Added documentation

Added suitable documentation to Substructure.jl
Will add more to jetreco-substructure.jl

src/Substructure.jl

@@ -1,17 +1,39 @@
-# function to see if  a jet has parent jets
-function has_parents(jet, history)
+"""
+    has_parents(p, history) -> (boolean, Int64, Int64)
+
+Checks if the jet `p` is a child of two other jets, after clustering 
+
+# Arguments
+- `p`: The jet to check.
+- `history`: The vector of history element obtained from the cluster sequence after clustering.
+
+# Returns
+- (boolean, Int64, Int64): true or false depending on if the jet has a parent or not. If the jet has a parent, returns the indices of the parent jets in the history element. Otherwise, returns -2 (NonexistentParent).
+"""
+function has_parents(p::PseudoJet, history::Vector{HistoryElement})
 
-    N = jet._cluster_hist_index
+    N = p._cluster_hist_index
     p1 = history[N].parent1
     p2 = history[N].parent2
 
     p1 == p2 == NonexistentParent ? result = false : result = true
-    return result, p1, p2
+    return (result, p1, p2)
 
 end
 
-# Function to calculate ΔR
-function delta_R(jet1, jet2)
+"""
+    delta_R(jet1, jet2) -> Float64
+
+Function to calculate the distance in the y-ϕ plane between two jets `jet1` and `jet2`
+
+# Arguments
+- `jet1`: The first jet.
+- `jet2`: The second jet.
+
+# Returns
+- Float64: The Euclidean distance in the y-ϕ plane for the two jets.
+"""
+function delta_R(jet1::PseudoJet, jet2::PseudoJet)
 
     eta1, phi1 = rapidity(jet1), phi(jet1)
     eta2, phi2 = rapidity(jet2), phi(jet2)
@@ -33,7 +55,20 @@ function kt_distance(jet1::PseudoJet, jet2::PseudoJet, R = 1)
     return min(p1, p2) * (d_R^2 / R^2)
 end;
 
-# Function to recluster the constituents of a jet in a different method
+"""
+    recluster(jet, clusterseq, rad, mtd) -> ClusterSequence
+
+Reclusters the constituents of a given jet `jet` with a different clustering method `mtd` and different jet radius `rad`.
+
+# Arguments
+- `jet`: The jet whose constituents are to be reclustered.
+- `clusterseq`: The cluster sequence from which the original jet is obtained.
+- `rad`: The new jet radius.
+- `mtd`: The new clustering method.
+
+# Returns
+- ClusterSequence: The new cluster sequence.
+"""
 function recluster(jet::PseudoJet, clusterseq::ClusterSequence, rad = 1.0, mtd = 0)
     cons = constituents(jet, clusterseq)
     new_clusterseq = jet_reconstruct(cons; p = mtd, R = rad, strategy = RecoStrategy.N2Plain)
@@ -58,28 +93,83 @@ function join(jets::Vector{PseudoJet})
 end
 
 # Defining suitable structures to be used for jet grooming and tagging
+"""
+    struct MassDropTagger
 
-struct MassDropTagger
+Used for tagging jets that undergo mass drop, a common technique in jet substructure.
+
+Fields:
+- mu: Maximum allowed mass ratio for a jet to pass tagging
+- y: Minimum kT distance threshold for parent separation
+"""
+
+mutable struct MassDropTagger
     mu::Float64
     y::Float64
 end
 
-struct SoftDropTagger
+"""
+    struct SoftDropTagger
+
+Applies a soft-drop condition on jets, trimming away soft, wide-angle radiation.
+
+Fields:
+- zcut: Minimum allowed energy fraction for subjets
+- b: Angular exponent controlling soft radiation suppression
+"""
+
+mutable struct SoftDropTagger
     zcut::Float64
     b::Float64
 end
 
-struct Filter
+"""
+    struct Filter
+
+Filters jets based on radius and number of hardest subjets, reducing contamination.
+
+Fields:
+- filterRadius: Radius parameter to recluster subjets
+- numHardestJets: Number of hardest jets to retain in the filtered result
+"""
+
+mutable struct Filter
     filterRadius::Float64 
     numHardestJets::Int
 end
 
-struct Trim
+"""
+    struct Trim
+
+Trims soft, large-angle components from jets based on fraction and radius.
+
+Fields:
+- trimRadius: Radius used for reclustering in trimming
+- trimFraction: Minimum momentum fraction for retained subjets
+- reclusterMethod: Method identifier for reclustering
+"""
+
+mutable struct Trim
     trimRadius::Float64
     trimFraction::Float64
     reclusterMethod::Int
 end
 
+"""
+    massDrop(jet, clusterseq, tag) -> PseudoJet
+
+Identifies subjets in a jet that pass the mass drop tagging condition.
+The method stops at the first jet satisfying the mass and distance thresholds.
+
+Arguments:
+- jet: PseudoJet instance representing the jet to tag
+- clusterseq: ClusterSequence with jet clustering history
+- tag: MassDropTagger instance providing mass drop parameters
+
+Returns:
+- PseudoJet: The jet (or subjet) satisfying the mass drop conditions, if tagging is successful, otherwise a zero-momentum PseudoJet
+"""
+
 function massDrop(jet::PseudoJet, clusterseq::ClusterSequence, tag::MassDropTagger)
     allJets = clusterseq.jets
     hist = clusterseq.history
@@ -110,6 +200,22 @@ function massDrop(jet::PseudoJet, clusterseq::ClusterSequence, tag::MassDropTagg
 
 end
 
+"""
+    softDrop(jet, clusterseq, rad, tag) -> PseudoJet
+
+Applies soft-drop grooming to remove soft, wide-angle radiation from jets.
+This function reclusters the jet and iteratively checks the soft-drop condition on subjets.
+
+Arguments:
+- jet: PseudoJet instance to groom
+- clusterseq: ClusterSequence containing jet history
+- rad: Radius parameter for reclustering
+- tag: SoftDropTagger instance with soft-drop parameters
+
+Returns:
+- PseudoJet: Groomed jet or zero-momentum PseudoJet if grooming fails
+"""
+
 function softDrop(jet::PseudoJet, clusterseq::ClusterSequence, rad::Float64, tag::SoftDropTagger)
     new_clusterseq = recluster(jet, clusterseq, rad, 0)
     new_jet = inclusive_jets(new_clusterseq; T = PseudoJet)[1]
@@ -146,6 +252,20 @@ function softDrop(jet::PseudoJet, clusterseq::ClusterSequence, rad::Float64, tag
 
 end
 
+"""
+    jetFilter(jet, clusterseq, filter) -> PseudoJet
+
+Filters a jet to retain only the hardest subjets based on a specified radius and number.
+
+Arguments:
+- jet: PseudoJet instance representing the jet to filter
+- clusterseq: ClusterSequence containing jet history
+- filter: Filter instance specifying radius and number of subjets
+
+Returns:
+- PseudoJet: Filtered jet composed of the hardest subjets
+
+"""
 function jetFilter(jet::PseudoJet, clusterseq::ClusterSequence, filter::Filter)
     rad = filter.filterRadius;
     new_clusterseq = recluster(jet, clusterseq, rad, 0)
@@ -159,6 +279,20 @@ function jetFilter(jet::PseudoJet, clusterseq::ClusterSequence, filter::Filter)
     filtered    
 end
 
+"""
+    jetTrim(jet, clusterseq, trim) -> PseudoJet
+
+Trims a jet by removing subjets with transverse momentum below a specified fraction.
+
+Arguments:
+- jet: PseudoJet instance representing the jet to trim
+- clusterseq: ClusterSequence containing jet history
+- trim: Trim instance specifying trimming parameters
+
+Returns:
+- PseudoJet: Trimmed jet composed of retained subjets
+"""
+
 function jetTrim(jet::PseudoJet, clusterseq::ClusterSequence, trim::Trim)
     rad = trim.trimRadius;
     mtd = trim.reclusterMethod