public void DestroyGene(int i)
{
GeneID id = playerScript.genes[i].id;
foreach (Transform child in geneObjects[i].transform)
{
GeneDeathScript geneDeathScript = child.gameObject.GetComponent <GeneDeathScript>();
if (geneDeathScript != null)
{
geneDeathScript.enabled = true;
}
}
foreach (TextMeshPro textMeshPro in geneObjects[i].GetComponentsInChildren <TextMeshPro>())
{
Destroy(textMeshPro);
}
playerScript.genes.RemoveAt(i);
geneObjects.RemoveAt(i);
if (id == GeneID.Junk)
{
playerScript.genes.Insert(i, new Gene(GeneID.DamagedJunk));
AddGene(i);
}
popupTextScript.Display(Gene.NAME_LOOKUP[id] + " gene destroyed.");
}
public bool HasGene(GeneID id)
{
foreach (Gene gene in genes)
{
if (gene.id == id)
{
return(true);
}
}
return(false);
}
public void SetID(GeneID id)
{
this.id = id;
nameText.text = Gene.NAME_LOOKUP[id];
foreach (SpriteRenderer spriteRenderer in spriteObject.GetComponentsInChildren <SpriteRenderer>())
{
spriteRenderer.color = Gene.COLOR_LOOKUP[id];
}
int[] prices = Gene.PRICE_LOOKUP[id];
price = Random.Range(prices[0], prices[1] + 1);
priceText.text = price.ToString();
}
public int NumGene(GeneID id)
{
int ret = 0;
foreach (Gene gene in genes)
{
if (gene.id == id)
{
ret++;
}
}
return(ret);
}
public Gene(GeneID id)
{
this.id = id;
}
bool GetSpecialButtonDown(GeneID id)
{
return(HasGene(id) && Input.GetButtonDown("Special"));
}
/// <summary>
/// In this method we will take one dictionary to populate GeneId's and mapped read count and another dictionary
/// to populate GeneID's and their length. Take a list CHRData with data from chr1-250.fa file.
/// Pass read length value and a string variable which will return the GeneID and their corresponding mappability value.
/// </summary>
/// <param name="FilePath"></param>
/// <param name="GeneData"></param>
/// <param name="GeneDataLength"></param>
/// <param name="CHRData"></param>
/// <param name="Values"></param>
/// <param name="readLength"></param>
public static void MappabilityFunction(string FilePath, Dictionary <string, int> GeneData, Dictionary <string, int> GeneDataLength, List <KeyValuePair <string, string> > CHRData, ref string Values, int readLength)
{
//Clear the list as there might be values for previous read length Bowtie file.
GeneData.Clear();
//Loop through the Bowtie output (BED format) to get the unique GeneId's and there mapped read count
foreach (string GeneID in File.ReadAllLines(FilePath))
{
string[] BToutDetails = GeneID.Split('\t');
string[] GeneNameDetails = BToutDetails[3].Split('.');
//Build the gene name
string GeneName = ">" + GeneNameDetails[0] + "." + GeneNameDetails[1] + "." + GeneNameDetails[2] + "." + GeneNameDetails[3] + "." + GeneNameDetails[4];// GeneNameDetails[3];
//Check if there exists Gene Name in dictionary and add 1 to the value.
if (GeneData.ContainsKey(GeneName))
{
//Add 1 to existing value for particular GeneID. If Map start and end are in range of Gene ID.
if ((Convert.ToInt32(BToutDetails[1]) >= Convert.ToInt32(GeneNameDetails[1])) &&
(Convert.ToInt32(BToutDetails[2]) <= Convert.ToInt32(GeneNameDetails[2])))
{
GeneData[GeneName] = GeneData[GeneName] + 1;
}
}
else
{
//Add GeneID and 1 as initial value. If Map start and end are in range of Gene ID.
if ((Convert.ToInt32(BToutDetails[1]) >= Convert.ToInt32(GeneNameDetails[1])) &&
(Convert.ToInt32(BToutDetails[2]) <= Convert.ToInt32(GeneNameDetails[2])))
{
GeneData.Add(GeneName, 1);
}
}
}
//Clear the dictionary before we put some information into it.
GeneDataLength.Clear();
//Loop through CHRData which contains information of Chr1-250.fa file and populate the unique GeneID's and their length.
foreach (KeyValuePair <string, string> GeneLengthData in CHRData)
{
string[] GeneAnnotData_Array = GeneLengthData.Key.Split('.');
string GeneName = GeneLengthData.Key;//GeneAnnotData_Array[3];
int GeneLength = 0;
//If we have duplicate GeneID then we will consider only the last GeneID found and its corresponding length.
if (GeneDataLength.ContainsKey(GeneName))
{
//Replace new length with the existing Value for particular GeneID which is duplicate.
GeneDataLength[GeneName] = Convert.ToInt32(GeneAnnotData_Array[2]) - Convert.ToInt32(GeneAnnotData_Array[1]);
}
else
{
//Add GeneID and its length.
GeneLength = Convert.ToInt32(GeneAnnotData_Array[2]) - Convert.ToInt32(GeneAnnotData_Array[1]);
GeneDataLength.Add(GeneName, GeneLength);
}
}
//Linq query to get data present in disctionary.
var items = from pair in GeneData
select pair;
//Initialize KeyValuePair List for storing data from GeneData dictionary.
List <KeyValuePair <string, int> > med1 = new List <KeyValuePair <string, int> >(items);
//Linq query to get data present in disctionary.
var items1 = from pair in GeneDataLength
select pair;
//Initialize KeyValuePair List for storing data from GeneDataLength dictionary.
List <KeyValuePair <string, int> > med2 = new List <KeyValuePair <string, int> >(items1);
//Set read_Length value.
int read_length = readLength;
double FinalValue = 0.0;
bool present = false;
//Loop through the list which contains GeneID and its length values.
foreach (KeyValuePair <string, int> GeneLengthValue in med2)
{
//Loop through the list which contains GeneID and its mapped reads.
foreach (KeyValuePair <string, int> GeneDataValue in med1)
{
//Check if GeneID exists or not
if (GeneDataValue.Key == GeneLengthValue.Key)//&& GeneLengthValue.Key == "NR_026818")
{
//Calculate the mappability value in percentile.
double totaltiles = 0.0;
//if gene length less than or equal to current read length then set total tiles as 1 other wise calculate.
if (GeneLengthValue.Value <= read_length)
{
totaltiles = 1.0;
}
else
{
totaltiles = GeneLengthValue.Value - read_length + 1;
}
FinalValue = ((Convert.ToDouble(GeneDataValue.Value) / totaltiles)) * 100;
string vl = Math.Round(FinalValue, 2).ToString();
if (vl.IndexOf('.') != -1)
{
Values += GeneDataValue.Key + "$" + vl + ";";
}
else
{
Values += GeneDataValue.Key + "$" + vl + ".0" + ";";
}
present = true;
}
}
//Based on flag value above, if GeneID doesnt exists then we will set value as '0.0'
if (!present)
{
Values += GeneLengthValue.Key + "$" + "0.0;";
present = false;
}
else
{
present = false;
}
}
}
// Start is called before the first frame update
void Start()
{
playerScript = GameObject.FindGameObjectWithTag("Player").GetComponent <PlayerScript>();
// Pick 3 weighted genes.
GeneID[] ids = new List <GeneID>(Gene.SHOP_WEIGHT_LOOKUP.Keys).ToArray();
float[] weights = new float[ids.Length];
for (int i = 0; i < ids.Length; i++)
{
GeneID id = ids[i];
float baseWeight = Gene.SHOP_WEIGHT_LOOKUP[id];
// No repeat powers.
if (id == GeneID.Blink || id == GeneID.Glide)
{
weights[i] = playerScript.HasGene(id) ? 0 : baseWeight;
continue;
}
if (id == GeneID.DoubleJump)
{
weights[i] = baseWeight / (1 + playerScript.NumGene(GeneID.DoubleJump));
continue;
}
weights[i] = baseWeight;
}
float totalWeight = 0;
foreach (float f in weights)
{
totalWeight += f;
}
List <GeneID> chosen = new List <GeneID>();
while (chosen.Count < 4)
{
float selector = Random.value * totalWeight;
int targetIndex = 0;
for (; targetIndex < weights.Length; targetIndex++)
{
selector -= weights[targetIndex];
if (selector < 0)
{
break;
}
}
GeneID id = ids[targetIndex];
if (chosen.Contains(id))
{
continue;
}
chosen.Add(id);
}
float spacing = 2.5f / chosen.Count;
for (int i = 0; i < chosen.Count; i++)
{
float xMult = i - (chosen.Count - 1) / 2;
GameObject shopGene = Instantiate(shopGenePrefab, transform.parent, false);
shopGene.transform.localPosition = new Vector3(xMult * spacing, -2);
ShopGeneScript shopGeneScript = shopGene.GetComponent <ShopGeneScript>();
shopGeneScript.SetID(chosen[i]);
}
}
