Generate hash seed with a delimiter

GeUtilities/Intervals/Functions/HashFunctions.cs

@@ -9,6 +9,12 @@ public static class HashFunctions
         private const uint _FNVPrime_32 = 16777619;
         private const uint _FNVOffsetBasis_32 = 2166136261;
 
+        /// <summary>
+        /// Sets and gets a string used as a delimiter separating 
+        /// properties used as hash seed.
+        /// </summary>
+        public const string HashSeedDelimiter = ";;";
+
         public static uint FNVHashFunction(string bytes)
         {
             uint hash = _FNVOffsetBasis_32;
@@ -20,5 +26,10 @@ public static uint FNVHashFunction(string bytes)
 
             return hash;
         }
+
+        public static string GetHashSeed(params string[] properties)
+        {
+            return string.Join(HashSeedDelimiter, properties);
+        }
     }
 }

GeUtilities/Intervals/Genome/Chromosome.cs

@@ -20,12 +20,20 @@ public Chromosome()
             Strands = new Dictionary<char, Strand<I>>();
         }
 
-        public void Add(I interval, char strand)
+        public bool TryAdd(I interval, char strand)
         {
             if (!Strands.ContainsKey(strand))
                 Strands.Add(strand, new Strand<I>());
+
             if (Strands[strand].TryAdd(interval))
+            {
                 Statistics.Update(interval);
+                return true;
+            }
+            else
+            {
+                return false;
+            }
         }
     }
 }

GeUtilities/Intervals/Model/GeneralFeature.cs

@@ -3,14 +3,15 @@
 // See the LICENSE file in the project root for more information.
 
 using Genometric.GeUtilities.IGenomics;
+using Genometric.GeUtilities.Intervals.Functions;
 
 namespace Genometric.GeUtilities.Intervals.Model
 {
     public class GeneralFeature : Interval, IGeneralFeature
     {
         public GeneralFeature(int left, int right, string source, string feature, double score,
             string frame, string attribute, string hashSeed = "") :
-            base(left, right, source + feature + score.ToString() + frame + attribute + hashSeed)
+            base(left, right, HashFunctions.GetHashSeed(source, feature, score.ToString(), frame, attribute, hashSeed))
         {
             Source = source;
             Feature = feature;

GeUtilities/Intervals/Model/Interval.cs

@@ -16,7 +16,7 @@ public Interval(int left, int right, string hashSeed = "")
 
             unchecked
             {
-                _hashKey = (int)HashFunctions.FNVHashFunction(left.ToString() + right.ToString() + hashSeed);
+                _hashKey = (int)HashFunctions.FNVHashFunction(HashFunctions.GetHashSeed(left.ToString(), right.ToString(), hashSeed));
             }
         }
 

GeUtilities/Intervals/Model/Peak.cs

@@ -3,13 +3,14 @@
 // See the LICENSE file in the project root for more information.
 
 using Genometric.GeUtilities.IGenomics;
+using Genometric.GeUtilities.Intervals.Functions;
 
 namespace Genometric.GeUtilities.Intervals.Model
 {
     public class Peak : Interval, IPeak
     {
         public Peak(int left, int right, double value, string name = null, int summit = -1, string hashSeed = "") :
-            base(left, right, value.ToString() + summit.ToString() + name + hashSeed)
+            base(left, right, HashFunctions.GetHashSeed(value.ToString(), summit.ToString(), name, hashSeed))
         {
             Value = value;
             Summit = summit != -1 ? summit : (right - left) / 2;

GeUtilities/Intervals/Model/RefSeqGene.cs

@@ -3,13 +3,14 @@
 // See the LICENSE file in the project root for more information.
 
 using Genometric.GeUtilities.IGenomics;
+using Genometric.GeUtilities.Intervals.Functions;
 
 namespace Genometric.GeUtilities.Intervals.Model
 {
     public class RefSeqGene : Interval, IRefSeqGene
     {
         public RefSeqGene(int left, int right, string refSeqID, string geneSymbol, string hashSeed = "") :
-            base(left, right, refSeqID + geneSymbol + hashSeed)
+            base(left, right, HashFunctions.GetHashSeed(refSeqID, geneSymbol, hashSeed))
         {
             RefSeqID = refSeqID;
             GeneSymbol = geneSymbol;

GeUtilities/Intervals/Model/Variant.cs

@@ -3,15 +3,16 @@
 // See the LICENSE file in the project root for more information.
 
 using Genometric.GeUtilities.IGenomics;
+using Genometric.GeUtilities.Intervals.Functions;
 
 namespace Genometric.GeUtilities.Intervals.Model
 {
     public class Variant : Interval, IVariant
     {
         public Variant(int left, int right, string id, Base[] refBase, Base[] altBase, double quality,
             string filter, string info, string hashSeed = "") :
-            base(left, right, id + (refBase == null ? "" : refBase.ToString())
-                + (altBase == null ? "" : altBase.ToString()) + quality.ToString() + filter + info + hashSeed)
+            base(left, right, HashFunctions.GetHashSeed(id, (refBase == null ? "" : refBase.ToString()),
+                (altBase == null ? "" : altBase.ToString()), quality.ToString(), filter, info, hashSeed))
         {
             ID = id;
             RefBase = refBase;

GeUtilities/Intervals/Parsers/Model/ParsedIntervals.cs

@@ -29,12 +29,19 @@ protected ParsedIntervals()
             Statistics = new S();
         }
 
-        public void Add(I interval, string chr, char strand)
+        public bool TryAdd(I interval, string chr, char strand)
         {
             if (!Chromosomes.ContainsKey(chr))
                 Chromosomes.Add(chr, new Chromosome<I, S>());
-            Chromosomes[chr].Add(interval, strand);
-            Statistics.Update(interval);
+            if (Chromosomes[chr].TryAdd(interval, strand))
+            {
+                Statistics.Update(interval);
+                return true;
+            }
+            else
+            {
+                return false;
+            }
         }
     }
 }

GeUtilities/Intervals/Parsers/Parser.cs

@@ -262,7 +262,7 @@ private void Parse()
                         continue;
                     }
 
-                    I readingInterval = BuildInterval(left, right, splittedLine, lineCounter, _data.FileHashKey + lineCounter.ToString());
+                    I readingInterval = BuildInterval(left, right, splittedLine, lineCounter, HashFunctions.GetHashSeed(_data.FileHashKey.ToString(), lineCounter.ToString()));
                     if (DropReadingPeak)
                         continue;
 
@@ -291,8 +291,13 @@ private void Parse()
                        (char.TryParse(splittedLine[_strandColumn], out strand) && strand != '+' && strand != '-' && strand != UnspecifiedStrandChar))
                         strand = UnspecifiedStrandChar;
 
-                    _data.Add(readingInterval, chrName, strand);
-                    _data.IntervalsCount++;
+                    if (_data.TryAdd(readingInterval, chrName, strand))
+                        _data.IntervalsCount++;
+                    else
+                    {
+                        DropLine("\tLine " + lineCounter.ToString() + "\t:\tPossibly Hash key collision.");
+                        continue;
+                    }
                 }
             }
         }