);
}
else if (psm1_score < psm2_score)
{
return(-1);
}
return(0);
}
else
{
if (psm1_score > psm2_score)
{
return(-1);
}
else if (psm1_score < psm2_score)
{
return(1);
}
return(0);
}
}
else if (header_name == "Ratio")
{
double psm1_ratio = psm1.Ratio;
double psm2_ratio = psm2.Ratio;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_ratio > psm2_ratio)
{
return(1);
}
else if (psm1_ratio < psm2_ratio)
{
return(-1);
}
return(0);
}
else
{
if (psm1_ratio > psm2_ratio)
{
return(-1);
}
else if (psm1_ratio < psm2_ratio)
{
return(1);
}
return(0);
}
}
else if (header_name == "Sigma")
{
double psm1_sigma = psm1.Sigma;
double psm2_sigma = psm2.Sigma;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_sigma > psm2_sigma)
{
return(1);
}
else if (psm1_sigma < psm2_sigma)
{
return(-1);
}
return(0);
}
else
{
if (psm1_sigma > psm2_sigma)
{
return(-1);
}
else if (psm1_sigma < psm2_sigma)
{
return(1);
}
return(0);
}
}
else if (header_name == "AC")
{
string psm1_ac = psm1.AC;
string psm2_ac = psm2.AC;
if (this.direction == ListSortDirection.Ascending)
{
if (string.Compare(psm1_ac, psm2_ac) > 0)
{
return(1);
}
else if (string.Compare(psm1_ac, psm2_ac) < 0)
{
return(-1);
}
return(0);
}
else
{
if (string.Compare(psm1_ac, psm2_ac) > 0)
{
return(-1);
}
else if (string.Compare(psm1_ac, psm2_ac) < 0)
{
return(1);
}
return(0);
}
}
else if (header_name == "Target_Decoy")
{
string psm1_is_target_flag = psm1.Is_target_flag.ToString();
string psm2_is_target_flag = psm2.Is_target_flag.ToString();
if (this.direction == ListSortDirection.Ascending)
{
if (string.Compare(psm1_is_target_flag, psm2_is_target_flag) > 0)
{
return(1);
}
else if (string.Compare(psm1_is_target_flag, psm2_is_target_flag) < 0)
{
return(-1);
}
return(0);
}
else
{
if (string.Compare(psm1_is_target_flag, psm2_is_target_flag) > 0)
{
return(-1);
}
else if (string.Compare(psm1_is_target_flag, psm2_is_target_flag) < 0)
{
return(1);
}
return(0);
}
}
else if (header_name == "Label_Name")
{
string psm1_N15 = psm1.Pep_flag;
string psm2_N15 = psm2.Pep_flag;
if (this.direction == ListSortDirection.Ascending)
{
if (string.Compare(psm1_N15, psm2_N15) > 0)
{
return(1);
}
else if (string.Compare(psm1_N15, psm2_N15) < 0)
{
return(-1);
}
return(0);
}
else
{
if (string.Compare(psm1_N15, psm2_N15) > 0)
{
return(-1);
}
else if (string.Compare(psm1_N15, psm2_N15) < 0)
{
return(1);
}
return(0);
}
}
else if (header_name == "Detla_Mass (Da)")
{
double psm1_da_mass = psm1.Delta_mass;
double psm2_da_mass = psm2.Delta_mass;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_da_mass > psm2_da_mass)
{
return(1);
}
else if (psm1_da_mass < psm2_da_mass)
{
return(-1);
}
return(0);
}
else
{
if (psm1_da_mass > psm2_da_mass)
{
return(-1);
}
else if (psm1_da_mass < psm2_da_mass)
{
return(1);
}
return(0);
}
}
else if (header_name == "Detla_Mass (PPM)")
{
double psm1_ppm_mass = psm1.Delta_mass_PPM;
double psm2_ppm_mass = psm2.Delta_mass_PPM;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_ppm_mass > psm2_ppm_mass)
{
return(1);
}
else if (psm1_ppm_mass < psm2_ppm_mass)
{
return(-1);
}
return(0);
}
else
{
if (psm1_ppm_mass > psm2_ppm_mass)
{
return(-1);
}
else if (psm1_ppm_mass < psm2_ppm_mass)
{
return(1);
}
return(0);
}
}
else if (header_name == "MS2 Ratio")
{
double psm1_ms2_ratio = psm1.Ms2_ratio;
double psm2_ms2_ratio = psm2.Ms2_ratio;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_ms2_ratio > psm2_ms2_ratio)
{
return(1);
}
else if (psm1_ms2_ratio < psm2_ms2_ratio)
{
return(-1);
}
return(0);
}
else
{
if (psm1_ms2_ratio > psm2_ms2_ratio)
{
return(-1);
}
else if (psm1_ms2_ratio < psm2_ms2_ratio)
{
return(1);
}
return(0);
}
}
else if (header_name == "MS2 Ratio a1")
{
double psm1_ms2_ratio = psm1.Ms2_ratio_a1;
double psm2_ms2_ratio = psm2.Ms2_ratio_a1;
if (this.direction == ListSortDirection.Ascending)
{
if (psm1_ms2_ratio > psm2_ms2_ratio)
{
return(1);
}
else if (psm1_ms2_ratio < psm2_ms2_ratio)
{
return(-1);
}
return(0);
}
else
{
if (psm1_ms2_ratio > psm2_ms2_ratio)
{
return(-1);
}
else if (psm1_ms2_ratio < psm2_ms2_ratio)
{
return(1);
}
return(0);
}
}
else
{
return(0);
}
}