/// <summary>
/// Constructor
/// </summary>
/// <param name="type">type of fragment</param>
/// <param name="messageSeqNumber">message sequence number</param>
/// <param name="isAckRequired">is ack required</param>
/// <param name="fragmentSeqNumber">fragment sequence number</param>
public FragmentHeader(FragmentType type, byte messageSeqNumber, bool isAckRequired, byte fragmentSeqNumber)
{
_type = type;
_messageSeqNumber = messageSeqNumber;
_isAckRequired = isAckRequired;
_fragmentSeqNumber = fragmentSeqNumber;
}
public void TestStateAddWithFragmentWithArguments()
{
var fragmentType = new FragmentType("fields", "state_type");
TypeQL typeQL = new TypeQL(
new Fragments(
new Fragment(
new QueryType(fragmentType,
new Fields(new Field("id"), new Field("name"))
)
)
),
new QueryType(
"state_add",
new Fields(
new Field(fragmentType)
),
new Arguments(
new Argument("input",
new State {
Id = 0, Name = "MINAS GERAIS", Cities = new List <City>()
}
)
)
)
);
var text = typeQL.ToBodyJson();
IExecutionResult result = RequestExecutor.Execute(text);
var json = result.ToJson();
Assert.IsNull(result.Errors);
}
/// <summary>
/// Initializes a new instance of the <see cref="FragmentToken"/> class.
/// </summary>
/// <param name="type">
/// The type of fragment.
/// </param>
/// <param name="name">
/// The name of the fragment if it has one.
/// </param>
/// <param name="content">
/// The content of the fragment if it has any.
/// </param>
public FragmentToken(FragmentType type, string name, object content)
{
this.Type = type;
this.Name = name;
this.Content = content;
this.ContentString = content as string ?? string.Empty;
}
public void TestStateWithFragment()
{
FragmentType fragmentType = new FragmentType("fields", "state_type");
TypeQL typeQL = new TypeQL(
new Fragments(
new Fragment(
new QueryType(fragmentType,
new Fields(new Field("id"), new Field("name"))
)
)
),
new QueryType(
"states",
new Fields(
new Field(fragmentType)
)
)
);
var text = typeQL.ToBodyJson();
//var text0 = typeQL.ToStringJson();
IExecutionResult result = RequestExecutor.Execute(text);
var json = result.ToJson();
Assert.IsNull(result.Errors);
}
public void TestCarAddWithFragmentWithVariables()
{
Car car = new Car
{
Active = true,
Purchase = DateTime.Parse("02/01/1999"),
Time = TimeSpan.Parse("13:14:55"),
Title = "Car One",
Value = 10000M,
Id = 0
};
var fragmentType = new FragmentType("fields", "car_type");
var fragments = new Fragments(new Fragment(new QueryType(fragmentType,
new Fields(new Field("id"), new Field("title"), new Field("active")))));
var arguments = new Arguments(new Argument(new Parameter("input")));
var variables = new Variables("getCar", new Variable <object>("input", car, "car_input"));
var queryTypes = new QueryType("car_add", new Fields(new Field(fragmentType)), arguments);
TypeQL typeQL = new TypeQL(variables, fragments, queryTypes);
var text = typeQL.ToBodyJson();
//var textComplete = typeQL.ToStringJson();
var varDic = typeQL.Variables.ToDictionary();
IExecutionResult result = RequestExecutor.Execute(text, varDic);
var json = result.ToJson();
Assert.IsNull(result.Errors);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="type">type of fragment</param>
/// <param name="messageSeqNumber">message sequence number</param>
/// <param name="isAckRequired">is ack required</param>
/// <param name="fragmentSeqNumber">fragment sequence number</param>
public FragmentHeader(FragmentType type, byte messageSeqNumber, bool isAckRequired, byte fragmentSeqNumber)
{
_type = type;
_messageSeqNumber = messageSeqNumber;
_isAckRequired = isAckRequired;
_fragmentSeqNumber = fragmentSeqNumber;
}
public TabFragPackage(FragmentType fragType)
{
Icon = GetTabIconFromString(fragType.ToString());
Title = fragType.ToString();
RootUrl = Https.URLs.GetUrlStringFromPref(fragType.ToString());
WebViewClient = GetWebViewClientByType(FragmentType.None, fragType.ToString());
}
private MessageFragment(String text, TimeSpanWrapper timeSpanWrapper, OpponentData opponent, FragmentType type)
{
this.text = text;
this.timeSpanWrapper = timeSpanWrapper;
this.opponent = opponent;
this.type = type;
}
public ProfileTextPositionParams(bool expected, int position, string message, FragmentType fragmentType, string newProfileText)
{
Expected = expected;
Position = position;
Message = message;
FragmentType = fragmentType;
NewProfileText = newProfileText;
}
public AScoreParameters(FragmentType f, double tol)
{
staticMods = new List <Mod.Modification>();
terminiMods = new List <Mod.TerminiModification>();
// dynamMods = new List<Mod.DynamicModification>();
fragmentType = f;
fragmentMassTolerance = tol;
}
protected GenFragmentParams(GenDataDef genDataDef, Fragment fragment, FragmentType fragmentType)
{
Contract.Requires(fragment != null && fragment.GetType().Name == fragmentType.ToString());
Contract.Ensures(Fragment != null && Fragment.GetType().Name == FragmentType.ToString());
_fragment = fragment;
GenDataDef = genDataDef;
FragmentType = fragmentType;
}
public Fragment(int Start, int End, int Line, string Text, FragmentType Type)
{
this.Start = Start;
this.End = End;
this.Line = Line;
this.Text = Text;
this.Type = Type;
}
static IRule <Fragment> ThenCreateFragment(this IRule <int> rule, FragmentType type) => rule.Map(x =>
{
var fragment = new Fragment
{
FragmentType = type
};
fragment.Trivia.StartPosition = x;
return(fragment);
});
public void GeneratorFragment(FragmentType type)
{
Vector3 dir =Vector3.Normalize(new Vector3(Random.Range(-1f,1f),0,Random.Range(-1f,1f)));
Vector3 generatorPos = transform.position+dir*radius;
generatorPos.y =Random.Range(0.25f,0.5f);
GameObject newObj = GameObject.Instantiate(FragmentPrefab)as GameObject;
newObj.transform.position = generatorPos;
}
public AScoreParameters(List <Mod.Modification> stat, List <Mod.TerminiModification> term,
List <Mod.DynamicModification> dynam, FragmentType f, double tol)
{
staticMods = stat;
terminiMods = term;
dynamMods = dynam;
fragmentType = f;
fragmentMassTolerance = tol;
}
private void CheckFragment(FragmentType fragmentType, FragmentBody fragmentBody)
{
Contract.Ensures(Fragment != null);
if (FragmentExists)
{
return;
}
var fragmentName = fragmentBody.FragmentName(fragmentType);
switch (fragmentType)
{
case FragmentType.Profile:
Fragment = fragmentBody.AddProfile();
break;
case FragmentType.Text:
Fragment = fragmentBody.AddText(fragmentName);
break;
case FragmentType.Placeholder:
Fragment = fragmentBody.AddPlaceholder(fragmentName);
break;
case FragmentType.Segment:
var segmentParams = ((GenSegmentParams)this);
Fragment = fragmentBody.AddSegment(segmentParams.ClassName, segmentParams.Cardinality.ToString());
break;
case FragmentType.Annotation:
Fragment = fragmentBody.AddAnnotation();
break;
case FragmentType.Block:
Fragment = fragmentBody.AddBlock();
break;
case FragmentType.Lookup:
Fragment = fragmentBody.AddLookup();
break;
case FragmentType.Condition:
Fragment = fragmentBody.AddCondition();
break;
case FragmentType.Function:
Fragment = fragmentBody.AddFunction();
break;
case FragmentType.TextBlock:
Fragment = fragmentBody.AddTextBlock();
break;
default:
throw new ArgumentOutOfRangeException("fragmentType");
}
}
public PresentationContextInputStream(DicomConnection connection, FragmentType fragmentType)
{
_connection = connection;
_fragmentType = fragmentType;
StartReadFragment(isFirstFragment: true);
PresentationContextID = _fragmentHeader.PresentationContextID;
}
public SingleFragment AddFragmentAtScreenPos(Vector3 viewPos, FragmentType type)
{
viewPos.z = 10;
Vector3 wordPos = Camera.main.ViewportToWorldPoint (viewPos);
wordPos = GetPosInRange (wordPos);
SingleFragment fragment = AddNewFragment(wordPos, type);
fragment.SetRandomMoveActive(false);
fragment.IsBeginnerGuideFragment = true;
return fragment;
}
public SingleFragment AddNewFragment(Vector3 pos,FragmentType type,bool showEffect = false)
{
// Debug.Log("AddFragment");
SingleFragment newFragment = (GameObject.Instantiate(FragmentPrefab) as GameObject).GetComponent<SingleFragment>();
newFragment.transform.position = pos;
newFragment.Init(type, showEffect);
newFragment.transform.parent = Root.transform;
mFragmentGroup.Add(newFragment);
return newFragment;
}
public static IFragment GetFragment(FragmentType type, int id)
{
switch (type)
{
case FragmentType.Guard: return(GetGuardFrag(id));
case FragmentType.Demon: return(GetDemonFrag(id));
}
throw new System.Exception("no but try get it");
}
public void Init(FragmentType type,bool isShowEffect = false)
{
mFragmentType = type;
transform.localScale *= (int)type;
mFragmentStatus = FragmentStatus.Stay;
SetRandomMoveActive(true);
}
public GenFragmentLabel(Fragment fragment)
{
Contract.Ensures(Fragment == fragment);
Contract.Ensures(Fragment.GetType().Name == FragmentType.ToString());
Fragment = fragment;
//FragmentType fragmentType;
//Contract.Assert(Enum.TryParse(Fragment.GetType().Name, out fragmentType), "Fragment type invalid: " + Fragment.GetType().Name);
//FragmentType = fragmentType;
FragmentType = fragment.FragmentType;
}
public void TestFragmentType()
{
IFragmentType fragmentType = new FragmentType("fields", "state_type");
Assert.IsInstanceOfType(fragmentType.GetType(), typeof(IFragmentType).GetType());
Assert.IsInstanceOfType(fragmentType.GetType(), typeof(FragmentType).GetType());
Assert.AreEqual(fragmentType.FragmentName, "...fields");
Assert.AreEqual(fragmentType.FragmentNameAndType, "fragment fields on state_type");
Assert.AreEqual(fragmentType.Name, "fields");
Assert.AreEqual(fragmentType.NameType, "state_type");
}
public AttachFragmentCommand(
IPowerPlant powerPlant,
FragmentType lateInstantiationFragmentType,
string lateInstantiationFragmentName,
int lateInstantiationFragmentPressureAffection)
: base(powerPlant)
{
this.LateInstantiationFragmentType = lateInstantiationFragmentType;
this.LateInstantiationFragmentName = lateInstantiationFragmentName;
this.LateInstantiationFragmentPressureAffection = lateInstantiationFragmentPressureAffection;
}
public string GetSource(FragmentType mediaType, long bitrate)
{
ISMElement ismElement = GetISMElement(mediaType, bitrate);
if (ismElement != null)
{
return(ismElement.Source);
}
return(null);
}
public ISMElement GetISMElement(FragmentType fragmentType, long bitrate)
{
foreach (ISMElement ismElement in _ismElements)
{
if (ismElement.FragmentType == fragmentType && ismElement.Bitrate == bitrate)
{
return(ismElement);
}
}
return(null);
}
public GenFragmentParams SetFragmentType(FragmentType fragmentType)
{
Contract.Requires(Container != null || Fragment != null);
Contract.Ensures(Fragment != null && Fragment.GetType().Name == FragmentType.ToString());
FragmentType = fragmentType;
if (FragmentExists)
{
return(this);
}
var fragmentBody = IsPrimary ? Container.CheckBody() : Container.CheckSecondaryBody();
CheckFragment(fragmentType, fragmentBody);
return(this);
}
public IFragment CreateFragment(FragmentType fragmentType, string name, int pressureAffection)
{
IFragment fragment = null;
switch (fragmentType)
{
case FragmentType.Cooling:
fragment = new CoolingFragment(name, pressureAffection);
break;
case FragmentType.Nuclear:
fragment = new NuclearFragment(name, pressureAffection);
break;
}
return fragment;
}
public Fragment(string name, FragmentType type, List <Instruction> instructions)
{
this.Name = name;
this.Type = type;
this.Instructions = new ReadOnlyCollection <Instruction>(instructions);
this.Labels = new Dictionary <string, int>();
for (int i = 0; i < instructions.Count; i++)
{
if (instructions[i].Label == null)
{
continue;
}
this.Labels[instructions[i].Label.Name] = i;
}
}
public void AddComponent(string name, FragmentType type, string parent)
{
TreeNode newGuy = new TreeNode(name);
newGuy.Name = name;
// TODO: Change icon based on FragmentType
if (!string.IsNullOrEmpty(parent))
{
foreach (TreeNode t in treeFragments.Nodes)
{
if (t.Name == parent)
t.Nodes.Add(newGuy);
}
}
else
treeFragments.Nodes.Add(newGuy);
}
public Fragment CalculateFragment(FragmentType fragmentIonType, int fragmentNumber)
{
switch (fragmentIonType)
{
case FragmentType.b:
case FragmentType.c:
return(new Fragment(fragmentIonType, fragmentNumber, cumulativeNTerminalMass[fragmentNumber] + ION_CAPS[fragmentIonType].Mass));
case FragmentType.y:
case FragmentType.zdot:
return(new Fragment(fragmentIonType, fragmentNumber, cumulativeCTerminalMass[fragmentNumber] + ION_CAPS[fragmentIonType].Mass));
default:
return(null);
}
}
/// <summary>
/// Convert UInt16 into a FragmentHeader
/// </summary>
/// <param name="value">encode header value</param>
/// <returns>a new FragmentHeade</returns>
static public FragmentHeader Decode(UInt16 value)
{
ushort mask = 0x0001; // 1 bit for type
byte btype = (byte)((value >> (byte)FragmentHeaderField.Type) & mask);
FragmentType type = (FragmentType)btype;
mask = 0x0001 << (byte)FragmentHeaderField.RequireAck;
bool isAckRequired = ((value & mask) > 0);
mask = 0x00FF; // 8 bits for MessageNumber
byte messageNumber = (byte)((value >> (byte)FragmentHeaderField.MessageNumber) & mask);
mask = 0x003F; // 6 bits for FragmentSeqNumber
byte fragmentSeqNumber = (byte)((value >> (byte)FragmentHeaderField.FragmentSeqNumber) & mask);
return(new FragmentHeader(type, messageNumber, isAckRequired, fragmentSeqNumber));
}
/// <summary>
/// Method to get fragment type from xml
/// </summary>
/// <param name="fragmentType">xmlnode with fragment type info</param>
/// <returns>the type of fragmentation</returns>
private static FragmentType GetFragmentType(XmlNode fragmentType)
{
FragmentType f = FragmentType.CID;
if (Regex.IsMatch(fragmentType.InnerText, "CID"))
{
f = FragmentType.CID;
}
else if (Regex.IsMatch(fragmentType.InnerText, "ETD"))
{
f = FragmentType.ETD;
}
else if (Regex.IsMatch(fragmentType.InnerText, "HCD"))
{
f = FragmentType.HCD;
}
return(f);
}
public override int GetHashCode()
{
unchecked
{
int hash = 13;
hash = (hash * 7) + FragmentType.GetHashCode();
if (Value != null)
{
hash = (hash * 7) + Value.GetHashCode();
}
if (Attributes != null)
{
hash = (hash * 7) + Attributes.GetHashCode();
}
hash = (hash * 7) + IsSelfClosing.GetHashCode();
return(hash);
}
}
//IEnumerator Start()
//{
// yield return new WaitForSeconds(1);
// SetRandomFly();
//}
public void Init(FragmentType type)
{
mType = type;
switch (type)
{
case FragmentType.Big:
mSPrite.spriteName = "Fragment_Big";
break;
case FragmentType.Medium:
mSPrite.spriteName = "Fragment_Medium";
break;
case FragmentType.Small:
mSPrite.spriteName = "Fragment_Small";
break;
}
//mSPrite.transform.localScale *= (int)type;
float scale = 0.5f+((int)type)*0.5f;
mSPrite.transform.localScale*= scale;
}
public static object GetWebViewClientByType(FragmentType fragtype = FragmentType.None, string type = null)
{
if (fragtype != FragmentType.None)
{
type = fragtype.ToString();
}
switch (type)
{
case "Home": return(new Home());
case "Subs": return(new Subs());
case "Feed": return(new Feed());
case "MyChannel": return(new MyChannel());
case "Settings": return(new Settings());
}
return(new Subs());
}
public void SetMyFragments(int num,FragmentType type)
{
mBottleObjGroup.ApplyAllItem(C=>GameObject.Destroy(C.gameObject));
mBottleObjGroup.Clear();
for(int i = 0;i<num;i++)
{
GameObject newFrag = NGUITools.AddChild(gameObject, BottleFlyEffectPrefab);
BottleFragRandomFly randomFly = newFrag.AddComponent<BottleFragRandomFly>();
float scale = 0.5f+((int)type)*0.5f;
newFrag.transform.localScale*= scale/2;
int randomX = Random.Range(20, 30);
int randomY = Random.Range(20, 30);
Vector3 targetPos = new Vector3(Random.Range(-1f, 1f) > 0 ? randomX : -randomX, Random.Range(-1f, 1f) > 0 ? randomY : -randomY, 0);
randomFly.transform.localPosition = targetPos;
randomFly.SetFlyPosRange(20,30);
randomFly.mSPrite.depth = 3;
randomFly.SetActive(true);
mBottleObjGroup.Add(newFrag);
}
}
public void TestStateAddWithFragmentWithVariables()
{
var state = new State {
Id = 0, Name = "MINAS GERAIS", Cities = new List <City>()
};
var fragmentType = new FragmentType("fields", "state_type");
var fragments = new Fragments(new Fragment(new QueryType(fragmentType, new Fields(new Field("id"), new Field("name")))));
var arguments = new Arguments(new Argument(new Parameter("input")));
var variables = new Variables("getState", new Variable <object>("input", state, "state_input"));
var queryTypes = new QueryType("state_add", new Fields(new Field(fragmentType)), arguments);
TypeQL typeQL = new TypeQL(variables, fragments, queryTypes);
var text = typeQL.ToBodyJson();
//var textComplete = typeQL.ToStringJson();
var varDic = typeQL.Variables.ToDictionary();
IExecutionResult result = RequestExecutor.Execute(text, varDic);
var json = result.ToJson();
Assert.IsNull(result.Errors);
}
public ModelComponent(string _name, string _parent)
{
name = _name;
type = FragmentType.MODEL;
parent = _parent;
}
public ModelComponent(string _name, FragmentType _type, string _parent)
{
name = _name;
type = _type;
parent = _parent;
}
protected BaseFragment(string name, FragmentType fragmentType, int pressureAffection)
{
this.Name = name;
this.FragmentType = fragmentType;
this.PressureAffection = pressureAffection;
}
public void AddComponent(string name, FragmentType type)
{
AddComponent(name, type, "");
}
public ISMElement GetISMElement(FragmentType fragmentType, long bitrate)
{
foreach (ISMElement ismElement in ismElements) {
if (ismElement.FragmentType == fragmentType && ismElement.Bitrate == bitrate) {
return (ismElement);
}
}
return (null);
}
public Fragment(FragmentType type, string value)
{
Type = type;
Value = value;
}
public Fragment(FragmentType fragmentType, int number, double mass)
{
this.fragmentType = fragmentType;
this.number = number;
this.mass = mass;
}
public Fragment(string text, FragmentType type)
: this(text, type, -1)
{
}
private Fragment(string text, FragmentType type, int indent)
{
_text = text;
_type = type;
_indent = indent;
}
public void Write(FragmentType type)
{
Write(type, null);
}
public void Write(FragmentType type, string text)
{
_fragments.Add(new Fragment(text, type));
}
public Fragment CalculateFragment(FragmentType fragmentIonType, int fragmentNumber)
{
switch(fragmentIonType)
{
case FragmentType.b:
case FragmentType.c:
return new Fragment(fragmentIonType, fragmentNumber, cumulativeNTerminalMass[fragmentNumber] + ION_CAPS[fragmentIonType].Mass);
case FragmentType.y:
case FragmentType.zdot:
return new Fragment(fragmentIonType, fragmentNumber, cumulativeCTerminalMass[fragmentNumber] + ION_CAPS[fragmentIonType].Mass);
default:
return null;
}
}
public string GetSource(FragmentType mediaType, long bitrate)
{
ISMElement ismElement = GetISMElement(mediaType, bitrate);
if (ismElement != null) {
return (ismElement.Source);
}
return (null);
}
public ModelComponent(string _name, FragmentType _type)
{
name = _name;
type = _type;
parent = "";
}
/// <summary>
/// Sends a fragment.
/// </summary>
private Task SendFragment(Message message, byte[] fragment, FragmentType type)
{
// create a task
return Task.Run(() => {
// check the listening state
if (_listening) {
// error
Log.Singleton.LogError("Can't send a fragment while listening");
// delete message
lock (message) {
MessageCenter.Singleton.Messages.Remove(BitConverter.ToUInt16(message.ID, 0));
}
// cancel
return;
}
// append CRC checksum
CRC.GenerateChecksum(ref fragment);
// need to lock to prevent multiple tasks trying to send simultaneously
lock (_clientMutex) {
// check if we want to lose some fragments
if (Options.LoseFragments) {
// get a random value
var random = new Random();
if ((ushort) random.Next() % 100 < 30) {
// 30% of fragments will be lost
// log that
Log.Singleton.LogMessage($"Purposefully losing a fragment of type <{type}>");
// exit
return;
}
}
// check if we want to corrupt some fragments
if (Options.SendCorrupt) {
// get a random value
var random = new Random();
if ((ushort) random.Next() % 100 < 40) {
// 40% of fragments will be corrupted
// log that
Log.Singleton.LogMessage($"Purposefully corrupting a fragment of type <{type}>");
// change random bytes
for (int i = 0, imax = Math.Abs(random.Next() + 2) % 16; i < imax; ++i) {
fragment[random.Next() % fragment.Length] = (byte) random.Next();
}
}
}
// create a client
_client = new UdpClient();
// bind it
try {
_client.Client.Bind(new IPEndPoint(IPAddress.Any, Options.Port));
}
catch (SocketException) {
// nope, can't bind to that port
Log.Singleton.LogError($"Failed to bind the sending socket to the port <{Options.Port}>");
// remove client
_client = null;
// remove message
lock (message) {
MessageCenter.Singleton.Messages.Remove(BitConverter.ToUInt16(message.ID, 0));
}
// stop
return;
}
// log
lock (message) {
Log.Singleton.LogMessage(
$"Sending a <{type}> fragment for message <{message.ID[0].ToString("00")}{message.ID[1].ToString("00")}> to <{message.RemoteEndPoint}>");
}
// send the fragment
lock (message) {
_client.Send(fragment, fragment.Length, message.RemoteEndPoint);
}
// close and remove client
_client.Close();
_client = null;
}
});
}
public ModelComponent(string _name)
{
name = _name;
type = FragmentType.MODEL;
parent = "";
}
protected Fragment(FragmentType fragmentType, string fragmentName, bool undefined)
{
_fragmentType = fragmentType;
_fragmentName = fragmentName;
_undefined = undefined;
}
/// <summary>
/// Finds the next delimiter from the starting index.
/// </summary>
static Fragment ParseFragment(string format, int startIndex, out int fragmentEndIndex)
{
bool foundEscapedDelimiter = false;
FragmentType type = FragmentType.Literal;
int numChars = format.Length;
for (int i = startIndex; i < numChars; i++)
{
char currChar = format[i];
bool isOpenBrace = currChar == OpeningDelimiter;
bool isCloseBrace = isOpenBrace ? false : currChar == ClosingDelimiter;
if (!isOpenBrace && !isCloseBrace)
{
continue;
}
else if (i < (numChars - 1) && format[i + 1] == currChar)
{ //{{ or }}
i++;
foundEscapedDelimiter = true;
}
else if (isOpenBrace)
{
if (i == startIndex)
{
type = FragmentType.FormatItem;
}
else
{
if (type == FragmentType.FormatItem)
{
throw new FormatException("Two consequtive unescaped { format item openers were found. Either close the first or escape any literals with another {.");
}
//curr character is the opening of a new format item. so we close this literal out
string literal = format.Substring(startIndex, i - startIndex);
if (foundEscapedDelimiter)
{
literal = ReplaceEscapes(literal);
}
fragmentEndIndex = i - 1;
return(new Fragment(FragmentType.Literal, literal));
}
}
else
{ //close bracket
if (i == startIndex || type == FragmentType.Literal)
{
throw new FormatException("A } closing brace existed without an opening { brace.");
}
string formatItem = format.Substring(startIndex + 1, i - startIndex - 1);
if (foundEscapedDelimiter)
{
formatItem = ReplaceEscapes(formatItem); //a format item with a { or } in its name is crazy but it could be done
}
fragmentEndIndex = i;
return(new Fragment(FragmentType.FormatItem, formatItem));
}
}
if (type == FragmentType.FormatItem)
{
throw new FormatException("A format item was opened with { but was never closed.");
}
fragmentEndIndex = numChars - 1;
string literalValue = format.Substring(startIndex);
if (foundEscapedDelimiter)
{
literalValue = ReplaceEscapes(literalValue);
}
return(new Fragment(FragmentType.Literal, literalValue));
}
public void Phosphinate()
{
StreamWriter log = null;
IXRawfile2 raw = null;
StreamReader csv = null;
StreamWriter non_phospho_output = null;
StreamWriter localized_phospho_output = null;
StreamWriter unlocalized_phospho_output = null;
StreamWriter motifX = null;
try
{
onStarting(new EventArgs());
onUpdateProgress(new ProgressEventArgs(0));
StringBuilder fixed_modifications_sb = new StringBuilder();
foreach (Modification modification in fixedModifications)
{
fixed_modifications_sb.Append(modification.Name + ", ");
}
if (fixed_modifications_sb.Length > 0)
{
fixed_modifications_sb = fixed_modifications_sb.Remove(fixed_modifications_sb.Length - 2, 2);
}
string fixed_modifications = fixed_modifications_sb.ToString();
if (!Directory.Exists(outputFolder))
{
Directory.CreateDirectory(outputFolder);
}
log = new StreamWriter(Path.Combine(outputFolder, "Phosphinator_log.txt"));
log.AutoFlush = true;
log.WriteLine("Phosphinator PARAMETERS");
log.WriteLine("Fixed Modifications: " + fixed_modifications);
log.WriteLine("Fragment Intensity Threshold: " + intensityThreshold.ToString() + " (" + intensityThresholdType.ToString() + ')');
log.WriteLine("Fragment m/z Tolerance (Th): " + mzTolerance.ToString());
log.WriteLine("Ambiguity Score Threshold: " + ambiguityScoreThreshold.ToString());
log.WriteLine("Eliminate Precursor Interference: " + eliminatePrecursorInterference.ToString());
if (eliminatePrecursorInterference)
{
log.WriteLine("Precursor Interference Threshold: " + precursorInterferenceThreshold.ToString());
}
if (motifXOutput)
{
log.WriteLine("Motif-X Fasta Protein Database Filepath: " + motifXFastaProteinDatabaseFilepath);
log.WriteLine("Motif-X Window Size: " + motifXWindowSize.ToString());
}
log.WriteLine();
ProteinSiteCounter identified_sites_by_protein = new ProteinSiteCounter();
ProteinSiteCounter localized_sites_by_protein = new ProteinSiteCounter();
ProteinSiteCounter unlocalized_sites_by_protein = new ProteinSiteCounter();
Dictionary<string, Dictionary<KeyValuePair<int, string>, List<string>>> localized =
new Dictionary<string, Dictionary<KeyValuePair<int, string>, List<string>>>();
Dictionary<string, Dictionary<KeyValuePair<int, string>, List<string>>> unlocalized =
new Dictionary<string, Dictionary<KeyValuePair<int, string>, List<string>>>();
non_phospho_output = new StreamWriter(Path.Combine(outputFolder, "non_phospho.csv"));
localized_phospho_output = new StreamWriter(Path.Combine(outputFolder, "localized_phospho.csv"));
unlocalized_phospho_output = new StreamWriter(Path.Combine(outputFolder, "unlocalized_phospho.csv"));
ProteinDictionary proteins = null;
Dictionary<string, int> motifs = null;
if (motifXOutput)
{
proteins = new ProteinDictionary(motifXFastaProteinDatabaseFilepath);
motifs = new Dictionary<string, int>();
motifX = new StreamWriter(Path.Combine(outputFolder, "motif-x.txt"));
}
raw = (IXRawfile2) new MSFileReader_XRawfile();
string header_line = null;
string[] headers = null;
bool quant = false;
foreach (string csv_filepath in csvFilepaths)
{
onStartingFile(new FilepathEventArgs(csv_filepath));
csv = new StreamReader(csv_filepath);
using (CsvReader reader = new CsvReader(csv, true))
{
headers = reader.GetFieldHeaders();
header_line = string.Join(",", headers);
quant = headers.Contains("Channels Detected");
string[] lineData = new string[headers.Length];
//header_line = csv.ReadLine();
//quant = header_line.Contains("TQ_");
non_phospho_output.WriteLine(header_line);
localized_phospho_output.WriteLine(header_line +
", Number of Theoretical Fragments, Identified Phosphoisoform, Identified Phosphoisoform Number of Matching Fragments, Best Phosphoisoforms, Best Phosphoisoform, Best Phosphoisoform Number of Matching Fragments, Second-Best Phosphoisoform, Second-Best Phosphoisoform Number of Matching Fragments, Identified Phosphoisoform Correct?, Preliminary Localization of All Phosphorylations?, Peptide Phosphorylation Sites, Probability of Spurious Fragment Match, Number of Theoretical Site-Determining Fragment Ions, Number of Matching Site-Determining Fragment Ions, Matching Site-Determining Fragment Ions, Probability Values, Ambiguity Scores, Phosphorylation Sites Localized?, All Phosphorylation Sites Localized?");
unlocalized_phospho_output.WriteLine(header_line +
", Number of Theoretical Fragments, Identified Phosphoisoform, Identified Phosphoisoform Number of Matching Fragments, Best Phosphoisoforms, Best Phosphoisoform, Best Phosphoisoform Number of Matching Fragments, Second-Best Phosphoisoform, Second-Best Phosphoisoform Number of Matching Fragments, Identified Phosphoisoform Correct?, Preliminary Localization of All Phosphorylations?, Peptide Phosphorylation Sites, Probability of Spurious Fragment Match, Number of Theoretical Site-Determining Fragment Ions, Number of Matching Site-Determining Fragment Ions, Matching Site-Determining Fragment Ions, Probability Values, Ambiguity Scores, Phosphorylation Sites Localized?, All Phosphorylation Sites Localized?");
while (reader.ReadNextRecord())
{
//string line = csv.ReadLine();
//string[] fields = Regex.Split(line,
// @",(?!(?<=(?:^|,)\s*\x22(?:[^\x22]|\x22\x22|\\\x22)*,)(?:[^\x22]|\x22\x22|\\\x22)*\x22\s*(?:,|$))");
// // crazy regex to parse CSV with internal double quotes from http://regexlib.com/REDetails.aspx?regexp_id=621
string sequence = reader["Peptide"];
string dynamic_modifications = reader["Mods"];
if (!dynamic_modifications.Contains("phosphorylation"))
{
//non_phospho_output.WriteLine(line);
}
else
{
Peptide identified_phosphopeptide = new Peptide(sequence, fixedModifications,
dynamic_modifications);
int start_residue = int.Parse(reader["Start"]);
int stop_residue = int.Parse(reader["Stop"]);
string protein_description = reader["Defline"].Trim('"');
StringBuilder sb = new StringBuilder();
reader.CopyCurrentRecordTo(lineData);
foreach (string datum in lineData)
{
if (datum.Contains(','))
sb.Append("\"" + datum + "\"");
else
sb.Append(datum);
sb.Append(',');
}
sb.Remove(sb.Length - 1, 1);
string line = sb.ToString();
if (!identified_sites_by_protein.ContainsKey(protein_description))
{
identified_sites_by_protein.Add(protein_description, new Dictionary<string, int>());
}
foreach (KeyValuePair<int, string> kvp in identified_phosphopeptide.DynamicModifications)
{
if (kvp.Value.Contains("phosphorylation"))
{
string site = sequence[kvp.Key - 1] + (start_residue + kvp.Key).ToString();
if (!identified_sites_by_protein[protein_description].ContainsKey(site))
{
identified_sites_by_protein[protein_description].Add(site, 0);
}
identified_sites_by_protein[protein_description][site]++;
}
}
int scan_number = int.Parse(reader["Spectrum number"]);
string filenameID = reader["Filename/id"];
FragmentType[] fragment_types = null;
if (filenameID.Contains(".ETD.") || filenameID.Contains(".ECD."))
{
fragment_types = new FragmentType[] {FragmentType.c, FragmentType.zdot};
}
else
{
fragment_types = new FragmentType[] {FragmentType.b, FragmentType.y};
}
string raw_filename = filenameID.Substring(0, filenameID.IndexOf('.')) + ".raw";
int charge = int.Parse(reader["Charge"]);
string current_raw_filename = null;
raw.GetFileName(ref current_raw_filename);
if (current_raw_filename == null ||
!raw_filename.Equals(Path.GetFileName(current_raw_filename),
StringComparison.InvariantCultureIgnoreCase))
{
raw.Close();
string[] raw_filepaths = null;
if (!string.IsNullOrEmpty(rawFolder) && Directory.Exists(rawFolder))
{
raw_filepaths = Directory.GetFiles(rawFolder, raw_filename,
SearchOption.AllDirectories);
}
else
{
raw_filepaths = Directory.GetFiles(Path.GetDirectoryName(csv_filepath),
raw_filename, SearchOption.AllDirectories);
}
if (raw_filepaths.Length == 0)
{
throw new FileNotFoundException("No corresponding .raw file found for " +
csv_filepath);
}
if (raw_filepaths.Length > 1)
{
throw new Exception("Multiple corresponding .raw files found for " +
csv_filepath);
}
raw.Open(raw_filepaths[0]);
raw.SetCurrentController(0, 1);
}
string scan_filter = null;
raw.GetFilterForScanNum(scan_number, ref scan_filter);
string low_mz_scan_filter = scan_filter.Substring(scan_filter.IndexOf('[') + 1);
double low_mz =
double.Parse(low_mz_scan_filter.Substring(0, low_mz_scan_filter.IndexOf('-')));
string high_mz_scan_filter = scan_filter.Substring(scan_filter.LastIndexOf('-') + 1);
double high_mz =
double.Parse(high_mz_scan_filter.Substring(0, high_mz_scan_filter.IndexOf(']')));
double[,] spectrum = null;
if (scan_filter.Contains("FTMS"))
{
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scan_number);
spectrum = (double[,]) labels_obj;
}
else
{
double centroid_width = double.NaN;
object spectrum_obj = null;
object flags = null;
int size = -1;
raw.GetMassListFromScanNum(ref scan_number, null, 0, -1, 0, 1, ref centroid_width,
ref spectrum_obj, ref flags, ref size);
spectrum = (double[,]) spectrum_obj;
}
double base_peak_mz = double.NaN;
double base_peak_intensity = double.NaN;
for (int i = spectrum.GetLowerBound(1); i <= spectrum.GetUpperBound(1); i++)
{
if (double.IsNaN(base_peak_mz) ||
spectrum[(int) RawLabelDataColumn.Intensity, i] > base_peak_intensity)
{
base_peak_mz = spectrum[(int) RawLabelDataColumn.MZ, i];
base_peak_intensity = spectrum[(int) RawLabelDataColumn.Intensity, i];
}
}
double intensity_threshold = intensityThreshold;
if (intensityThresholdType == IntensityThresholdType.Relative)
{
intensity_threshold = (intensityThreshold/100.0)*base_peak_intensity;
}
double[] parameters = new double[4];
if (!scan_filter.Contains("FTMS") &&
intensityThresholdType == IntensityThresholdType.SignalToNoiseRatio)
{
List<double> relative_intensities = new List<double>();
for (int i = spectrum.GetLowerBound(1); i <= spectrum.GetUpperBound(1); i++)
{
relative_intensities.Add(spectrum[(int) RawLabelDataColumn.Intensity, i]/
base_peak_intensity);
}
double bin_width = 0.001;
int bins = 101;
double[][] relative_intensity_histogram = new double[2][];
relative_intensity_histogram[0] = new double[bins];
relative_intensity_histogram[1] = new double[bins];
for (int i = relative_intensity_histogram[0].GetLowerBound(0);
i <= relative_intensity_histogram[0].GetUpperBound(0);
i++)
{
relative_intensity_histogram[0][i] = i*bin_width;
}
foreach (double relative_intensity in relative_intensities)
{
int bin_number = (int) Math.Floor(relative_intensity/bin_width);
if (bin_number < bins)
{
relative_intensity_histogram[1][bin_number]++;
}
}
parameters[0] = 0.0;
parameters[1] = 100.0;
parameters[2] = 0.0;
parameters[3] = 0.001;
double[] weights = new double[relative_intensity_histogram[1].Length];
for (int i = weights.GetLowerBound(0); i <= weights.GetUpperBound(0); i++)
{
weights[i] = 1.0;
}
LMA lma = new LMA(new GaussianFunctionWithPartials(), parameters,
relative_intensity_histogram, weights, new DotNetMatrix.GeneralMatrix(4, 4),
0.001, 5000);
lma.Fit();
}
List<Peptide> peptides = GetAlternativePhosphoisoformPeptides(
identified_phosphopeptide, fixedModifications);
List<PhosphopeptideStatistics> all_phosphopeptide_stats =
new List<PhosphopeptideStatistics>(peptides.Count);
PhosphopeptideStatistics identified_phosphoisoform = null;
List<double> ms2_mz_peaks = new List<double>(spectrum.GetLength(1));
for (int i = spectrum.GetLowerBound(1); i <= spectrum.GetUpperBound(1); i++)
{
double signal_to_noise = scan_filter.Contains("FTMS")
? (spectrum[(int) RawLabelDataColumn.Intensity, i] -
spectrum[(int) RawLabelDataColumn.NoiseBaseline, i])/
spectrum[(int) RawLabelDataColumn.NoiseLevel, i]
: ((spectrum[(int) RawLabelDataColumn.Intensity, i]/base_peak_intensity) -
parameters[2])/parameters[3];
if ((intensityThresholdType == IntensityThresholdType.SignalToNoiseRatio
&& signal_to_noise >= intensity_threshold)
|| (intensityThresholdType != IntensityThresholdType.SignalToNoiseRatio
&& spectrum[(int) RawLabelDataColumn.Intensity, i] >= intensity_threshold))
{
ms2_mz_peaks.Add(spectrum[(int) RawLabelDataColumn.MZ, i]);
}
}
double mz_range = high_mz - low_mz;
Dictionary<double, bool> searched_fragment_mzs = new Dictionary<double, bool>();
foreach (Peptide peptide in peptides)
{
PhosphopeptideStatistics phosphopeptide_stats = new PhosphopeptideStatistics(peptide);
if (peptide.Sequence == identified_phosphopeptide.Sequence)
{
identified_phosphoisoform = phosphopeptide_stats;
}
FragmentDictionary fragments = peptide.CalculateFragments(fragment_types);
foreach (KeyValuePair<string, Fragment> kvp in fragments)
{
phosphopeptide_stats.Fragments.Add(kvp.Key, new Dictionary<int, bool>());
for (int fragment_charge = 1;
fragment_charge <= (charge >= 3 ? 2 : 1);
fragment_charge++)
{
if (fragment_charge > 1 &&
fragment_charge >
(double) kvp.Value.Number/peptide.Sequence.Length*charge)
{
break;
}
double mz = MZFromMassAndCharge(kvp.Value.Mass, fragment_charge);
if (mz < low_mz || mz > high_mz)
{
continue;
}
if (!searched_fragment_mzs.ContainsKey(mz))
{
bool found = false;
foreach (double ms2_mz_peak in ms2_mz_peaks)
{
if (Math.Abs(ms2_mz_peak - mz) <= mzTolerance)
{
found = true;
break;
}
else if (ms2_mz_peak > mz + mzTolerance)
{
break;
}
}
searched_fragment_mzs.Add(mz, found);
}
phosphopeptide_stats.Fragments[kvp.Key].Add(fragment_charge,
searched_fragment_mzs[mz]);
}
}
all_phosphopeptide_stats.Add(phosphopeptide_stats);
}
all_phosphopeptide_stats.Sort(ComparePhosphopeptidesByDescendingMatchingFragments);
PhosphopeptideStatistics best_phosphoisoform = all_phosphopeptide_stats[0];
PhosphopeptideStatistics second_best_phosphoisoform = all_phosphopeptide_stats.Count > 1
? all_phosphopeptide_stats[1]
: null;
List<string> best_sequences = new List<string>();
foreach (PhosphopeptideStatistics phosphopeptide_stats in all_phosphopeptide_stats)
{
if (phosphopeptide_stats.NumberOfMatchingFragments ==
best_phosphoisoform.NumberOfMatchingFragments)
{
best_sequences.Add(phosphopeptide_stats.Peptide.Sequence);
}
else
{
break;
}
}
bool preliminary_localization = second_best_phosphoisoform == null
||
best_phosphoisoform.NumberOfMatchingFragments >
second_best_phosphoisoform.NumberOfMatchingFragments;
bool all_sites_localized = preliminary_localization;
Dictionary<string, bool> peptide_sites = new Dictionary<string, bool>();
Dictionary<string, bool> protein_sites = new Dictionary<string, bool>();
string best_sequence = best_phosphoisoform.Peptide.Sequence;
for (int i = 0; i < best_sequence.Length; i++)
{
if (char.IsLower(best_sequence[i]))
{
if (preliminary_localization && second_best_phosphoisoform == null)
{
peptide_sites.Add(best_sequence[i] + (i + 1).ToString(), true);
protein_sites.Add(best_sequence[i] + (start_residue + i).ToString(), true);
if (!localized_sites_by_protein.ContainsKey(protein_description))
{
localized_sites_by_protein.Add(protein_description,
new Dictionary<string, int>());
}
string site = best_sequence[i] + (start_residue + i).ToString();
if (!localized_sites_by_protein[protein_description].ContainsKey(site))
{
localized_sites_by_protein[protein_description].Add(site, 0);
}
localized_sites_by_protein[protein_description][site]++;
if (motifXOutput)
{
ExtractMotifs(motifs, proteins, protein_description, best_sequence,
start_residue, i);
}
}
else
{
peptide_sites.Add(best_sequence[i] + (i + 1).ToString(), false);
protein_sites.Add(best_sequence[i] + (start_residue + i).ToString(), false);
}
}
}
double probability_of_success = double.NaN;
List<string> theoretical_site_determining_fragment_ions = new List<string>();
List<string> matching_site_determining_fragment_ions = new List<string>();
List<string> left_site_determining_fragments = new List<string>();
List<string> right_site_determining_fragments = new List<string>();
List<string> site_determining_fragments = new List<string>();
List<string> p_values = new List<string>();
List<string> a_scores = new List<string>();
List<string> sites_localized = new List<string>();
if (preliminary_localization && second_best_phosphoisoform != null)
{
probability_of_success = (ms2_mz_peaks.Count*2*mzTolerance)/mz_range;
for (int i = 0; i < best_sequence.Length; i++)
{
if (char.IsLower(best_sequence[i]))
{
int first_phosphorylatable_residue = i - 1;
while (first_phosphorylatable_residue >= 0)
{
if (best_sequence[first_phosphorylatable_residue] == 'S'
|| best_sequence[first_phosphorylatable_residue] == 'T'
|| best_sequence[first_phosphorylatable_residue] == 'Y')
{
break;
}
else
{
first_phosphorylatable_residue--;
}
}
int? num_left_theoretical_site_determining_fragment_ions = null;
int? num_left_matching_site_determining_fragment_ions = null;
double left_p_value = double.NaN;
double left_a_score = double.NaN;
if (first_phosphorylatable_residue >= 0)
{
num_left_theoretical_site_determining_fragment_ions = 0;
num_left_matching_site_determining_fragment_ions = 0;
for (int j = first_phosphorylatable_residue + 1; j <= i; j++)
{
string n_terminal_fragment = fragment_types[0].ToString() +
j.ToString();
if (best_phosphoisoform.Fragments.ContainsKey(n_terminal_fragment))
{
foreach (
KeyValuePair<int, bool> kvp in
best_phosphoisoform.Fragments[n_terminal_fragment])
{
num_left_theoretical_site_determining_fragment_ions++;
if (kvp.Value)
{
num_left_matching_site_determining_fragment_ions++;
string n_terminal_fragment_string =
n_terminal_fragment + "(+" + kvp.Key.ToString() +
')';
if (
!left_site_determining_fragments.Contains(
n_terminal_fragment_string))
{
left_site_determining_fragments.Add(
n_terminal_fragment_string);
}
}
}
}
string c_terminal_fragment = fragment_types[1].ToString() +
(best_sequence.Length - j).ToString();
if (best_phosphoisoform.Fragments.ContainsKey(c_terminal_fragment))
{
foreach (
KeyValuePair<int, bool> kvp in
best_phosphoisoform.Fragments[c_terminal_fragment])
{
num_left_theoretical_site_determining_fragment_ions++;
if (kvp.Value)
{
num_left_matching_site_determining_fragment_ions++;
string c_terminal_fragment_string =
c_terminal_fragment + "(+" + kvp.Key.ToString() +
')';
if (
!left_site_determining_fragments.Contains(
c_terminal_fragment_string))
{
left_site_determining_fragments.Add(
c_terminal_fragment_string);
}
}
}
}
}
left_p_value =
alglib.binomialdistr.binomialcdistribution(
num_left_matching_site_determining_fragment_ions.Value - 1,
num_left_theoretical_site_determining_fragment_ions.Value,
probability_of_success);
left_a_score = -10*Math.Log10(left_p_value);
}
int last_phosphorylatable_residue = i + 1;
while (last_phosphorylatable_residue < best_sequence.Length)
{
if (best_sequence[last_phosphorylatable_residue] == 'S'
|| best_sequence[last_phosphorylatable_residue] == 'T'
|| best_sequence[last_phosphorylatable_residue] == 'Y')
{
break;
}
else
{
last_phosphorylatable_residue++;
}
}
int? num_right_theoretical_site_determining_fragment_ions = null;
int? num_right_matching_site_determining_fragment_ions = null;
double right_p_value = double.NaN;
double right_a_score = double.NaN;
if (last_phosphorylatable_residue < best_sequence.Length)
{
num_right_theoretical_site_determining_fragment_ions = 0;
num_right_matching_site_determining_fragment_ions = 0;
for (int j = last_phosphorylatable_residue; j > i; j--)
{
string n_terminal_fragment = fragment_types[0].ToString() +
j.ToString();
if (best_phosphoisoform.Fragments.ContainsKey(n_terminal_fragment))
{
foreach (
KeyValuePair<int, bool> kvp in
best_phosphoisoform.Fragments[n_terminal_fragment])
{
num_right_theoretical_site_determining_fragment_ions++;
if (kvp.Value)
{
num_right_matching_site_determining_fragment_ions++;
string n_terminal_fragment_string =
n_terminal_fragment + "(+" + kvp.Key.ToString() +
')';
if (
!right_site_determining_fragments.Contains(
n_terminal_fragment_string))
{
right_site_determining_fragments.Add(
n_terminal_fragment_string);
}
}
}
}
string c_terminal_fragment = fragment_types[1].ToString() +
(best_sequence.Length - j).ToString();
if (best_phosphoisoform.Fragments.ContainsKey(c_terminal_fragment))
{
foreach (
KeyValuePair<int, bool> kvp in
best_phosphoisoform.Fragments[c_terminal_fragment])
{
num_right_theoretical_site_determining_fragment_ions++;
if (kvp.Value)
{
num_right_matching_site_determining_fragment_ions++;
string c_terminal_fragment_string =
c_terminal_fragment + "(+" + kvp.Key.ToString() +
')';
if (
!right_site_determining_fragments.Contains(
c_terminal_fragment_string))
{
right_site_determining_fragments.Add(
c_terminal_fragment_string);
}
}
}
}
}
right_p_value =
alglib.binomialdistr.binomialcdistribution(
num_right_matching_site_determining_fragment_ions.Value - 1,
num_right_theoretical_site_determining_fragment_ions.Value,
probability_of_success);
right_a_score = -10*Math.Log10(right_p_value);
}
theoretical_site_determining_fragment_ions.Add(
(num_left_theoretical_site_determining_fragment_ions.HasValue
? num_left_theoretical_site_determining_fragment_ions.ToString()
: "n/a") + " | " +
(num_right_theoretical_site_determining_fragment_ions.HasValue
? num_right_theoretical_site_determining_fragment_ions.ToString()
: "n/a"));
matching_site_determining_fragment_ions.Add(
(num_left_matching_site_determining_fragment_ions.HasValue
? num_left_matching_site_determining_fragment_ions.ToString()
: "n/a") + " | " +
(num_right_matching_site_determining_fragment_ions.HasValue
? num_right_matching_site_determining_fragment_ions.ToString()
: "n/a"));
site_determining_fragments.Add((left_site_determining_fragments.Count > 0
? string.Join(",", left_site_determining_fragments.ToArray())
: "n/a") + " | " +
(right_site_determining_fragments.Count > 0
? string.Join(",",
right_site_determining_fragments
.ToArray())
: "n/a"));
p_values.Add((double.IsNaN(left_p_value) ? "n/a" : left_p_value.ToString()) +
" | " +
(double.IsNaN(right_p_value) ? "n/a" : right_p_value.ToString()));
a_scores.Add((double.IsNaN(left_a_score) ? "n/a" : left_a_score.ToString()) +
" | " +
(double.IsNaN(right_a_score) ? "n/a" : right_a_score.ToString()));
bool site_localized = (double.IsNaN(left_a_score) ||
left_a_score >= ambiguityScoreThreshold) &&
(double.IsNaN(right_a_score) ||
right_a_score >= ambiguityScoreThreshold);
sites_localized.Add(site_localized.ToString().ToUpper());
if (site_localized)
{
peptide_sites[best_sequence[i] + (i + 1).ToString()] = true;
protein_sites[best_sequence[i] + (start_residue + i).ToString()] = true;
if (!localized_sites_by_protein.ContainsKey(protein_description))
{
localized_sites_by_protein.Add(protein_description,
new Dictionary<string, int>());
}
string site = best_sequence[i] + (start_residue + i).ToString();
if (!localized_sites_by_protein[protein_description].ContainsKey(site))
{
localized_sites_by_protein[protein_description].Add(site, 0);
}
localized_sites_by_protein[protein_description][site]++;
if (motifXOutput)
{
ExtractMotifs(motifs, proteins, protein_description, best_sequence,
start_residue, i);
}
}
if (!site_localized)
{
all_sites_localized = false;
}
}
}
}
int phosphorylations = 0;
foreach (
string dynamic_modification in
best_phosphoisoform.Peptide.DynamicModifications.Values)
{
if (dynamic_modification.Contains("phosphorylation"))
{
phosphorylations++;
}
}
string isoform = null;
if (all_sites_localized)
{
foreach (KeyValuePair<string, bool> kvp in protein_sites)
{
isoform += kvp.Key + ',';
}
isoform = isoform.Substring(0, isoform.Length - 1);
KeyValuePair<int, string> isoform_kvp =
new KeyValuePair<int, string>(phosphorylations, isoform);
if (!localized.ContainsKey(protein_description))
{
localized.Add(protein_description,
new Dictionary<KeyValuePair<int, string>, List<string>>());
}
if (!localized[protein_description].ContainsKey(isoform_kvp))
{
localized[protein_description].Add(isoform_kvp, new List<string>());
}
localized[protein_description][isoform_kvp].Add(line);
}
else
{
if (preliminary_localization)
{
foreach (KeyValuePair<string, bool> kvp in protein_sites)
{
isoform += kvp.Key;
if (!kvp.Value)
{
isoform += '?';
}
isoform += ',';
}
}
else
{
for (int i = 0; i < best_sequence.Length; i++)
{
bool phospho = false;
for (int j = 0; j < all_phosphopeptide_stats.Count; j++)
{
if (all_phosphopeptide_stats[j].NumberOfMatchingFragments <
best_phosphoisoform.NumberOfMatchingFragments)
{
break;
}
if (char.IsLower(all_phosphopeptide_stats[j].Peptide.Sequence[i]))
{
phospho = true;
}
}
if (phospho)
{
isoform += char.ToLower(best_sequence[i]) +
(start_residue + i).ToString() + "?,";
}
}
}
isoform = isoform.Substring(0, isoform.Length - 1);
KeyValuePair<int, string> isoform_kvp =
new KeyValuePair<int, string>(phosphorylations, isoform);
if (!unlocalized.ContainsKey(protein_description))
{
unlocalized.Add(protein_description,
new Dictionary<KeyValuePair<int, string>, List<string>>());
}
if (!unlocalized[protein_description].ContainsKey(isoform_kvp))
{
unlocalized[protein_description].Add(isoform_kvp, new List<string>());
}
unlocalized[protein_description][isoform_kvp].Add(line);
}
StreamWriter output = all_sites_localized
? localized_phospho_output
: unlocalized_phospho_output;
output.Write(line + ',');
output.Write(identified_phosphoisoform.NumberOfTotalFragments.ToString() + ',');
output.Write(identified_phosphoisoform.Peptide.Sequence + ',');
output.Write(identified_phosphoisoform.NumberOfMatchingFragments.ToString() + ',');
for (int s = 0; s < best_sequences.Count; s++)
{
output.Write(best_sequences[s]);
if (s < best_sequences.Count - 1)
{
output.Write('/');
}
}
output.Write(',');
output.Write(best_phosphoisoform.Peptide.Sequence + ',');
output.Write(best_phosphoisoform.NumberOfMatchingFragments.ToString() + ',');
if (second_best_phosphoisoform != null)
{
output.Write(second_best_phosphoisoform.Peptide.Sequence + ',');
output.Write(second_best_phosphoisoform.NumberOfMatchingFragments.ToString() + ',');
}
else
{
output.Write("n/a,n/a,");
}
output.Write(
(identified_phosphoisoform.NumberOfMatchingFragments ==
best_phosphoisoform.NumberOfMatchingFragments).ToString() + ',');
output.Write(preliminary_localization.ToString() + ',');
string[] peptide_sites_array = new string[peptide_sites.Count];
peptide_sites.Keys.CopyTo(peptide_sites_array, 0);
string peptide_sites_array_string = string.Join("; ", peptide_sites_array);
AppendFieldToCsv(peptide_sites_array_string, output);
output.Write((!double.IsNaN(probability_of_success)
? probability_of_success.ToString()
: string.Empty) + ',');
string theoretical_site_determining_fragment_ions_string = string.Join("; ",
theoretical_site_determining_fragment_ions.ToArray());
AppendFieldToCsv(theoretical_site_determining_fragment_ions_string, output);
string matching_site_determining_fragment_ions_string = string.Join("; ",
matching_site_determining_fragment_ions.ToArray());
AppendFieldToCsv(matching_site_determining_fragment_ions_string, output);
string site_determining_fragments_string = string.Join("; ",
site_determining_fragments.ToArray());
AppendFieldToCsv(site_determining_fragments_string, output);
string p_values_string = string.Join("; ", p_values.ToArray());
AppendFieldToCsv(p_values_string, output);
string a_scores_string = string.Join("; ", a_scores.ToArray());
AppendFieldToCsv(a_scores_string, output);
string sites_localized_string = string.Join("; ", sites_localized.ToArray());
AppendFieldToCsv(sites_localized_string, output);
output.Write(all_sites_localized.ToString().ToUpper());
output.WriteLine();
}
double progress = (double) csv.BaseStream.Position/csv.BaseStream.Length;
onUpdateProgress(new ProgressEventArgs((int) Math.Round(progress*100.0)));
}
}
csv.Close();
onFinishedFile(new EventArgs());
}
raw.Close();
non_phospho_output.Close();
localized_phospho_output.Close();
unlocalized_phospho_output.Close();
log.WriteLine("Identified Phosphoproteins: " + identified_sites_by_protein.Proteins.ToString());
log.WriteLine("Identified Phosphosites: " + identified_sites_by_protein.Sites.ToString());
log.WriteLine();
log.WriteLine("Localized Phosphoproteins: " + localized_sites_by_protein.Proteins.ToString());
log.WriteLine("Localized Phosphosites: " + localized_sites_by_protein.Sites.ToString());
log.WriteLine();
int localized_phosphoisoforms = 0;
foreach (KeyValuePair<string, Dictionary<KeyValuePair<int, string>, List<string>>> kvp in localized)
{
foreach (KeyValuePair<KeyValuePair<int, string>, List<string>> kvp2 in kvp.Value)
{
localized_phosphoisoforms++;
}
}
int unlocalized_phosphoisoforms = 0;
foreach (KeyValuePair<string, Dictionary<KeyValuePair<int, string>, List<string>>> kvp in unlocalized)
{
foreach (KeyValuePair<KeyValuePair<int, string>, List<string>> kvp2 in kvp.Value)
{
unlocalized_phosphoisoforms++;
}
}
log.WriteLine("Localized Phosphoisoforms: " + localized_phosphoisoforms.ToString());
log.WriteLine("Unlocalized Phosphoisoforms: " + unlocalized_phosphoisoforms.ToString());
log.Close();
using (StreamWriter protein_sites = new StreamWriter(Path.Combine(outputFolder, "localized_protein_phosphosites.csv")))
{
protein_sites.WriteLine("Protein Description, Number of Localized Phosphosites");
protein_sites.WriteLine(", Localized Phosphosite");
foreach (KeyValuePair<string, Dictionary<string, int>> kvp in localized_sites_by_protein)
{
protein_sites.WriteLine((kvp.Key.Contains(",") ? '"' + kvp.Key + '"' : kvp.Key) + ',' + kvp.Value.Count.ToString());
foreach (KeyValuePair<string, int> kvp2 in kvp.Value)
{
protein_sites.WriteLine(',' + kvp2.Key);
}
}
}
using (StreamWriter full_localized_output = new StreamWriter(Path.Combine(outputFolder, "full_localized_phosphoisoforms.csv")))
{
//int interference_index = -1;
int first_quant_index = -1;
int last_quant_index = -1;
if (!quant)
{
full_localized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites, PSMs Identified, Peptides Identified");
}
else
{
full_localized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites, PSMs Identified, PSMs Quantified, Peptides Identified, Peptides Quantified,");
for (int i = 0; i < headers.Length; i++)
{
if (headers[i].EndsWith("NL)"))
{
if (first_quant_index < 0)
{
first_quant_index = i;
}
}
if (first_quant_index >= 0)
full_localized_output.Write(' ' + headers[i] + ',');
if (headers[i].Equals("Channels Detected"))
{
last_quant_index = i;
}
}
full_localized_output.Write(" Phosphoisoform Quantified?");
}
full_localized_output.WriteLine();
full_localized_output.WriteLine(", " + header_line);
using (StreamWriter reduced_localized_output = new StreamWriter(Path.Combine(outputFolder, "reduced_localized_phosphoisoforms.csv")))
{
if (!quant)
{
reduced_localized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites,Peptides , PSMs Identified, Peptides Identified");
}
else
{
reduced_localized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites,Peptides , PSMs Identified, PSMs Quantified, Peptides Identified, Peptides Quantified,");
for (int i = first_quant_index; i <= last_quant_index; i++)
{
reduced_localized_output.Write(' ' + headers[i] + ',');
}
reduced_localized_output.Write(" Phosphoisoform Quantified?");
}
reduced_localized_output.WriteLine();
foreach (KeyValuePair<string, Dictionary<KeyValuePair<int, string>, List<string>>> kvp in localized)
{
foreach (KeyValuePair<KeyValuePair<int, string>, List<string>> kvp2 in kvp.Value)
{
full_localized_output.Write((kvp.Key.Contains(",") ? '"' + kvp.Key + '"' : kvp.Key) + ',');
reduced_localized_output.Write((kvp.Key.Contains(",") ? '"' + kvp.Key + '"' : kvp.Key) + ',');
full_localized_output.Write((kvp2.Key.Value.Contains(",") ? '"' + kvp2.Key.Value + '"' : kvp2.Key.Value) + ',');
reduced_localized_output.Write((kvp2.Key.Value.Contains(",") ? '"' + kvp2.Key.Value + '"' : kvp2.Key.Value) + ',');
full_localized_output.Write(kvp2.Key.Key.ToString() + ',');
reduced_localized_output.Write(kvp2.Key.Key.ToString() + ',');
double[] isoform_quantitation = new double[last_quant_index - first_quant_index + 1];
isoform_quantitation = Array.ConvertAll<double, double>(isoform_quantitation, SET_DOUBLE_VALUE_TO_NAN);
int spectra_identified = 0;
int spectra_quantified = 0;
Dictionary<string, int> unique_peptides_identified = new Dictionary<string, int>();
Dictionary<string, int> unique_peptides_quantified = new Dictionary<string, int>();
StringBuilder peptides = new StringBuilder();
foreach (string line in kvp2.Value)
{
string[] fields = Regex.Split(line, @",(?!(?<=(?:^|,)\s*\x22(?:[^\x22]|\x22\x22|\\\x22)*,)(?:[^\x22]|\x22\x22|\\\x22)*\x22\s*(?:,|$))"); // crazy regex to parse CSV with internal double quotes from http://regexlib.com/REDetails.aspx?regexp_id=621
spectra_identified++;
string peptide_sequence = fields[2];
peptides.Append(peptide_sequence + " ");
if (!unique_peptides_identified.ContainsKey(peptide_sequence))
{
unique_peptides_identified.Add(peptide_sequence, 0);
}
unique_peptides_identified[peptide_sequence]++;
if (quant)
{
spectra_quantified++;
if (double.IsNaN(isoform_quantitation[0]))
{
isoform_quantitation = Array.ConvertAll<double, double>(isoform_quantitation, SET_DOUBLE_VALUE_TO_ZERO);
}
if (!unique_peptides_quantified.ContainsKey(peptide_sequence))
{
unique_peptides_quantified.Add(peptide_sequence, 0);
}
unique_peptides_quantified[peptide_sequence]++;
for (int i = first_quant_index; i <= last_quant_index; i++)
{
double val = 0;
double.TryParse(fields[i], out val);
isoform_quantitation[i - first_quant_index] += val;
}
}
}
full_localized_output.Write(peptides.ToString() + ',');
reduced_localized_output.Write(peptides.ToString() + ',');
full_localized_output.Write(spectra_identified.ToString() + ',');
reduced_localized_output.Write(spectra_identified.ToString() + ',');
if (quant)
{
full_localized_output.Write(spectra_quantified.ToString() + ',');
reduced_localized_output.Write(spectra_quantified.ToString() + ',');
}
full_localized_output.Write(unique_peptides_identified.Count.ToString() + ',');
reduced_localized_output.Write(unique_peptides_identified.Count.ToString() + ',');
if (quant)
{
full_localized_output.Write(unique_peptides_quantified.Count.ToString() + ',');
reduced_localized_output.Write(unique_peptides_quantified.Count.ToString() + ',');
for (int i = isoform_quantitation.GetLowerBound(0); i <= isoform_quantitation.GetUpperBound(0); i++)
{
full_localized_output.Write(isoform_quantitation[i].ToString() + ',');
reduced_localized_output.Write(isoform_quantitation[i].ToString() + ',');
}
full_localized_output.Write((spectra_quantified > 0).ToString());
reduced_localized_output.Write((spectra_quantified > 0).ToString());
}
full_localized_output.WriteLine();
reduced_localized_output.WriteLine();
foreach (string line in kvp2.Value)
{
full_localized_output.WriteLine(',' + line);
}
}
}
}
}
using (StreamWriter full_unlocalized_output = new StreamWriter(Path.Combine(outputFolder, "full_unlocalized_phosphoisoforms.csv")))
{
int first_quant_index = -1;
int last_quant_index = -1;
if (!quant)
{
full_unlocalized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites,Peptides, PSMs Identified, Peptides Identified");
}
else
{
full_unlocalized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites,Peptides, PSMs Identified, PSMs Quantified, Peptides Identified, Peptides Quantified,");
for (int i = 0; i < headers.Length; i++)
{
if (headers[i].EndsWith("NL)"))
{
if (first_quant_index < 0)
{
first_quant_index = i;
}
}
if (first_quant_index >= 0)
full_unlocalized_output.Write(' ' + headers[i] + ',');
if (headers[i].Equals("Channels Detected"))
{
last_quant_index = i;
}
}
full_unlocalized_output.Write(" Phosphoisoform Quantified?");
}
full_unlocalized_output.WriteLine();
full_unlocalized_output.WriteLine(", " + header_line);
using (StreamWriter reduced_unlocalized_output = new StreamWriter(Path.Combine(outputFolder, "reduced_unlocalized_phosphoisoforms.csv")))
{
if (!quant)
{
reduced_unlocalized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites,Peptides, PSMs Identified, Peptides Identified");
}
else
{
reduced_unlocalized_output.Write("Protein Description, Phosphoisoform, Phosphoisoform Sites,Peptides, PSMs Identified, PSMs Quantified, Peptides Identified, Peptides Quantified,");
for (int i = first_quant_index; i <= last_quant_index; i++)
{
reduced_unlocalized_output.Write(' ' + headers[i] + ',');
}
reduced_unlocalized_output.Write(" Phosphoisoform Quantified?");
}
reduced_unlocalized_output.WriteLine();
foreach (KeyValuePair<string, Dictionary<KeyValuePair<int, string>, List<string>>> kvp in unlocalized)
{
foreach (KeyValuePair<KeyValuePair<int, string>, List<string>> kvp2 in kvp.Value)
{
full_unlocalized_output.Write((kvp.Key.Contains(",") ? '"' + kvp.Key + '"' : kvp.Key) + ',');
reduced_unlocalized_output.Write((kvp.Key.Contains(",") ? '"' + kvp.Key + '"' : kvp.Key) + ',');
full_unlocalized_output.Write((kvp2.Key.Value.Contains(",") ? '"' + kvp2.Key.Value + '"' : kvp2.Key.Value) + ',');
reduced_unlocalized_output.Write((kvp2.Key.Value.Contains(",") ? '"' + kvp2.Key.Value + '"' : kvp2.Key.Value) + ',');
full_unlocalized_output.Write(kvp2.Key.Key.ToString() + ',');
reduced_unlocalized_output.Write(kvp2.Key.Key.ToString() + ',');
double[] isoform_quantitation = new double[last_quant_index - first_quant_index + 1];
isoform_quantitation = Array.ConvertAll<double, double>(isoform_quantitation, SET_DOUBLE_VALUE_TO_NAN);
int spectra_identified = 0;
int spectra_quantified = 0;
Dictionary<string, int> unique_peptides_identified = new Dictionary<string, int>();
Dictionary<string, int> unique_peptides_quantified = new Dictionary<string, int>();
StringBuilder peptides = new StringBuilder();
foreach (string line in kvp2.Value)
{
string[] fields = Regex.Split(line, @",(?!(?<=(?:^|,)\s*\x22(?:[^\x22]|\x22\x22|\\\x22)*,)(?:[^\x22]|\x22\x22|\\\x22)*\x22\s*(?:,|$))"); // crazy regex to parse CSV with internal double quotes from http://regexlib.com/REDetails.aspx?regexp_id=621
spectra_identified++;
string peptide_sequence = fields[2];
peptides.Append(peptide_sequence + " ");
if (!unique_peptides_identified.ContainsKey(peptide_sequence))
{
unique_peptides_identified.Add(peptide_sequence, 0);
}
unique_peptides_identified[peptide_sequence]++;
if (quant)
{
spectra_quantified++;
if (double.IsNaN(isoform_quantitation[0]))
{
isoform_quantitation = Array.ConvertAll<double, double>(isoform_quantitation, SET_DOUBLE_VALUE_TO_ZERO);
}
if (!unique_peptides_quantified.ContainsKey(peptide_sequence))
{
unique_peptides_quantified.Add(peptide_sequence, 0);
}
unique_peptides_quantified[peptide_sequence]++;
for (int i = first_quant_index; i <= last_quant_index; i++)
{
double val = 0;
double.TryParse(fields[i], out val);
isoform_quantitation[i - first_quant_index] += val;
}
}
}
full_unlocalized_output.Write(peptides.ToString() + ',');
reduced_unlocalized_output.Write(peptides.ToString() + ',');
full_unlocalized_output.Write(spectra_identified.ToString() + ',');
reduced_unlocalized_output.Write(spectra_identified.ToString() + ',');
if (quant)
{
full_unlocalized_output.Write(spectra_quantified.ToString() + ',');
reduced_unlocalized_output.Write(spectra_quantified.ToString() + ',');
}
full_unlocalized_output.Write(unique_peptides_identified.Count.ToString() + ',');
reduced_unlocalized_output.Write(unique_peptides_identified.Count.ToString() + ',');
if (quant)
{
full_unlocalized_output.Write(unique_peptides_quantified.Count.ToString() + ',');
reduced_unlocalized_output.Write(unique_peptides_quantified.Count.ToString() + ',');
for (int i = isoform_quantitation.GetLowerBound(0); i <= isoform_quantitation.GetUpperBound(0); i++)
{
full_unlocalized_output.Write(isoform_quantitation[i].ToString() + ',');
reduced_unlocalized_output.Write(isoform_quantitation[i].ToString() + ',');
}
full_unlocalized_output.Write((spectra_quantified > 0).ToString());
reduced_unlocalized_output.Write((spectra_quantified > 0).ToString());
}
full_unlocalized_output.WriteLine();
reduced_unlocalized_output.WriteLine();
foreach (string line in kvp2.Value)
{
full_unlocalized_output.WriteLine(',' + line);
}
}
}
}
}
if (motifXOutput)
{
foreach (string motif in motifs.Keys)
{
motifX.WriteLine(motif);
}
motifX.Close();
using (StreamWriter motif_fasta = new StreamWriter(Path.Combine(outputFolder, "motif-x.fasta")))
{
foreach (KeyValuePair<string, string> kvp in proteins)
{
if (!kvp.Key.Contains("DECOY") && !kvp.Key.Contains("REVERSED"))
{
motif_fasta.WriteLine('>' + kvp.Key);
motif_fasta.WriteLine(kvp.Value);
}
}
}
}
onFinished(new EventArgs());
//}
//catch(Exception ex)
//{
// onThrowException(new ExceptionEventArgs(ex));
//}
//finally
//{
if (log != null)
{
log.Close();
}
if (raw != null)
{
raw.Close();
}
if (csv != null)
{
csv.Close();
}
if (non_phospho_output != null)
{
non_phospho_output.Close();
}
if (localized_phospho_output != null)
{
localized_phospho_output.Close();
}
if (unlocalized_phospho_output != null)
{
unlocalized_phospho_output.Close();
}
if (motifX != null)
{
motifX.Close();
}
}
catch (Exception e)
{
MessageBox.Show(e.Message + " " + e.StackTrace);
}
}
public Fragment(FragmentType type, string value)
{
Type = type;
Value = value;
}
private MessageFragment(String text, OpponentData opponent, FragmentType type)
{
this.text = text;
this.opponent = opponent;
this.type = type;
}