private void method_9(CodeFile codeFile_0, AllSequences allSequences_0)
{
if (allSequences_0.Sequences.Count != 0)
{
int i = 0;
IL_A1:
while (i < codeFile_0.Similarities.Count)
{
Similarity similarity = codeFile_0.Similarities[i];
bool flag = false;
int j = 0;
while (j < allSequences_0.Sequences.Count)
{
Sequence sequence = allSequences_0.Sequences[j];
if (sequence.FirstCoord.J < similarity.MyHashIndexRange.Start || sequence.LastCoord.J > similarity.MyHashIndexRange.End)
{
j++;
}
else
{
codeFile_0.Similarities.Remove(similarity);
flag = true;
IL_9A:
if (!flag)
{
i++;
goto IL_A1;
}
goto IL_A1;
}
}
goto IL_9A;
}
}
}
internal void method7()
{
if (File.Exists("ignoreCode.txt"))
{
string str;
using (StreamReader streamReader = new StreamReader("ignoreCode.txt"))
{
str = streamReader.ReadToEnd();
}
List <CodeFile> list = method8(str);
foreach (CodeFile current in list)
{
foreach (CodeFile file in Files)
{
AllSequences allSequences = Analysis.smethod1(current, file, current.Hashes.Length - 1);
method9(file, allSequences);
}
}
method2(RootDirectories.First <CodeDir>());
method3();
}
}
private static AllSequences smethod2(CodeFile codeFile, int int2)
{
int[] hashes = codeFile.Hashes;
int[] hashes2 = codeFile.Hashes;
AllSequences allSequences = new AllSequences();
AllSequences result;
if (hashes.Length == 0)
{
result = allSequences;
}
else
{
int[] array = new int[hashes2.Length];
int[] array2 = new int[hashes2.Length];
for (int i = 0; i < hashes.Length; i++)
{
for (int j = i; j < hashes2.Length; j++)
{
if (i != j)
{
if (hashes[i] != hashes2[j])
{
array2[j] = 0;
}
else
{
if (i == 0 || j == 0)
{
array2[j] = 1;
}
else
{
array2[j] = 1 + array[j - 1];
}
if (array2[j] > int2)
{
allSequences.AddCoordToAppropriateSequence(new Coord
{
I = i,
J = j,
Size = array2[j]
});
}
}
}
}
int[] array3 = array;
array = array2;
array2 = array3;
}
result = allSequences;
}
return(result);
}
internal void method_7()
{
if (File.Exists("ignoreCode.txt"))
{
string string_;
using (StreamReader streamReader = new StreamReader("ignoreCode.txt"))
{
string_ = streamReader.ReadToEnd();
}
List <CodeFile> list = this.method_8(string_);
foreach (CodeFile current in list)
{
foreach (CodeFile current2 in this.observableCollection_1)
{
AllSequences allSequences_ = Analysis.smethod_1(current, current2, current.Hashes.Length - 1);
this.method_9(current2, allSequences_);
}
}
this.method_2(this.observableCollection_0.First <CodeDir>());
this.method_3();
}
}
private void method9(CodeFile codeFile, AllSequences allSequences)
{
if (allSequences.Sequences.Count != 0)
{
int i = 0;
IL_A1:
while (i < codeFile.Similarities.Count)
{
Similarity similarity = codeFile.Similarities[i];
bool flag = false;
int j = 0;
while (j < allSequences.Sequences.Count)
{
Sequence sequence = allSequences.Sequences[j];
if (sequence.FirstCoord.J < similarity.MyHashIndexRange.Start || sequence.LastCoord.J > similarity.MyHashIndexRange.End)
{
j++;
}
else
{
codeFile.Similarities.Remove(similarity);
flag = true;
//IL_9A:
if (!flag)
{
i++;
goto IL_A1;
}
goto IL_A1;
}
}
//goto IL_9A;
}
}
}
private static AllSequences smethod2(CodeFile codeFile, int int2)
{
int[] hashes = codeFile.Hashes;
int[] hashes2 = codeFile.Hashes;
AllSequences allSequences = new AllSequences();
AllSequences result;
if (hashes.Length == 0)
{
result = allSequences;
}
else
{
int[] array = new int[hashes2.Length];
int[] array2 = new int[hashes2.Length];
for (int i = 0; i < hashes.Length; i++)
{
for (int j = i; j < hashes2.Length; j++)
{
if (i != j)
{
if (hashes[i] != hashes2[j])
{
array2[j] = 0;
}
else
{
if (i == 0 || j == 0)
{
array2[j] = 1;
}
else
{
array2[j] = 1 + array[j - 1];
}
if (array2[j] > int2)
{
allSequences.AddCoordToAppropriateSequence(new Coord
{
I = i,
J = j,
Size = array2[j]
});
}
}
}
}
int[] array3 = array;
array = array2;
array2 = array3;
}
result = allSequences;
}
return result;
}
internal static AllSequences smethod1(CodeFile codeFile1, CodeFile codeFile2, int int2)
{
AllSequences result;
if (codeFile1 == codeFile2)
{
result = Analysis.smethod2(codeFile1, int2);
}
else
{
int[] hashes = codeFile1.Hashes;
int[] hashes2 = codeFile2.Hashes;
AllSequences allSequences = new AllSequences();
if (hashes.Intersect(hashes2).Count<int>() == 0)
{
Analysis.int0++;
result = allSequences;
}
else if (hashes.Length == 0 || hashes2.Length == 0)
{
result = allSequences;
}
else
{
int[] array = new int[hashes2.Length];
int[] array2 = new int[hashes2.Length];
for (int i = 0; i < hashes.Length; i++)
{
for (int j = 0; j < hashes2.Length; j++)
{
if (hashes[i] != hashes2[j])
{
array2[j] = 0;
}
else
{
if (i == 0 || j == 0)
{
array2[j] = 1;
}
else
{
array2[j] = 1 + array[j - 1];
}
if (array2[j] > int2)
{
allSequences.AddCoordToAppropriateSequence(new Coord
{
I = i,
J = j,
Size = array2[j]
});
}
}
}
int[] array3 = array;
array = array2;
array2 = array3;
}
result = allSequences;
}
}
return result;
}
private void method_10()
{
try
{
DirectoryInfo directoryInfo = new DirectoryInfo(this.string_0);
int minSimilarityLineLength = this.options_0.MinSimilarityLineLength;
FileInfo[] files = directoryInfo.GetFiles(this.options_0.FileSearchPattern, SearchOption.AllDirectories);
int num = 0;
List <Regex> excludeRegexes = this.options_0.GetExcludeRegexes();
FileInfo[] array = files;
int i = 0;
IL_98:
while (i < array.Length)
{
FileInfo fileInfo = array[i];
bool flag = false;
for (int j = 0; j < excludeRegexes.Count; j++)
{
if (excludeRegexes[j].IsMatch(fileInfo.FullName))
{
flag = true;
IL_87:
if (!flag)
{
num++;
}
i++;
goto IL_98;
}
}
goto IL_87;
}
if (num == 0)
{
this.AlertAction("No " + this.options_0.FileSearchPattern + " Files Found");
this.Done();
}
else
{
this.UpdateProgressAction(0, num, "Loading Files...");
CodeDir codeDir = this.method_4(directoryInfo, this.options_0.MinSimilarityLineLength, "");
this.observableCollection_0.Add(codeDir);
ObservableCollection <CodeFile> observableCollection = this.observableCollection_1;
this.UpdateProgressAction(0, observableCollection.Count * observableCollection.Count / 2, "Comparing Files...");
int num2 = 0;
StringBuilder stringBuilder = new StringBuilder();
for (int j = 0; j < observableCollection.Count; j++)
{
CodeFile codeFile = observableCollection[j];
for (int k = j; k < observableCollection.Count; k++)
{
num2++;
if (num2 % 500 == 0)
{
this.UpdateProgressValue(num2);
}
try
{
CodeFile codeFile_ = observableCollection[k];
AllSequences allSequences = Analysis.smethod_1(codeFile, codeFile_, minSimilarityLineLength);
foreach (Sequence current in allSequences.Sequences)
{
Analysis.smethod_4(codeFile, codeFile_, current);
}
goto IL_24D;
}
catch (Exception ex)
{
stringBuilder.AppendLine(codeFile.Name + " - " + observableCollection[k].Name);
goto IL_24D;
}
break;
IL_24D :;
}
codeFile.method_1();
codeFile.Similarities.Sort(new Comparison <Similarity>(Analysis.smethod_0));
}
this.method_2(codeDir);
this.method_3();
this.method_7();
if (stringBuilder.Length > 0)
{
this.AlertAction("Atomiq experienced an error with the following file combinations: " + stringBuilder.ToString());
}
this.bool_0 = true;
this.Done();
}
}
catch (Exception ex)
{
if (!(ex is ThreadAbortException))
{
this.CaughtException = ex;
}
this.Done();
}
}
internal static AllSequences smethod_1(CodeFile codeFile_0, CodeFile codeFile_1, int int_2)
{
AllSequences result;
if (codeFile_0 == codeFile_1)
{
result = Analysis.smethod_2(codeFile_0, int_2);
}
else
{
int[] hashes = codeFile_0.Hashes;
int[] hashes2 = codeFile_1.Hashes;
AllSequences allSequences = new AllSequences();
if (hashes.Intersect(hashes2).Count <int>() == 0)
{
Analysis.int_0++;
result = allSequences;
}
else if (hashes.Length == 0 || hashes2.Length == 0)
{
result = allSequences;
}
else
{
int[] array = new int[hashes2.Length];
int[] array2 = new int[hashes2.Length];
for (int i = 0; i < hashes.Length; i++)
{
for (int j = 0; j < hashes2.Length; j++)
{
if (hashes[i] != hashes2[j])
{
array2[j] = 0;
}
else
{
if (i == 0 || j == 0)
{
array2[j] = 1;
}
else
{
array2[j] = 1 + array[j - 1];
}
if (array2[j] > int_2)
{
allSequences.AddCoordToAppropriateSequence(new Coord
{
I = i,
J = j,
Size = array2[j]
});
}
}
}
int[] array3 = array;
array = array2;
array2 = array3;
}
result = allSequences;
}
}
return(result);
}