public static void PrintTree(DictionaryNode root)
{
if(!String.IsNullOrEmpty(root.Payload))
{
Console.WriteLine();
}
foreach(KeyValuePair<char,DictionaryNode> entry in root.Children )
{
Console.Write(entry.Key + "-");
PrintTree(entry.Value);
}
return;
}
//This function searches through a prie tree and returns the string if there was a match or returns empty String
public static String SearchTree(DictionaryNode root,string testString)
{
string result="";
//if we have payload we are at the leaf of the tree
if (!String.IsNullOrEmpty(root.Payload))
{
return root.Payload;
}
// else we have to recurse by checking if current character exists in the tree and send the remaining characters for further recursion
Char c= Char.ToUpper(testString[0]);
if(root.Children.ContainsKey(c))
{
result = SearchTree(root.Children[c],testString.Substring(1));
}
return result;
}
static void Main(string[] args)
{
DictionaryNode root = new DictionaryNode();
DictionaryNode child = new DictionaryNode();
int i = 0;
int maxTarget = 0;
int minTarget = int.MaxValue;
string payload;
int count_target = 0;
Stopwatch timer = new Stopwatch();
timer.Start();
string TargetFile = (args.Length > 0) ? @args[0] :@"/opt/dropbox/15-16/473/project4/targets";
//Create a prie tree
using (StreamReader sr = new StreamReader(TargetFile))
{
string line;
while ((line = sr.ReadLine()) != null)
{
line = line.ToUpper();
count_target++;
maxTarget = Math.Max(maxTarget, line.Length);
minTarget = Math.Min(minTarget, line.Length);
for (int x = 0; x < line.Length; x++)
{
char c = line[x];
payload = (x == (line.Length - 1)) ? line : "";
if (i == 0)
{
child = GetChild(root, c, payload);
i++;
}
else
{
child = GetChild(child, c, payload);
}
}
i = 0;
}
line = null;
}
timer.Stop();
Console.WriteLine("total number of targets is " + count_target);
Console.WriteLine("timeElapsed for building a tree : "+timer.ElapsedMilliseconds);
timer.Start();
//Search through the prie tree
string SequenceFolder = (args.Length>1) ? @args[1]: @"/opt/dropbox/15-16/473/project4/hg19-GRCh37";
CheckDir(SequenceFolder);
string match = "";
Dictionary<String, List<String>> Matches = new Dictionary<string, List<string>>();
foreach (string file in Directory.EnumerateFiles(SequenceFolder, "*"))
{
using (StreamReader reader = new StreamReader(file))
{
StringBuilder sb = new StringBuilder(reader.ReadToEnd());
string fileName = Path.GetFileName(file);
int sbLength = sb.Length;
for (int n = 0; n < sbLength; n++)
{
int displacement = Math.Min(sbLength - n, maxTarget);
//if length of remaining sequence is less than mintarget size we can leave
if(displacement<minTarget)
break;
match = SearchTree(root, sb.ToString(n, displacement));
if (!String.IsNullOrEmpty(match))
{
if (Matches.ContainsKey(match))
Matches[match].Add(n + "\t" + fileName);
else
Matches.Add(match, new List<String>(new String[] { n + "\t" + fileName }));
}
}
}
}
timer.Stop();
StreamWriter writer = new StreamWriter("output.txt");
writer.WriteLine("timeElapsed for running through the tree : " + timer.ElapsedMilliseconds);
foreach(KeyValuePair<String,List<String>> entry in Matches)
{
writer.WriteLine(entry.Key);
foreach(String s in entry.Value)
{
writer.WriteLine(s);
}
}
writer.Close();
//PrintTree(root);
Console.WriteLine("Finished");
Console.ReadLine();
}
public static DictionaryNode GetChild(DictionaryNode root,char value,string payload)
{
if (!root.Children.ContainsKey(value))
root.Children.Add(value, new DictionaryNode(payload));
return root.Children[value];
}
