public List <peak> get_target_range(List <peak> peaks, double mono_mz, int charge, IsotopeSplineDB splinedb)
{
List <peak> .Enumerator copier = peaks.GetEnumerator();
List <peak> .Enumerator look_ahead = peaks.GetEnumerator();
List <peak> light_spec = new List <peak>();
List <peak> iso_hits = new List <peak>();
IsotopeDistribution id;
id = splinedb.estimateFromPeptideWeight(charge * mono_mz, 5);
double[] target_isos = { mono_mz, (mono_mz + (massDiff / charge)), (mono_mz + 2 * (massDiff / charge)), (mono_mz + 3 * (massDiff / charge)), (mono_mz + 4 * (massDiff / charge)) };
double tol = 20 * mono_mz * charge * (1 / 1000000.0);
int curr_iso = 0;
bool hit_iso = false;
double iso_comp = target_isos[0];
double[] target_intensities = { 0.0, 0.0, 0.0, 0.0, 0.0 };
while (look_ahead.MoveNext() && look_ahead.Current.mz < (mono_mz - 0.1))
{
copier.MoveNext();
}
double best_diff = 100000.0;
double best_old_inten = 0.0;
//double mono_intensity = 0.0;
if (Math.Abs(target_isos[curr_iso] - copier.Current.mz) < tol)
{
light_spec.Add(new peak(copier.Current.mz, copier.Current.intensity));
best_diff = Math.Abs(target_isos[curr_iso] - copier.Current.mz);
best_old_inten = copier.Current.intensity;
target_intensities[0] = best_old_inten;
}
bool early_exit = false;
while (copier.Current.mz < (mono_mz + 4 * (massDiff / charge) + 0.1))
{
if (curr_iso < 5)
{
double curr_diff = Math.Abs(target_isos[curr_iso] - copier.Current.mz);
if (curr_diff < tol)
{
if (curr_diff < best_diff)
{
if (best_diff < 99999.0)
{
light_spec[light_spec.Count - 1] = new peak(light_spec.ElementAt(light_spec.Count - 1).mz, -1 * best_old_inten);
}
best_diff = curr_diff;
best_old_inten = copier.Current.intensity;
if (curr_iso == 0)
{
target_intensities[0] = best_old_inten;
}
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity + 2 * target_intensities[curr_iso]));
}
else
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
}
if (!copier.MoveNext())
{
early_exit = true;
break;
}
}
else if (copier.Current.mz > target_isos[curr_iso])
{
if (curr_iso == 0)
{
for (int other_iso = 1; other_iso < 5; ++other_iso)
{
target_intensities[other_iso] = target_intensities[0] * (id.getIntensity(other_iso) / id.getIntensity(0));
}
}
++curr_iso;
best_diff = 100000.0;
best_old_inten = 0.0;
}
else
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
if (!copier.MoveNext())
{
early_exit = true;
break;
}
}
}
else
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
if (!copier.MoveNext())
{
early_exit = true;
break;
}
}
}
if (!early_exit)
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
}
return(light_spec);
}
static void Main(string[] args)
{
string line;
var driver = new DynWinDriver();
Console.WriteLine(args[0]);
bool write_out = System.Convert.ToBoolean(args[0]);
//bad practice but honestly whatever
int charge = 2;
string temp;
double mono_mz = 821.399475097656;
System.IO.StreamReader file = new System.IO.StreamReader(args[1]);
List <peak> temp_scan = new List <peak>();
while ((line = file.ReadLine()) != null)
{
if (line == "BREAK")
{
break;
}
string[] peak = line.Split('\t');
temp_scan.Add(new peak(System.Convert.ToDouble(peak[0]), System.Convert.ToDouble(peak[1])));
}
List <peak> .Enumerator copier = temp_scan.GetEnumerator();
List <peak> .Enumerator look_ahead = temp_scan.GetEnumerator();
List <peak> light_spec = new List <peak>();
List <peak> iso_hits = new List <peak>();
/*
*
* NEW CODE BE CAREFUL
*
*
*/
IsotopeSplineDB splineDB = new IsotopeSplineDB("C:/dev/workspace/IsotopeSplines_10kDa_21isotopes.xml");
IsotopeDistribution id;
id = splineDB.estimateFromPeptideWeight(charge * mono_mz, 5);
double[] target_isos = { mono_mz, (mono_mz + (massDiff / charge)), (mono_mz + 2 * (massDiff / charge)), (mono_mz + 3 * (massDiff / charge)), (mono_mz + 4 * (massDiff / charge)) };
//new variable, be wise
double[] target_intensities = { 0.0, 0.0, 0.0, 0.0, 0.0 };
double tol = 20 * mono_mz * charge * (1 / 1000000.0) * 2;
int curr_iso = 0;
bool hit_iso = false;
double iso_comp = target_isos[0];
while (look_ahead.MoveNext() && look_ahead.Current.mz < (mono_mz - 0.1))
{
copier.MoveNext();
}
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
bool normal_exit = false;
while (copier.MoveNext())
{
if (copier.Current.mz < (mono_mz + 4 * (massDiff / charge) + 0.1))
{
if (curr_iso < 5 && Math.Abs(target_isos[curr_iso] - copier.Current.mz) < tol)
{
iso_hits.Add(new peak(copier.Current.mz, copier.Current.intensity));
hit_iso = true;
}
else if (hit_iso)
{
int best_match = 0;
double min_diff = Math.Abs(iso_hits[0].mz - target_isos[curr_iso]);
for (int i = 0; i < iso_hits.Count(); i++)
{
if (Math.Abs(iso_hits[i].mz - target_isos[curr_iso]) < min_diff)
{
best_match = i;
min_diff = Math.Abs(iso_hits[i].mz - target_isos[curr_iso]);
}
}
for (int i = 0; i < iso_hits.Count(); i++)
{
//new version
if (i == best_match)
{
//everything in this block is the new code
if (curr_iso == 0)
{
target_intensities[0] = iso_hits[i].intensity;
for (int other_iso = 1; other_iso < 5; ++other_iso)
{
target_intensities[other_iso] = iso_hits[i].intensity * (id.getIntensity(other_iso) / id.getIntensity(0));
}
}
light_spec.Add(new peak(iso_hits[i].mz, iso_hits[i].intensity));
}
//
// old version
//
//if (i == best_match)
// light_spec.Add(new peak(iso_hits[i].mz, iso_hits[i].intensity));
else
{
light_spec.Add(new peak(iso_hits[i].mz, -1 * iso_hits[i].intensity));
}
}
iso_hits.Clear();
curr_iso++;
if (curr_iso == 5)
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
hit_iso = false;
}
else if (Math.Abs(target_isos[curr_iso] - copier.Current.mz) < tol)
{
iso_hits.Add(new peak(copier.Current.mz, copier.Current.intensity));
hit_iso = true;
}
else
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
hit_iso = false;
}
}
else
{
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
}
}
else
{
//clean up
normal_exit = true;
if (iso_hits.Count() > 0)
{
int best_match = 0;
double min_diff = Math.Abs(iso_hits[0].mz - target_isos[curr_iso]);
for (int i = 0; i < iso_hits.Count(); i++)
{
if (Math.Abs(iso_hits[i].mz - target_isos[curr_iso]) < min_diff)
{
best_match = i;
min_diff = Math.Abs(iso_hits[i].mz - target_isos[curr_iso]);
}
}
for (int i = 0; i < iso_hits.Count(); i++)
{
if (i == best_match)
{
//light_spec.Add(new peak(iso_hits[i].mz, iso_hits[i].intensity));
light_spec.Add(new peak(iso_hits[i].mz, iso_hits[i].intensity));
}
else
{
light_spec.Add(new peak(iso_hits[i].mz, -1 * iso_hits[i].intensity));
}
}
}
light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
break;
}
}
//new code to account for "full iso_hits" issue
if (!normal_exit)
{
if (iso_hits.Count() > 0)
{
int best_match = 0;
double min_diff = Math.Abs(iso_hits[0].mz - target_isos[curr_iso]);
for (int i = 0; i < iso_hits.Count(); i++)
{
if (Math.Abs(iso_hits[i].mz - target_isos[curr_iso]) < min_diff)
{
best_match = i;
min_diff = Math.Abs(iso_hits[i].mz - target_isos[curr_iso]);
}
}
for (int i = 0; i < iso_hits.Count(); i++)
{
if (i == best_match)
{
//light_spec.Add(new peak(iso_hits[i].mz, iso_hits[i].intensity));
light_spec.Add(new peak(iso_hits[i].mz, iso_hits[i].intensity));
}
else
{
light_spec.Add(new peak(iso_hits[i].mz, -1 * iso_hits[i].intensity));
}
}
}
}
//look_ahead = copier;
//if (look_ahead.MoveNext())
// light_spec.Add(new peak(copier.Current.mz, -1 * copier.Current.intensity));
int front_index = 0;
//IEnumerator<ICentroid> walker = temp_ms1.Centroids.GetEnumerator();
//walker.MoveNext();
//this is likely unnecessary now
while (light_spec[front_index].mz < (mono_mz - 0.1))
{
front_index++;
}
List <peak> light_spec_2 = driver.get_target_range(temp_scan, mono_mz, charge, splineDB);
for (int i = 0; i < light_spec_2.Count; i++)
{
Console.WriteLine("Old: ({0}, {1}) New: ({2}, {3})", light_spec[i].mz, light_spec[i].intensity, light_spec_2[i].mz, light_spec_2[i].intensity);
if (Math.Abs(light_spec[i].mz - light_spec_2[i].mz) >= 0.0001 || Math.Abs(light_spec[i].intensity - light_spec_2[i].intensity) >= 0.0001)
{
Console.WriteLine("Something is wrong with modular function");
//System.Environment.Exit(1);
}
}
int back_index = front_index;
double temp_score;
double min_window = 0.4;
double default_width = 4.0;
double margin = 0.1;
int precision = 1;
//old implementation
/*
* double window_limit;
*
* if ((light_spec[front_index].mz - light_spec[front_index - 1].mz) > 0.2)
* window_limit = (light_spec[front_index].mz + light_spec[front_index - 1].mz) / 2.0;
*
* else
* window_limit = light_spec[front_index].mz - 0.1;
*
* while (back_index < light_spec.Count() && (light_spec[back_index].mz - window_limit) < 0.4)
* back_index++;
*
* int min_index = back_index;
* List<subarrNode> first_scores = new List<subarrNode>();
* while (back_index < (light_spec.Count()))
* {
* int temp_index = front_index;
* temp_score = 0.0;
* while (temp_index <= back_index)
* {
* temp_score += light_spec[temp_index].intensity;
* temp_index++;
* }
*
* first_scores.Add(new subarrNode(front_index, back_index, temp_score));
* back_index++;
* if (back_index >= light_spec.Count())
* break;
* while ((light_spec[back_index].mz - light_spec[front_index].mz) >= 0.4)
* front_index++;
*
* front_index--;
* }
*
* List<subarrNode> final_scores = new List<subarrNode>();
* back_index = min_index + 1;
* final_scores.Add(first_scores[0]);
*
* while (back_index < (light_spec.Count() - 1))
* {
* subarrNode previous = final_scores[back_index - min_index - 1];
* double extended = previous.score + light_spec[back_index].intensity;
* if (extended > first_scores[back_index - min_index].score)
* {
* final_scores.Add(new subarrNode(previous.front, previous.back + 1, extended));
* }
*
* else
* final_scores.Add(first_scores[back_index - min_index]);
*
* back_index++;
*
* }
*
* subarrNode best = final_scores[0];
* for (int i = 1; i < final_scores.Count(); i++)
* {
* if (final_scores[i].score > best.score)
* best = final_scores[i];
* }
*/
//NEW IMPLEMENTATION
List <subarrNode> first_scores = new List <subarrNode>();
first_scores.Add(new subarrNode(0, 0, light_spec[0].intensity));
for (int i = 1; i < light_spec.Count; i++)
{
double new_score = light_spec[i].intensity + first_scores[i - 1].score;
if (new_score > light_spec[i].intensity)
{
first_scores.Add(new subarrNode(first_scores[i - 1].front, i, new_score));
}
else
{
first_scores.Add(new subarrNode(i, i, light_spec[i].intensity));
}
}
double local_sum = light_spec[0].intensity;
int j = 0;
subarrNode best = new subarrNode(0, 0, 0);
while (j < light_spec.Count)
{
j++;
if (light_spec[j].mz - light_spec[0].mz >= min_window)
{
best.back = --j;
break;
}
local_sum += light_spec[j].intensity;
}
best.score = local_sum;
int front = best.front;
int back = best.back;
while (back < (light_spec.Count - 1))
{
double next_mz = light_spec[back + 1].mz;
int num_peaks = (back - front) + 1;
if (num_peaks > 1 && (next_mz - light_spec[front].mz) > min_window)
{
local_sum -= light_spec[front].intensity;
front++;
}
else if ((next_mz - light_spec[front].mz) < min_window)
{
local_sum += light_spec[back + 1].intensity;
back++;
}
else if ((next_mz - light_spec[front].mz) > min_window || (next_mz - light_spec[front].mz) == min_window)
{
local_sum = local_sum + light_spec[back + 1].intensity - light_spec[front].intensity;
front++;
back++;
}
if (local_sum > best.score)
{
best = new subarrNode(front, back, local_sum);
}
if (local_sum + first_scores[front - 1].score > best.score)
{
best = new subarrNode(first_scores[front - 1].front, back, local_sum + first_scores[front - 1].score);
}
}
if (write_out)
{
using (StreamWriter writetext = new StreamWriter(args[2]))
{
for (int i = 0; i < light_spec_2.Count; i++)
{
string spec = (light_spec_2[i].mz).ToString() + '\t' + (light_spec_2[i].intensity).ToString();
writetext.WriteLine(spec);
}
string break_spec = "BREAK";
writetext.WriteLine(break_spec);
}
}
double upper, lower;
/*
* if ((light_spec[best.front].mz - light_spec[best.front - 1].mz) > 0.2)
* lower = (light_spec[best.front].mz + light_spec[best.front - 1].mz) / 2.0;
*
* else
* lower = light_spec[best.front].mz - 0.1;
*
* if ((light_spec[best.back + 1].mz - light_spec[best.back].mz) > 0.2)
* upper = (light_spec[best.back].mz + light_spec[best.back + 1].mz) / 2.0;
*
* else
* upper = light_spec[best.back].mz + 0.1;
*
* if (upper - lower > 4.0)
* upper = lower + 4.0;
*
* double offset = ((upper + lower) / 2.0) - mono_mz;
* double width = upper - lower;
*/
//lower = Math.Min(light_spec[best.front - 1].mz + margin, (light_spec[best.front].mz + light_spec[best.front - 1].mz) / 2.0);
//upper = Math.Max(light_spec[best.back + 1].mz - margin, (light_spec[best.back].mz + light_spec[best.back + 1].mz) / 2.0);
roundedWindow dyn_win = driver.calculate_window(light_spec_2, mono_mz);
upper = dyn_win.upper;
lower = dyn_win.lower;
//this line should ensure windows no larger than 4.0 MZ
//if (upper - lower > 4.0)
// upper = lower + 4.0;
double offset = ((upper + lower) / 2.0) - mono_mz;
double width = upper - lower;
//using (StreamWriter writetext = new StreamWriter("C:\\dev\\real_time_seq\\diw_testing\\diw_testing\\tests\\standard_noisy_answers.txt", true))
if (write_out)
{
using (StreamWriter writetext = new StreamWriter(args[2], true))
{
string window_rep = dyn_win.offset.ToString() + '\t' + dyn_win.width.ToString() + '\t' + dyn_win.upper.ToString() + '\t' + dyn_win.lower.ToString();
writetext.WriteLine(window_rep);
}
}
if (Math.Abs(dyn_win.width - width) >= 0.0001 || Math.Abs(dyn_win.offset - offset) >= 0.0001)
{
Console.WriteLine("Something is wrong with modular function");
//System.Environment.Exit(1);
}
if (width > 4.0)
{
/*
* if (lower < target_isos[0] && upper > target_isos[4])
* {
* lower = target_isos[2] - 2.0;
* upper = target_isos[2] + 2.0;
* }
*
* if (offset < 0.0)
* {
* lower = upper - 4.0;
* }
* else if (offset > (4 * (massDiff / charge)))
* {
* upper = lower + 4.0;
* }
*
*/
double deficit = width - 4.0;
double right_gap = upper - target_isos[4];
double left_gap = target_isos[0] - lower;
if (left_gap < 0.0)
{
upper = lower + 4.0;
}
else if (right_gap < 0.0)
{
lower = upper - 4.0;
}
else
{
double ratio_right = right_gap / (right_gap + left_gap);
upper = upper - ratio_right * deficit;
lower = lower + (1 - ratio_right) * deficit;
}
offset = ((upper + lower) / 2.0) - mono_mz;
width = upper - lower;
}
double width_rounded;
if (width > 4.0)
{
width_rounded = 4.0;
}
else
{
width_rounded = Math.Ceiling(width * 10) / 10;
}
Console.WriteLine("Old Beyond Edges {0} - {1}", light_spec_2[dyn_win.front - 1].mz, light_spec_2[dyn_win.back + 1].mz);
Console.WriteLine("Rounded Edges {0} - {1}", mono_mz + offset - (width_rounded / 2), mono_mz + offset + (width_rounded / 2));
dyn_win = driver.fix_window(light_spec_2, dyn_win, mono_mz, charge, target_isos);
Console.WriteLine("Old Beyond Edges {0} - {1}", light_spec_2[dyn_win.front - 1].mz, light_spec_2[dyn_win.back + 1].mz);
Console.WriteLine("Rounded Edges {0} - {1}", mono_mz + offset - (width_rounded / 2), mono_mz + offset + (width_rounded / 2));
if (write_out)
{
using (StreamWriter writetext = new StreamWriter(args[2], true))
{
string window_rep = dyn_win.offset.ToString() + '\t' + dyn_win.width.ToString() + '\t' + dyn_win.upper.ToString() + '\t' + dyn_win.lower.ToString();
writetext.WriteLine(window_rep);
}
}
//offset = 10.12356456;
//offset = -1.23856;
Console.WriteLine("Original Offset: {0}", offset);
double off_rounded = (double)(Math.Round((double)offset, 1));
width_rounded = (double)(Math.Round((double)width_rounded, 1));
double less_rounded = (double)(Math.Round((double)offset, 5));
double first_few = (double)(Math.Round((double)offset, 2));
double low_mass = 200.0 + first_few * 10;
double remain_offset = less_rounded - first_few;
double high_mass = 2000.0 + remain_offset * 10000;
double recon_offset = (high_mass - 2000.0) / 10000 + (low_mass - 200.0) / 10;
Console.WriteLine("Low: {0}, High: {1}, Reconstructed Offset: {2}", low_mass, high_mass, recon_offset);
Console.WriteLine("Offset: {0}, Width {1}", off_rounded, width_rounded);
temp_score = 0.0;
}