Merge pull request #17 from CIDARLAB/feature/compensation

Compensation Matrix scripts linked to Website

Author: PrashantVaidyanathan

fpSelectionWebApp/src/main/java/org/cidarlab/fpSelection/servlets/Compensation.java

@@ -0,0 +1,51 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.cidarlab.fpSelection.servlets;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import javax.servlet.ServletConfig;
+import javax.servlet.ServletContext;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+
+/**
+ *
+ * @author prash
+ */
+public class Compensation extends HttpServlet {
+
+    private ServletContext context;
+
+    public void init(ServletConfig config) throws ServletException
+    {
+        this.context = config.getServletContext();
+    }
+    
+    @Override
+    protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+        BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(context.getRealPath("/")+"/_LayoutHeader.html")));
+        String str;
+        PrintWriter out = response.getWriter();
+        while ((str = in.readLine()) != null) {
+            out.println(str);
+        }
+        in = new BufferedReader(new InputStreamReader(new FileInputStream(context.getRealPath("/")+"/Compensation.html")));
+        while ((str = in.readLine()) != null) {
+            out.println(str);
+        }
+        in = new BufferedReader(new InputStreamReader(new FileInputStream(context.getRealPath("/")+"/_LayoutFooter.html")));
+        while ((str = in.readLine()) != null) {
+            out.println(str);
+        }
+    }
+}

fpSelectionWebApp/src/main/webapp/Compensation.html

@@ -0,0 +1,10 @@
+
+<ul class="nav nav-tabs" style="margin-top: 100px;">
+    <li class="tooltipNav false" title="Generate custom cytometer settings"><a href="/Tools">Instrument Config Generator</a></li>
+    <li class="tooltipNav active" title="Scripts to create compensation matrices"><a href="/Compensation">Compensation Matrix Creation</a></li>
+</ul>
+</br>
+<p style="font-size:20px"> The <a href="https://github.com/CIDARLAB/fpSelection" target="_blank">fpSelection GitHub repository</a> contains scripts for creating compensation matrices from raw cytometry data using R Bioconductor packages. 
+    The files are in the <a href= "https://github.com/CIDARLAB/fpSelection/tree/master/resources/bleedThroughAnalysis" target="_blank">resources folder</a>. 
+    Specific instructions to execute the scripts can be found in the <a href="https://github.com/CIDARLAB/fpSelection/blob/master/resources/bleedThroughAnalysis/README.md" target="_blank">README</a>. </p>
+  

fpSelectionWebApp/src/main/webapp/CytometerForm.html

@@ -1,10 +1,9 @@
-<!--
+
 <ul class="nav nav-tabs" style="margin-top: 100px;">
-    <li class="tooltipNav active" title="Generate custom cytometer settings"><a href="/Extras">Instrument Config Generator</a></li>
+    <li class="tooltipNav active" title="Generate custom cytometer settings"><a href="/Tools">Instrument Config Generator</a></li>
+    <li class="tooltipNav false" title="Scripts to create compensation matrices"><a href="/Compensation">Compensation Matrix Creation</a></li>
 </ul>
-<br>
--->
-<fieldset style="margin-top: 150px;">
+<fieldset >
     <!--FORM START-->
     <legend>Instrument Config Generator</legend>
     <div class="container cytoData">

fpSelectionWebApp/src/main/webapp/WEB-INF/web.xml

@@ -40,6 +40,10 @@
         <servlet-name>Documentation</servlet-name>
         <servlet-class>org.cidarlab.fpSelection.servlets.Documentation</servlet-class>
     </servlet>
+    <servlet>
+        <servlet-name>Compensation</servlet-name>
+        <servlet-class>org.cidarlab.fpSelection.servlets.Compensation</servlet-class>
+    </servlet>
     <servlet>
         <servlet-name>Tools</servlet-name>
         <servlet-class>org.cidarlab.fpSelection.servlets.Tools</servlet-class>
@@ -92,6 +96,10 @@
         <servlet-name>Tools</servlet-name>
         <url-pattern>/Tools</url-pattern>
     </servlet-mapping>
+    <servlet-mapping>
+        <servlet-name>Compensation</servlet-name>
+        <url-pattern>/Compensation</url-pattern>
+    </servlet-mapping>
     <servlet-mapping>
         <servlet-name>Attributions</servlet-name>
         <url-pattern>/Attributions</url-pattern>