/// <summary>
/// 6/21/2012
/// Links to Parts Registry pages and parses source code in order to obtain general information for a
/// particular part
/// @ Nicole Francisco & Veronica Lin
/// </summary>
/// <param name="link">Particular extension of URL specific to this page</param>
public RegDataSheet(string link)
{
_name = "";
_type = "";
_none = true;
_terminator = new Terminators();
_promoter = new Promoter();
_rbs = new RBS();
_gene = new Gene();
_basicInfo = new BasicInfo();
_description = new Description();
//_protocol = new Protocol();
_reference = new Reference();
bool linkValid = true;
#region HTML Web Request
//the first link was set to -1 if no results showed up
if (link.Equals("http://partsregistry.org/-1"))
{
linkValid = false;
}
if (linkValid)
{
try
{
//Open a connection to PubMed publication page to get the information
Uri uri = new Uri(link);
// used to build entire input
StringBuilder sb = new StringBuilder();
// used on each read operation
byte[] buf = new byte[8192];
// prepare the web page we will be asking for
HttpWebRequest request =
(HttpWebRequest)WebRequest.Create(uri);
// execute the request
HttpWebResponse response = (HttpWebResponse)request.GetResponse();
// we will read data via the response stream
Stream resStream = response.GetResponseStream();
string tempString = null;
int count = 0;
do
{
// fill the buffer with data
count = resStream.Read(buf, 0, buf.Length);
// make sure we read some data
if (count != 0)
{
// translate from bytes to ASCII text
tempString = Encoding.ASCII.GetString(buf, 0, count);
// continue building the string
sb.Append(tempString);
}
}
while (count > 0); // any more data to read?
#endregion
String htmlText = sb.ToString(); //keep original to have objects parse through and find
//specific information
String tempText = sb.ToString(); //will be parsed through in this top-level method to find name and type of part
String sourceText = sb.ToString(); //will be parsed for sections of source code each class needs
int index = 0;
//find name of page
string pageTitle = "<h1 class='firstHeading'>"; //length: 25
string typeImg = "<img style='padding-top:0px' src='http://partsregistry.org/images/partbypart/icon_";
string partLead = "Part:";
//strings needed for each big class
string descriptionText = "";
string referenceText = "";
string categoriesBox = "";
string parametersBox = "";
if (sourceText.Contains("Designed by"))
{
index = sourceText.IndexOf("Designed by ");
sourceText = sourceText.Substring(index);
referenceText = sourceText.Substring(0, sourceText.IndexOf("</div>"));
}
if (sourceText.Contains("Assembly Compatibility:<UL>"))
{
index = sourceText.IndexOf("Assembly Compatibility:<UL>");
sourceText = sourceText.Substring(index);
descriptionText = sourceText.Substring(0, sourceText.IndexOf("<DIV id='reviews'>"));
}
if (sourceText.Contains("<div style='border:1px solid #aaa;'>"))
{
index = sourceText.IndexOf("<div style='border:1px solid #aaa;'>");
sourceText = sourceText.Substring(index);
categoriesBox = sourceText.Substring(0, sourceText.IndexOf("</div>"));
}
if (sourceText.Contains("<div id='parameters'>"))
{
index = sourceText.IndexOf("<div id='parameters'>");
sourceText = sourceText.Substring(index);
parametersBox = sourceText.Substring(0, sourceText.IndexOf("<!--"));
}
if (tempText.Contains(typeImg)) //checks if this page is a parts page
{
//Find type of the part
index = tempText.IndexOf(typeImg) + typeImg.Length;
tempText = tempText.Substring(index);
string temp = tempText.Substring(0, tempText.IndexOf("'>"));
//first case, where the type of the part is RBS
if (htmlText.Contains("rbs"))
{
//if (temp == "rbs.png" || htmlText.Contains("//rbs/prokaryote/regulated/issacs"))
//{
_type = "rbs";
_rbs = new RBS(categoriesBox);
//}
//Console.WriteLine("RBS!");
}
//second case, where the type of the part is promoter (different images for
//different types of promoters)
else if (htmlText.Contains("//promoter"))
{
_type = "promoter";
_promoter = new Promoter(categoriesBox + " " + parametersBox);
//Console.WriteLine("PROMOTER!");
//if (temp == "regulatory.png" || temp == "reporter.png" ||
// temp == "generator.png" || temp == "signalling.png" ||
// temp == "intermediate.png" || temp == "composite.png")
//{
}
//third case, where the type of the part is terminator
else if (temp == "terminator.png")
{
_type = "terminator";
_terminator = new Terminators(parametersBox);
//Console.WriteLine("TERMINATOR!");
}
//fourth case, where the type of the part is gene or protein coding sequence
else if (temp == "coding.png")
{
_type = "gene";
_gene = new Gene(categoriesBox);
//Console.WriteLine("GENE!");
}
}
//last case, where type of part is none of the 4 classified parts above
else
{
_none = false;
}
//Finding page title
//case where page is not a parts page
if (_none == false)
{
index = tempText.IndexOf("<h1 class=\"firstHeading\">") + "<h1 class=\"firstHeading\">".Length;
tempText = tempText.Substring(index);
_name = tempText.Substring(0, tempText.IndexOf("</h1>"));
}
//case where page is a parts page
else
{
index = tempText.IndexOf(pageTitle) + pageTitle.Length + partLead.Length;
tempText = tempText.Substring(index);
_name = tempText.Substring(0, tempText.IndexOf("</h1>"));
}
//string protocolLink = "http://partsregistry.org/cgi/partsdb/related.cgi?part=" + _name;
//if the page is a parts page
if (_none)
{
_basicInfo = new BasicInfo(htmlText, _type, _name);
//Console.WriteLine(_basicInfo);
_description = new Description(descriptionText);
//Console.WriteLine(_description);
//_protocol = new Protocol(protocolLink);
//Console.WriteLine(_protocol);
_reference = new Reference(referenceText);
//Console.WriteLine(_reference);
}
resStream.Close();
response.Close();
}
catch (Exception ex)
{
Console.Write("Exception : " + ex.Message);
}
}
}
public RegDataSheet()
{
_name = "test";
_type = "test";
_none = true;
_terminator = new Terminators();
_promoter = new Promoter();
_rbs = new RBS();
_gene = new Gene();
_basicInfo = new BasicInfo();
_description = new Description();
//_protocol = new Protocol();
_reference = new Reference();
}
/// <summary>
/// 6/21/2012
/// Links to Parts Registry pages and parses source code in order to obtain general information for a
/// particular part
/// @ Nicole Francisco & Veronica Lin
/// </summary>
/// <param name="link">Particular extension of URL specific to this page</param>
public RegDataSheet(string link)
{
_name = "";
_type = "";
_none = true;
_terminator = new Terminators();
_promoter = new Promoter();
_rbs = new RBS();
_gene = new Gene();
_basicInfo = new BasicInfo();
_description = new Description();
//_protocol = new Protocol();
_reference = new Reference();
bool linkValid = true;
#region HTML Web Request
//the first link was set to -1 if no results showed up
if (link.Equals("http://partsregistry.org/-1"))
{
linkValid = false;
}
if (linkValid)
{
try
{
//Open a connection to PubMed publication page to get the information
Uri uri = new Uri(link);
// used to build entire input
StringBuilder sb = new StringBuilder();
// used on each read operation
byte[] buf = new byte[8192];
// prepare the web page we will be asking for
HttpWebRequest request =
(HttpWebRequest)WebRequest.Create(uri);
// execute the request
HttpWebResponse response = (HttpWebResponse)request.GetResponse();
// we will read data via the response stream
Stream resStream = response.GetResponseStream();
string tempString = null;
int count = 0;
do
{
// fill the buffer with data
count = resStream.Read(buf, 0, buf.Length);
// make sure we read some data
if (count != 0)
{
// translate from bytes to ASCII text
tempString = Encoding.ASCII.GetString(buf, 0, count);
// continue building the string
sb.Append(tempString);
}
}while (count > 0); // any more data to read?
#endregion
String htmlText = sb.ToString(); //keep original to have objects parse through and find
//specific information
String tempText = sb.ToString(); //will be parsed through in this top-level method to find name and type of part
String sourceText = sb.ToString(); //will be parsed for sections of source code each class needs
int index = 0;
//find name of page
string pageTitle = "<h1 class='firstHeading'>"; //length: 25
string typeImg = "<img style='padding-top:0px' src='http://partsregistry.org/images/partbypart/icon_";
string partLead = "Part:";
//strings needed for each big class
string descriptionText = "";
string referenceText = "";
string categoriesBox = "";
string parametersBox = "";
if (sourceText.Contains("Designed by"))
{
index = sourceText.IndexOf("Designed by ");
sourceText = sourceText.Substring(index);
referenceText = sourceText.Substring(0, sourceText.IndexOf("</div>"));
}
if (sourceText.Contains("Assembly Compatibility:<UL>"))
{
index = sourceText.IndexOf("Assembly Compatibility:<UL>");
sourceText = sourceText.Substring(index);
descriptionText = sourceText.Substring(0, sourceText.IndexOf("<DIV id='reviews'>"));
}
if (sourceText.Contains("<div style='border:1px solid #aaa;'>"))
{
index = sourceText.IndexOf("<div style='border:1px solid #aaa;'>");
sourceText = sourceText.Substring(index);
categoriesBox = sourceText.Substring(0, sourceText.IndexOf("</div>"));
}
if (sourceText.Contains("<div id='parameters'>"))
{
index = sourceText.IndexOf("<div id='parameters'>");
sourceText = sourceText.Substring(index);
parametersBox = sourceText.Substring(0, sourceText.IndexOf("<!--"));
}
if (tempText.Contains(typeImg)) //checks if this page is a parts page
{
//Find type of the part
index = tempText.IndexOf(typeImg) + typeImg.Length;
tempText = tempText.Substring(index);
string temp = tempText.Substring(0, tempText.IndexOf("'>"));
//first case, where the type of the part is RBS
if (htmlText.Contains("rbs"))
{
//if (temp == "rbs.png" || htmlText.Contains("//rbs/prokaryote/regulated/issacs"))
//{
_type = "rbs";
_rbs = new RBS(categoriesBox);
//}
//Console.WriteLine("RBS!");
}
//second case, where the type of the part is promoter (different images for
//different types of promoters)
else if (htmlText.Contains("//promoter"))
{
_type = "promoter";
_promoter = new Promoter(categoriesBox + " " + parametersBox);
//Console.WriteLine("PROMOTER!");
//if (temp == "regulatory.png" || temp == "reporter.png" ||
// temp == "generator.png" || temp == "signalling.png" ||
// temp == "intermediate.png" || temp == "composite.png")
//{
}
//third case, where the type of the part is terminator
else if (temp == "terminator.png")
{
_type = "terminator";
_terminator = new Terminators(parametersBox);
//Console.WriteLine("TERMINATOR!");
}
//fourth case, where the type of the part is gene or protein coding sequence
else if (temp == "coding.png")
{
_type = "gene";
_gene = new Gene(categoriesBox);
//Console.WriteLine("GENE!");
}
}
//last case, where type of part is none of the 4 classified parts above
else
{
_none = false;
}
//Finding page title
//case where page is not a parts page
if (_none == false)
{
index = tempText.IndexOf("<h1 class=\"firstHeading\">") + "<h1 class=\"firstHeading\">".Length;
tempText = tempText.Substring(index);
_name = tempText.Substring(0, tempText.IndexOf("</h1>"));
}
//case where page is a parts page
else
{
index = tempText.IndexOf(pageTitle) + pageTitle.Length + partLead.Length;
tempText = tempText.Substring(index);
_name = tempText.Substring(0, tempText.IndexOf("</h1>"));
}
//string protocolLink = "http://partsregistry.org/cgi/partsdb/related.cgi?part=" + _name;
//if the page is a parts page
if (_none)
{
_basicInfo = new BasicInfo(htmlText, _type, _name);
//Console.WriteLine(_basicInfo);
_description = new Description(descriptionText);
//Console.WriteLine(_description);
//_protocol = new Protocol(protocolLink);
//Console.WriteLine(_protocol);
_reference = new Reference(referenceText);
//Console.WriteLine(_reference);
}
resStream.Close();
response.Close();
}
catch (Exception ex)
{
Console.Write("Exception : " + ex.Message);
}
}
}