From 8ca6f814671463f2a39bec5b602ff7e0c7af63a4 Mon Sep 17 00:00:00 2001
From: Alexandra Kalinova <kalinal1@fit.cvut.cz>
Date: Tue, 12 Dec 2017 18:25:46 +0100
Subject: [PATCH] Added implementation of frontend
---
src/main/java/edu/cvut/fit/kw/vmm/Main.java | 4 +-
.../kw/vmm/backend/SimilarDnaFinderImpl.java | 7 +-
.../fit/kw/vmm/frontend/InputPageHandler.java | 23 ++-
.../kw/vmm/frontend/OutputPageHandler.java | 186 +++++++++++++++++-
4 files changed, 201 insertions(+), 19 deletions(-)
diff --git a/src/main/java/edu/cvut/fit/kw/vmm/Main.java b/src/main/java/edu/cvut/fit/kw/vmm/Main.java
index 2ad8681..54cf52c 100644
--- a/src/main/java/edu/cvut/fit/kw/vmm/Main.java
+++ b/src/main/java/edu/cvut/fit/kw/vmm/Main.java
@@ -47,8 +47,8 @@ public class Main {
//needleTest("I like trains!", "I like Bulánci sleeping!");
//needleTest("I like pizza!", "Ich mag nudeln!");
//needleTest("TRALALA", "Ich mag nudeln!");
- smithTest("CATAC", "ATCGAA");
- smithTest("GGTTGACTA","TGTTACGG");
+ //smithTest("CATAC", "ATCGAA");
+ //smithTest("GGTTGACTA","TGTTACGG");
String containerPath = args.length > 0 ? args[0] : DEFAULT_CONTAINER_PATH;
SequenceContainer container = new FileSequenceContainer(containerPath);
diff --git a/src/main/java/edu/cvut/fit/kw/vmm/backend/SimilarDnaFinderImpl.java b/src/main/java/edu/cvut/fit/kw/vmm/backend/SimilarDnaFinderImpl.java
index 4583470..fc0b665 100644
--- a/src/main/java/edu/cvut/fit/kw/vmm/backend/SimilarDnaFinderImpl.java
+++ b/src/main/java/edu/cvut/fit/kw/vmm/backend/SimilarDnaFinderImpl.java
@@ -55,10 +55,13 @@ public class SimilarDnaFinderImpl implements SimilarDnaFinder {
String seqString = sequence.getSequence();
SequenceComparator comparator = null;
if(alignmentType == AlignmentType.GLOBAL) {
- //comparator = new NeedlemanWunsch(inputSeqString, seqString);
- comparator = new SmithWaterman(inputSeqString, seqString);
+ comparator = new NeedlemanWunsch(inputSeqString, seqString);
AlignmentSolution alignment = comparator.solve();
similarSequences.tryAdd(inputSequence, sequence, alignment);
+ } else if (alignmentType == AlignmentType.LOCAL) {
+ comparator = new SmithWaterman(inputSeqString, seqString);
+ AlignmentSolution alignment = comparator.solve();
+ similarSequences.tryAdd(inputSequence, sequence, alignment);
}
}
return similarSequences.getList();
diff --git a/src/main/java/edu/cvut/fit/kw/vmm/frontend/InputPageHandler.java b/src/main/java/edu/cvut/fit/kw/vmm/frontend/InputPageHandler.java
index 6aa5f42..7926d2e 100644
--- a/src/main/java/edu/cvut/fit/kw/vmm/frontend/InputPageHandler.java
+++ b/src/main/java/edu/cvut/fit/kw/vmm/frontend/InputPageHandler.java
@@ -1,7 +1,9 @@
package edu.cvut.fit.kw.vmm.frontend;
import java.io.IOException;
+import java.io.InputStream;
import java.io.OutputStream;
+import java.util.Scanner;
import com.sun.net.httpserver.HttpExchange;
import com.sun.net.httpserver.HttpHandler;
@@ -13,17 +15,18 @@ public class InputPageHandler implements HttpHandler {
System.out.println("InputPage request.");
String response =
"<html><head><title>Lokalni a globalni zarovnavani DNA sekvenci</title></head>" +
- "<body><h2>Lokalni a globalni zarovnavani DNA sekvenci</h2><br>" +
+ "<body>" +
+ "<form action=\"../outputs/\" method=\"post\">" +
+ "<h2>Lokalni a globalni zarovnavani DNA sekvenci</h2><br>" +
"<label><b>Vyberte zarovnavaci algoritmus: </b></label><br><br>" +
- "<form action=\"../\" method=\"post\">" +
- " <label for=\"needlemanwunsch\">NeedlemanWunsch (globalni)<input type=\"radio\" name=\"aligmnenttype\" id=\"needlemanwunsch\" value=\"needlemanwunsch\"></label> " +
- "  <label for=\"smithwaterman\">SmithWaterman (lokalni)<input type=\"radio\" name=\"aligmnenttype\" id=\"smithwaterman\" value=\"smithwaterman\"></label><br><br><br>" +
- "<label><b>Vlozte vstupni DNA sekvenci ze souboru: </b></label><br><br>" +
- "<input name=\"myFile\" type=\"file\"><br><br><br>" +
- "<label><b>nebo vlozte vstupni sekvence rucne: </b></label><br><br>" +
- "<label>1. DNA sekvence: <input type=\"text\" name=\"DNA1\"/></label> <br><br>" +
- "<label>2. DNA sekvence: <input type=\"text\" name=\"DNA2\"/> </label> <br><br>" +
- "            <input type=\"submit\"/>" +
+ " <label for=\"needlemanwunsch\">NeedlemanWunsch (globalni)<input type=\"radio\" name=\"alignmentType\" id=\"needlemanwunsch\" value=\"needlemanwunsch\"></label> " +
+ "  <label for=\"smithwaterman\">SmithWaterman (lokalni)<input type=\"radio\" name=\"alignmentType\" id=\"smithwaterman\" value=\"smithwaterman\"></label><br><br><br>" +
+
+ "<label><b>Vlozte vstupni DNA sekvenci: </b></label><br><br>" +
+ "  <label><b>ze souboru: </b></label>   <input name=\"myFile\" type=\"file\"><br>" +
+ "      <label>nebo</label><br>" +
+ "  <label><b>z klavesnice: </b>   </label><input name=\"DNA\" type=\"text\"/><br><br><br>" +
+ "   <input type=\"submit\"/>" +
"</form></body></html>";
arg0.sendResponseHeaders(200, response.length());
OutputStream os = arg0.getResponseBody();
diff --git a/src/main/java/edu/cvut/fit/kw/vmm/frontend/OutputPageHandler.java b/src/main/java/edu/cvut/fit/kw/vmm/frontend/OutputPageHandler.java
index 07be8bc..b9c9bce 100644
--- a/src/main/java/edu/cvut/fit/kw/vmm/frontend/OutputPageHandler.java
+++ b/src/main/java/edu/cvut/fit/kw/vmm/frontend/OutputPageHandler.java
@@ -1,16 +1,192 @@
package edu.cvut.fit.kw.vmm.frontend;
+import java.io.File;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
import com.sun.net.httpserver.HttpExchange;
import com.sun.net.httpserver.HttpHandler;
+import edu.cvut.fit.kw.vmm.alignment_solution.AlignedSequencePair;
+import edu.cvut.fit.kw.vmm.alignment_solution.AlignmentSolution;
+import edu.cvut.fit.kw.vmm.alignment_solution.StringOperation;
+import edu.cvut.fit.kw.vmm.backend.AlignmentType;
+import edu.cvut.fit.kw.vmm.backend.SimilarDnaFinder;
+import edu.cvut.fit.kw.vmm.backend.SimilarDnaFinderImpl;
+import edu.cvut.fit.kw.vmm.backend.sequence_containers.FileSequenceContainer;
+import edu.cvut.fit.kw.vmm.backend.sequence_containers.SequenceContainer;
+
public class OutputPageHandler implements HttpHandler {
+ private static final String DEFAULT_CONTAINER_PATH = "." + File.separator + "data";
+ protected String response;
- @Override
public void handle(HttpExchange arg0) throws IOException {
- // TODO Auto-generated method stub
-
- }
+ System.out.println("OutputPage request.");
+ response = "";
+ logInputs(arg0);
+ arg0.sendResponseHeaders(200, response.length());
+ OutputStream os = arg0.getResponseBody();
+ os.write(response.getBytes());
+ os.close();
+ }
+
+ private void logInputs(HttpExchange t) {
+ InputStream inputStream = t.getRequestBody();
+ Scanner s = new Scanner(inputStream);
+ String result = s.hasNext() ? s.next() : "";
+ System.out.println("Pure result: " + result);
+
+ String algnmntType = "---unknown---";
+ String myFile = "---unknown---";
+ String DNA = "---unknown---";
-}
+ // Split it
+ String[] params = result.split("&");
+
+ for(String param : params) {
+ String[] paramParts = param.split("=");
+ if(paramParts.length != 2) {
+ continue; // Something weird
+ }
+ String key = paramParts[0];
+ String value = paramParts[1];
+ if(key.compareTo("alignmentType") == 0) {
+ algnmntType = value;
+ }
+ else if(key.compareTo("myFile") == 0) {
+ myFile = value;
+ }
+ else if(key.compareTo("DNA") == 0) {
+ DNA = value;
+ }
+ }
+
+ String containerPath = DEFAULT_CONTAINER_PATH;
+ SequenceContainer container = new FileSequenceContainer(containerPath);
+ SimilarDnaFinder similarDnaFinder = new SimilarDnaFinderImpl(container);
+ String inputSeq = DNA;
+ List<AlignedSequencePair> kSimilar = null;
+ if(algnmntType.compareTo("needlemanwunsch") == 0) {
+ kSimilar = similarDnaFinder.findKSimilar(inputSeq, AlignmentType.GLOBAL, 1);
+ } else if (algnmntType.compareTo("smithwaterman") == 0) {
+ kSimilar = similarDnaFinder.findKSimilar(inputSeq, AlignmentType.LOCAL, 1);
+ }
+ System.out.println(kSimilar);
+ for(AlignedSequencePair pair : kSimilar) {
+ response += "<html><head></head><body style=\"font-family:monospace\">" + pair.getSecondSequence().getAnimalName() + "<br>";
+ System.out.println("Animal: " + pair.getSecondSequence().getAnimalName());
+ printSolution(pair.getAlignment(), pair.getFirstSequence().getSequence(), pair.getSecondSequence().getSequence());
+
+ System.out.println(pair.getAlignment().getSimilarity());
+ response += pair.getAlignment().getSimilarity() + "<br>";
+ }
+
+ if (myFile !="---unknown---" && DNA !="---unknown---" || algnmntType == "---unknown---") {
+ response += "<html><head></head><body>Takhle by to neslo! Zadejte vstup ze souboru NEBO z klavesnice.</body></html>";
+ } else if (myFile !="---unknown---" || DNA !="---unknown---") {
+ response += myFile + " " + algnmntType + " " + DNA;
+ }
+
+ System.out.println("Params were:");
+ System.out.println("Alignment type: " + algnmntType);
+ System.out.println("myFile: " + myFile);
+ System.out.println("DNA: " + DNA);
+ }
+
+ /**
+ * Example how can printing the solution look like
+ * @param solution solved solution - how to transform the first string into the second one
+ * @param str0 first string
+ * @param str1 second string
+ */
+ private void printSolution(AlignmentSolution solution, String str0, String str1) {
+ List<StringOperation> operations = solution.getOperations();
+ int str0Pointer = solution.getStr0Beginning();
+ int str1Pointer = solution.getStr1Beginning();
+ String res0 = "";
+ String res1 = "";
+ String verticalLines = "";
+ System.out.println("====== Printing solution: ======");
+ System.out.println(str0);
+ System.out.println(str1);
+ // PRINT THE PART BEFORE ALIGNED SEQUENCE
+ for(int i = 0; i < Integer.min(str0Pointer, str1Pointer); i++) {
+ res0 += str0.charAt(i);
+ res1 += str1.charAt(i);
+ verticalLines += ".";
+ }
+ for(int i = Integer.min(str0Pointer, str1Pointer); i < str0Pointer; i++) {
+ res0 += str0.charAt(i);
+ res1 += "-";
+ verticalLines += ".";
+ }
+ for(int i = Integer.min(str0Pointer, str1Pointer); i < str1Pointer; i++) {
+ res0 += "-";
+ res1 += str1.charAt(i);
+ verticalLines += ".";
+ }
+ // ACTUAL ALIGNED SEQUENCE
+ for(StringOperation operation:operations) {
+ switch (operation) {
+ case COPY:
+ res0 += str0.charAt(str0Pointer);
+ res1 += str1.charAt(str1Pointer);
+ verticalLines += "|";
+ str0Pointer++;
+ str1Pointer++;
+ break;
+ case REPLACE:
+ res0 += str0.charAt(str0Pointer);
+ res1 += str1.charAt(str1Pointer);
+ verticalLines += ".";
+ str0Pointer++;
+ str1Pointer++;
+ break;
+ case ADD:
+ res0 += "-";
+ res1 += str1.charAt(str1Pointer);
+ verticalLines += ".";
+ str1Pointer++;
+ break;
+ case DELETE:
+ res0 += str0.charAt(str0Pointer);
+ res1 += "-";
+ verticalLines += ".";
+ str0Pointer++;
+ }
+ }
+ // PRINT THE PART AFTER ALIGNED SEQUENCE
+ while(str0Pointer < str0.length() && str1Pointer < str1.length()) {
+ res0 += str0.charAt(str0Pointer);
+ res1 += str1.charAt(str1Pointer);
+ verticalLines += ".";
+ str0Pointer++;
+ str1Pointer++;
+ }
+ while(str0Pointer < str0.length()) {
+ res0 += str0.charAt(str0Pointer);
+ res1 += "-";
+ verticalLines += ".";
+ str0Pointer++;
+ }
+ while(str1Pointer < str1.length()) {
+ res0 += "-";
+ res1 += str1.charAt(str1Pointer);
+ verticalLines += ".";
+ str1Pointer++;
+ }
+ // PRINT IT TO STDOUT
+
+ response += res0 + "<br>";
+ response += verticalLines + "<br>";
+ response += res1 + "<br>";
+
+ System.out.println(res0);
+ System.out.println(verticalLines);
+ System.out.println(res1);
+ }
+}
\ No newline at end of file
--
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