initial commit

.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>triage</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8

.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=9
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=9
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=9

.settings/org.eclipse.m2e.core.prefs

+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<groupId>tcdb</groupId>
+	<artifactId>triage</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<packaging>jar</packaging>
+
+	<name>triage</name>
+	<url>http://maven.apache.org</url>
+
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+	</properties>
+	
+	 <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.7.0</version>
+        <configuration>
+          <source>1.9</source>
+          <target>1.9</target>
+        </configuration>
+      </plugin>
+    </plugins>
+  </build>
+
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>3.8.1</version>
+			<scope>test</scope>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.apache.poi/poi -->
+		<dependency>
+			<groupId>org.apache.poi</groupId>
+			<artifactId>poi</artifactId>
+			<version>3.17</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.apache.xmlbeans/xmlbeans -->
+		<dependency>
+			<groupId>org.apache.xmlbeans</groupId>
+			<artifactId>xmlbeans</artifactId>
+			<version>2.6.0</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
+		<dependency>
+			<groupId>org.apache.poi</groupId>
+			<artifactId>poi-ooxml</artifactId>
+			<version>3.17</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml-schemas -->
+		<dependency>
+			<groupId>org.apache.poi</groupId>
+			<artifactId>poi-ooxml-schemas</artifactId>
+			<version>3.17</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.dom4j/dom4j -->
+		<dependency>
+			<groupId>org.dom4j</groupId>
+			<artifactId>dom4j</artifactId>
+			<version>2.1.0</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.jsoup/jsoup -->
+		<dependency>
+			<groupId>org.jsoup</groupId>
+			<artifactId>jsoup</artifactId>
+			<version>1.11.3</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/com.github.cliftonlabs/json-simple -->
+		<dependency>
+			<groupId>com.github.cliftonlabs</groupId>
+			<artifactId>json-simple</artifactId>
+			<version>3.0.2</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/com.googlecode.json-simple/json-simple -->
+		<dependency>
+			<groupId>com.googlecode.json-simple</groupId>
+			<artifactId>json-simple</artifactId>
+			<version>1.1.1</version>
+		</dependency>
+		
+		<!-- https://mvnrepository.com/artifact/org.seleniumhq.selenium/selenium-server -->
+<dependency>
+    <groupId>org.seleniumhq.selenium</groupId>
+    <artifactId>selenium-server</artifactId>
+    <version>3.9.1</version>
+</dependency>
+		
+
+	</dependencies>
+</project>

src/main/java/betaBarrels/Navigate.java

+package betaBarrels;
+
+import java.util.concurrent.TimeUnit;
+
+import org.openqa.selenium.By;
+import org.openqa.selenium.WebDriver;
+import org.openqa.selenium.WebElement;
+import org.openqa.selenium.htmlunit.HtmlUnitDriver;
+
+public class Navigate {
+
+	public static void main(String[] args) throws InterruptedException {
+		// Create a new instance of the html unit driver
+		// Notice that the remainder of the code relies on the interface, 
+		// not the implementation.
+		WebDriver driver = new HtmlUnitDriver();
+
+		// And now use this to visit Google
+		driver.get("http://195.251.108.230/PRED-TMBB2/");
+
+		// Find the text input element by its name
+		WebElement element = driver.findElement(By.name("sequence"));
+
+		// Enter something to search for
+		element.sendKeys(">2K4T_A Chain A, Solution Structure Of Human Vdac-1 In Ldao Micelles\nMAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQALEHHHHHH\n"+
+">5JDP_A Chain A, E73v Mutant Of The Human Voltage-dependent Anion Channel\nSAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTVKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQARS\n"+
+">2JK4_A Chain A, Structure Of The Human Voltage-Dependent Anion Channel\nMRGSAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQARSHHHHHH\n"+
+">5XDO_A Chain A, Crystal Structure Of Human Voltage-dependent Anion Channel 1 (hvdac1) In C222 Space Group\nMRGSHHHHHHGSMAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA\n");
+
+		System.out.println(driver.getCurrentUrl());
+		
+		element = driver.findElement(By.xpath("/html/body/form/input[2]"));
+		
+		element.click();
+		
+		System.out.println(element.isSelected());
+		
+		element = driver.findElement(By.xpath("/html/body/form/input[3]"));
+		
+		element.click();
+		
+		System.out.println(element.isSelected());
+		
+		// Now submit the form. WebDriver will find the form for us from the element
+//		element.submit();
+//		driver.findElement(By.tagName("Run prediction")).click();
+		WebElement element2 = driver.findElement(By.xpath("/html/body/form/input[7]"));
+		
+		element2.click();
+		
+//		TimeUnit.SECONDS.sleep();
+		 
+		System.out.println(driver.getCurrentUrl());
+//		System.out.println(driver.getPageSource());
+		
+//		System.out.println(driver.getCurrentUrl());
+		
+		// Check the title of the page
+		System.out.println("Page title is: " + driver.getTitle());
+	}
+}

src/main/java/betaBarrels/PREDTMBB2.java

+package betaBarrels;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+
+import org.openqa.selenium.By;
+import org.openqa.selenium.WebDriver;
+import org.openqa.selenium.WebElement;
+import org.openqa.selenium.htmlunit.HtmlUnitDriver;
+
+public class PREDTMBB2 {
+	
+	public static String getLink(String path){
+		
+		String query = getCorrectFormatFasta(path);
+
+		WebDriver driver = new HtmlUnitDriver();
+
+		// And now use this to visit Google
+		driver.get("http://195.251.108.230/PRED-TMBB2/");
+
+		// Find the text input element by its name
+		WebElement element = driver.findElement(By.name("sequence"));			//text area
+		element.sendKeys(query);
+		
+		element = driver.findElement(By.xpath("/html/body/form/input[2]"));		//check prediction for batch
+		element.click();
+		
+		element = driver.findElement(By.xpath("/html/body/form/input[3]"));		//uncheck Signal peptide predictions
+		element.click();
+		
+		element = driver.findElement(By.xpath("/html/body/form/input[7]"));		//run prediction
+		element.click();
+		
+//		TimeUnit.SECONDS.sleep();		see if necessary
+		 
+		return driver.getCurrentUrl();
+	}
+
+	public static String getCorrectFormatFasta(String path){
+		
+		String query = "";
+		
+		FileReader file;
+		
+		try {
+			
+			file = new FileReader(path);
+			BufferedReader br = new BufferedReader(file);
+
+			String sCurrentLine;
+
+			while ((sCurrentLine = br.readLine()) != null) {
+				
+				if(sCurrentLine.contains(">"))
+					query = query.concat("\n").concat(sCurrentLine).concat("\n");
+				else
+					query = query.concat(sCurrentLine);
+				
+			}
+			
+			br.close();
+			
+		} 
+		catch (FileNotFoundException e) {
+			System.out.println("FILE NOT FOUND");
+			e.printStackTrace();
+			
+		}
+		catch (Exception e) {
+			e.printStackTrace();
+		}
+
+		return query;
+	}
+	
+	
+	
+	
+	
+	
+	
+	
+}

src/main/java/betaBarrels/ReadResults.java

+package betaBarrels;
+
+import java.io.BufferedReader;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.concurrent.TimeUnit;
+
+import org.jsoup.Jsoup;
+import org.jsoup.nodes.Document;
+
+import tcdb.connection.LinkConnection;
+
+public class ReadResults {
+
+	public static Map<String, Integer> readResults(String link){
+
+		boolean go = false;
+		
+		Map<String, Integer> results = new HashMap<>();
+
+		try {
+			while(!go){
+
+				go = true;
+
+				LinkConnection conn = new LinkConnection();
+
+				conn.getCodeConnection(link);
+				BufferedReader in = conn.getPage();
+
+
+				if(in != null){
+					
+					String html;
+					Document doc;
+					String text;
+
+					int entry = -1, length = -1, sp = -1, score = -1, ompdbFamily = -1, tmNumber = -1, reliability = -1, image = -1;
+
+					String entryRes = "";
+					int tmNumberRes = 0;
+
+					boolean header = true;
+					int i = 0, lastCol = 0;
+
+					while ((html = in.readLine()) != null){
+
+						doc = Jsoup.parse(html);
+						text = doc.body().text().trim();
+						
+						System.out.println(text + "    >>>>>>>>> " + i);
+						
+						if(text.contains("This page will be automatically reloaded")){
+							go = false;
+						}
+
+						else{
+
+							if(header){
+
+								if(text.equalsIgnoreCase("Entry")){
+									entry = i;
+									i++;
+								}
+								else if(text.equalsIgnoreCase("Length")){
+									length = i;
+									i++;
+								}
+								else if(text.equalsIgnoreCase("SP")){
+									sp = i;
+									i++;
+								}
+								else if(text.contains("β-score")){
+									score = i;
+									i++;
+								}
+								else if(text.equalsIgnoreCase("OMPdb family")){
+									ompdbFamily = i;
+									i++;
+								}
+								else if(text.equalsIgnoreCase("#TM")){
+									tmNumber = i;
+									i++;
+								}
+								else if(text.equalsIgnoreCase("Reliability")){
+									reliability = i;
+									i++;
+								}
+								else if(text.equalsIgnoreCase("Image")){
+									image = i;
+
+									lastCol = i;
+									i = -2;
+									header = false;
+									
+//									System.out.println(entry + " " + length + " " + sp + " " + score + " " + ompdbFamily + " " + tmNumber + " " + reliability + " " + image );
+								}
+
+							}
+							else{
+
+								if (i < (lastCol)){
+
+									if(i == entry){
+										entryRes = text.trim();
+									}
+									else if(i == tmNumber){
+										
+										if(text.contains("--"))
+											tmNumberRes = 0;
+										else
+											tmNumberRes = Integer.parseInt(text);
+									}
+
+									i++;
+								}
+								else{
+									
+									results.put(entryRes, tmNumberRes);
+									i = -2;
+								}
+							}
+
+						}
+
+					}
+
+					if(!go){
+						System.out.println("Waiting...");
+						TimeUnit.MINUTES.sleep(1);
+					}
+					
+				}
+				
+				in.close();
+
+			}
+			
+		} 
+		catch (Exception e) {
+			e.printStackTrace();
+		}
+		return results;
+	}
+
+}

src/main/java/betaBarrels/main.java

+package betaBarrels;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class main {
+
+	public static void main(String[] args) {
+
+		try {
+			
+			String word = "rg2162.;47/fjds_ADSDpre";
+			
+			word = word.replaceAll("[^A-Za-z0-9]", "");
+			
+			System.out.println(word);
+			
+//			
+//			Map<String, Integer> res = ReadResults.readResults("http://195.251.108.230/PRED-TMBB2/index.php?id=2yyvNhmDuu");
+//			
+//			System.out.println("RESULTADOS ---> " + res);
+
+//			String link = PREDTMBB2.getLink("/Users/davidelagoa/Desktop/UMinho/Tese/Beta barrels/search.faa");
+			
+//			System.out.println(link);
+			
+//			LinkConnection conn = new LinkConnection();
+//			
+//			if(conn.getCodeConnection("http://195.251.108.230/PRED-TMBB2/index.php?id=VebVC1VSEi") == 200){
+//				BufferedReader in = conn.getPage();
+//			
+//				String html;
+//				
+//				while ((html = in.readLine()) != null){
+//					
+//					Document doc = Jsoup.parse(html);
+//					String text = doc.body().text().trim();
+//					
+//					System.out.println(text);
+//				}
+//			}
+			
+			
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+
+	}
+
+}

src/main/java/tcdb/capsules/ReactionContainer.java

+package tcdb.capsules;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import tcdb.tcdbTransportTypesRetriever.TypeOfTransporter;
+
+/**
+ * @author Davide
+ *
+ */
+public class ReactionContainer {
+	
+	public static final String REVERSIBLE_TOKEN = "$REV$";
+	public static final String IRREVERSIBLE_TOKEN = "$IRREV$";
+	public static final String REV_TOKEN = "\\$REV\\$";
+	public static final String IRREV_TOKEN = "\\$IRREV\\$";
+
+	private String originalReaction = "";
+	private String product = "";
+	private String reactant = "";
+	private Boolean reversible = false;
+	private TypeOfTransporter transportType;
+	private Map<String, String> properties;
+	private Integer reactionID = null;
+	private String confidenceLevel = "0";
+
+	/**
+	 * Changes the reactant of the reaction.
+	 * 
+	 * @param key
+	 * @param value
+	 */
+	public void replaceReactant(String reactant) {
+		
+		this.reactant = reactant;
+		
+	}
+	
+	/**
+	 * Changes the product of the reaction.
+	 * 
+	 * @param key
+	 * @param value
+	 */
+	public void replaceProduct(String product) {
+		
+		this.product = product;
+		
+	}
+	
+	/**
+	 * Add property to properties map.
+	 * 
+	 * @param key
+	 * @param value
+	 */
+	public void addProperty(String key, String value) {
+		
+		properties.put(key, value);
+		
+	}
+	
+	/**
+	 * @return the properties
+	 */
+	public Map<String, String> getProperties() {
+		return properties;
+	}
+
+	/**
+	 * Container to store information regarding a single reaction;
+	 * 
+	 * @param product
+	 * @param reactant
+	 * @param reversible
+	 */
+	public ReactionContainer(String reactant, String product, boolean reversible) {
+		
+		this.product = product;
+		this.reactant = reactant;
+		this.reversible = reversible;
+		
+		properties = new HashMap();
+	}
+	
+	/**
+	 * @return the product
+	 */
+	public String getProduct() {
+		return product;