Develop Reference

Calculating physico-chemical properties of amino acids in Biojava

I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava.
I have found in the BioJava tutorial how to read the Fasta files and implemented this code. But I have no ideas how to solve this problem.
If you have some ideas please help me.
Maybe there are some sources where I can check it.
This is the code.
package biojava.biojava_project;
import java.net.URL;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
public class BioSeq {
// Inserting the sequence from UNIPROT
public static ProteinSequence getSequenceForId(String uniProtId) throws Exception {
URL uniprotFasta = new URL(String.format("https://rest.uniprot.org/uniprotkb/P31574.fasta", uniProtId));
ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);
System.out.printf("id : P31574", uniProtId, seq, System.getProperty("line.separator"), seq.getOriginalHeader());
System.out.println();
return seq;
}
public static void main(String[] args) {
try {
System.out.println(getSequenceForId("P31574"));
} catch (Exception e) {
e.printStackTrace();
}
}
}

I don't know if BioJava stores these properties anywhere. But it's easy to just list all the amino acids with their properties manually. Then iterate over the sequence and count those that satisfy the property. Here's an example for the polarity:
import java.io.InputStream;
import java.net.URL;
import java.util.Set;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
public class BioSeq {
public static void main(String[] args) throws Exception {
ProteinSequence seq = loadFromUniprot("P31574");
int polarCount = numberOfOccurrences(seq, /*Polar AAs:*/ Set.of("Y", "S", "T", "N", "Q", "C"));
System.out.println("% of polar AAs: " + ((double)polarCount)/seq.getLength());
}
public static ProteinSequence loadFromUniprot(String uniProtId) throws Exception {
URL uniprotFasta = new URL(String.format("https://rest.uniprot.org/uniprotkb/%s.fasta", uniProtId));
try (InputStream is = uniprotFasta.openStream()) {
return FastaReaderHelper.readFastaProteinSequence(is).get(uniProtId);
}
}
private static int numberOfOccurrences(ProteinSequence seq, Set<String> bases) {
int count = 0;
for (AminoAcidCompound aminoAcid : seq)
if(bases.contains(aminoAcid.getBase()))
count++;
return count;
}
}
PS: don't forget to close IO streams after you used them. In the example above I used try-with-resources syntax which automatically closes the InputStream.

eclipse - testng the method is undefined for the type Utils

I am copying pasting code from here, the whole file, and then I would like to make changes to it and implement IReporter and I have done all necessary imports in my java file.
All the errors were gone except one related to below import:
import org.testng.internal.Utils;
The error is
The method longStackTrace(Throwable, boolean) is undefined for the type Utils
The method shortStackTrace(Throwable, boolean) is undefined for the type Utils
These two are defined , I can see it here and here . I tried to clean the project , restart eclipse but nothing worked.
in pom.xml
<testng.version>6.10</testng.version>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>${testng.version}</version>
<scope>test</scope>
<scope>compile</scope> //tried this also
</dependency>
below is the class
package firsttestngpackage;
import java.util.Map;
//import org.apache.xml.serializer.utils.Utils;
import org.testng.IReporter;
import org.testng.ISuite;
import org.testng.ISuiteResult;
import org.testng.reporters.TestHTMLReporter;
import org.testng.xml.XmlSuite;
import org.testng.ITestContext;
import org.testng.ITestNGMethod;
import org.testng.ITestResult;
import org.testng.Reporter;
import org.testng.TestListenerAdapter;
import org.testng.TestRunner;
import org.testng.internal.Utils;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.Serializable;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.Objects;
public class CustomReport implements IReporter {
#Override
public void generateReport(List<XmlSuite> xmlSuites, List<ISuite> suites,
String outputDirectory) {
}
public static void generateTable(PrintWriter pw, String title,
Collection<ITestResult> tests, String cssClass, Comparator<ITestResult> comparator)
{
pw.append("<table width='100%' border='1' class='invocation-").append(cssClass).append("'>\n")
.append("<tr><td colspan='4' align='center'><b>").append(title).append("</b></td></tr>\n")
.append("<tr>")
.append("<td><b>Test method</b></td>\n")
.append("<td width=\"30%\"><b>Exception</b></td>\n")
.append("<td width=\"10%\"><b>Time (seconds)</b></td>\n")
.append("<td><b>Instance</b></td>\n")
.append("</tr>\n");
if (tests instanceof List) {
Collections.sort((List<ITestResult>) tests, comparator);
}
// User output?
String id;
Throwable tw;
for (ITestResult tr : tests) {
pw.append("<tr>\n");
// Test method
ITestNGMethod method = tr.getMethod();
String name = method.getMethodName();
pw.append("<td title='").append(tr.getTestClass().getName()).append(".")
.append(name)
.append("()'>")
.append("<b>").append(name).append("</b>");
// Test class
String testClass = tr.getTestClass().getName();
if (testClass != null) {
pw.append("<br>").append("Test class: ").append(testClass);
// Test name
String testName = tr.getTestName();
if (testName != null) {
pw.append(" (").append(testName).append(")");
}
}
// Method description
if (! Utils.isStringEmpty(method.getDescription())) {
pw.append("<br>").append("Test method: ").append(method.getDescription());
}
Object[] parameters = tr.getParameters();
if (parameters != null && parameters.length > 0) {
pw.append("<br>Parameters: ");
for (int j = 0; j < parameters.length; j++) {
if (j > 0) {
pw.append(", ");
}
pw.append(parameters[j] == null ? "null" : parameters[j].toString());
}
}
//
// Output from the method, created by the user calling Reporter.log()
//
{
List<String> output = Reporter.getOutput(tr);
if (null != output && output.size() > 0) {
pw.append("<br/>");
// Method name
String divId = "Output-" + tr.hashCode();
pw.append("\n<a href=\"#").append(divId).append("\"")
.append(" onClick='toggleBox(\"").append(divId).append("\", this, \"Show output\", \"Hide output\");'>")
.append("Show output</a>\n")
.append("\n<a href=\"#").append(divId).append("\"")
.append(" onClick=\"toggleAllBoxes();\">Show all outputs</a>\n")
;
// Method output
pw.append("<div class='log' id=\"").append(divId).append("\">\n");
for (String s : output) {
pw.append(s).append("<br/>\n");
}
pw.append("</div>\n");
}
}
pw.append("</td>\n");
// Exception
tw = tr.getThrowable();
String stackTrace;
String fullStackTrace;
id = "stack-trace" + tr.hashCode();
pw.append("<td>");
if (null != tw) {
fullStackTrace = Utils.longStackTrace(tw, true);
stackTrace = "<div><pre>" + Utils.shortStackTrace(tw, true) + "</pre></div>";
pw.append(stackTrace);
// JavaScript link
pw.append("<a href='#' onClick='toggleBox(\"")
.append(id).append("\", this, \"Click to show all stack frames\", \"Click to hide stack frames\")'>")
.append("Click to show all stack frames").append("</a>\n")
.append("<div class='stack-trace' id='").append(id).append("'>")
.append("<pre>").append(fullStackTrace).append("</pre>")
.append("</div>")
;
}
pw.append("</td>\n");
// Time
long time = (tr.getEndMillis() - tr.getStartMillis()) / 1000;
String strTime = Long.toString(time);
pw.append("<td>").append(strTime).append("</td>\n");
// Instance
Object instance = tr.getInstance();
pw.append("<td>").append(Objects.toString(instance)).append("</td>");
pw.append("</tr>\n");
}
pw.append("</table><p>\n");
}
}

As per suggestion in above comments
updating testNG plugin through eclipse help--> check for updates --> then selecting testNG and updating, resolved the error

Apache flink pattern conditions with list

I wrote a pattern. I have a list for conditions(gettin rules from json).Data(json) is coming form kafka server . I want to filter the data with this list. But it is not working. How can I do that?
I am not sure about keyedstream and alarms in for. Can flink work like this?
main program:
package cep_kafka_eample.cep_kafka;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonParser;
import org.apache.flink.cep.CEP;
import org.apache.flink.cep.PatternSelectFunction;
import org.apache.flink.cep.PatternStream;
import org.apache.flink.cep.pattern.Pattern;
import org.apache.flink.streaming.api.TimeCharacteristic;
import org.apache.flink.streaming.api.datastream.DataStream;
import org.apache.flink.streaming.api.environment.StreamExecutionEnvironment;
import org.apache.flink.streaming.api.windowing.assigners.SlidingProcessingTimeWindows;
import org.apache.flink.streaming.api.windowing.time.Time;
import org.apache.flink.streaming.connectors.kafka.FlinkKafkaConsumer010;
import org.apache.flink.streaming.util.serialization.JSONDeserializationSchema;
import util.AlarmPatterns;
import util.Rules;
import util.TypeProperties;
import java.io.FileReader;
import java.util.*;
public class MainClass {
public static void main( String[] args ) throws Exception
{
ObjectMapper mapper = new ObjectMapper();
JsonParser parser = new JsonParser();
Object obj = parser.parse(new FileReader(
"c://new 5.json"));
JsonArray array = (JsonArray)obj;
Gson googleJson = new Gson();
List<Rules> ruleList = new ArrayList<>();
for(int i = 0; i< array.size() ; i++) {
Rules jsonObjList = googleJson.fromJson(array.get(i), Rules.class);
ruleList.add(jsonObjList);
}
//apache kafka properties
Properties properties = new Properties();
properties.setProperty("zookeeper.connect", "localhost:2181");
properties.setProperty("bootstrap.servers", "localhost:9092");
//starting flink
StreamExecutionEnvironment env = StreamExecutionEnvironment.getExecutionEnvironment();
env.enableCheckpointing(1000).setStreamTimeCharacteristic(TimeCharacteristic.EventTime);
//get kafka values
FlinkKafkaConsumer010<ObjectNode> myConsumer = new FlinkKafkaConsumer010<>("demo", new JSONDeserializationSchema(),
properties);
List<Pattern<ObjectNode,?>> patternList = new ArrayList<>();
DataStream<ObjectNode> dataStream = env.addSource(myConsumer);
dataStream.windowAll(SlidingProcessingTimeWindows.of(Time.seconds(10), Time.seconds(5)));
DataStream<ObjectNode> keyedStream = dataStream;
//get pattern list, keyeddatastream
for(Rules rules : ruleList){
List<TypeProperties> typePropertiesList = rules.getTypePropList();
for (int i = 0; i < typePropertiesList.size(); i++) {
TypeProperties typeProperty = typePropertiesList.get(i);
if (typeProperty.getGroupType() != null && typeProperty.getGroupType().equals("group")) {
keyedStream = keyedStream.keyBy(
jsonNode -> jsonNode.get(typeProperty.getPropName().toString())
);
}
}
Pattern<ObjectNode,?> pattern = new AlarmPatterns().getAlarmPattern(rules);
patternList.add(pattern);
}
//CEP pattern and alarms
List<DataStream<Alert>> alertList = new ArrayList<>();
for(Pattern<ObjectNode,?> pattern : patternList){
PatternStream<ObjectNode> patternStream = CEP.pattern(keyedStream, pattern);
DataStream<Alert> alarms = patternStream.select(new PatternSelectFunction<ObjectNode, Alert>() {
private static final long serialVersionUID = 1L;
public Alert select(Map<String, List<ObjectNode>> map) throws Exception {
return new Alert("new message");
}
});
alertList.add(alarms);
}
env.execute("Flink CEP monitoring job");
}
}
getAlarmPattern:
package util;
import org.apache.flink.cep.pattern.Pattern;
import org.apache.flink.cep.pattern.conditions.IterativeCondition;
import org.apache.flink.streaming.api.datastream.DataStream;
import com.fasterxml.jackson.databind.node.ObjectNode;
public class AlarmPatterns {
public Pattern<ObjectNode, ?> getAlarmPattern(Rules rules) {
//MySimpleConditions conditions = new MySimpleConditions();
Pattern<ObjectNode, ?> alarmPattern = Pattern.<ObjectNode>begin("first")
.where(new IterativeCondition<ObjectNode>() {
#Override
public boolean filter(ObjectNode jsonNodes, Context<ObjectNode> context) throws Exception {
for (Criterias criterias : rules.getCriteriaList()) {
if (criterias.getCriteriaType().equals("equals")) {
return jsonNodes.get(criterias.getPropName()).equals(criterias.getCriteriaValue());
} else if (criterias.getCriteriaType().equals("greaterThen")) {
if (!jsonNodes.get(criterias.getPropName()).equals(criterias.getCriteriaValue())) {
return false;
}
int count = 0;
for (ObjectNode node : context.getEventsForPattern("first")) {
count += node.get("value").asInt();
}
return Integer.compare(count, 5) > 0;
} else if (criterias.getCriteriaType().equals("lessThen")) {
if (!jsonNodes.get(criterias.getPropName()).equals(criterias.getCriteriaValue())) {
return false;
}
int count = 0;
for (ObjectNode node : context.getEventsForPattern("first")) {
count += node.get("value").asInt();
}
return Integer.compare(count, 5) < 0;
}
}
return false;
}
}).times(rules.getRuleCount());
return alarmPattern;
}
}

Thanks for using FlinkCEP!
Could you provide some more details about what exactly is the error message (if any)? This will help a lot at pinning down the problem.
From a first look at the code, I can make the following observations:
At first, the line:
dataStream.windowAll(SlidingProcessingTimeWindows.of(Time.seconds(10), Time.seconds(5)));
will never be executed, as you never use this stream in the rest of your program.
Second, you should specify a sink to be taken after the select(), e.g. print() method on each of your PatternStreams. If you do not do so, then your output gets discarded. You can have a look here for examples, although the list is far from exhaustive.
Finally, I would recommend adding a within() clause to your pattern, so that you do not run out of memory.

Error was from my json object. I will fix it. When i am run job on intellij cep doesn't work. When submit from flink console it works.

JNA: Missing some specifics methods

I'm wanting create a dll injector in Java ( and only in Java ) for educational proporses for myself and found a basic example in a website especialized in online game.
The autor only said that was made using JNA interface.
So, i'm studyng this piece of code and trying compile with success using NetBeans IDE and JNA, but seem that JNA interface that i have here ( 4.2.2 ) not have all methods and functions used on piece of code left by autor.
Are they:
GetProcAddress
VirtualAllocEx
VirtualFreeEx
So, i'm wanting some help here if possible, for try solved this trouble of missing of methods in JNA.
I had fixed big part these erros but still missing some methods in JNA like i will show following point to point with comments.
package inject;
//////////////////// JNA-4.2.2 /////////////////////
import com.sun.jna.Memory;
import com.sun.jna.Native;
import com.sun.jna.Pointer;
import com.sun.jna.platform.win32.Kernel32;
import com.sun.jna.platform.win32.Tlhelp32;
import com.sun.jna.platform.win32.WinDef;
import com.sun.jna.platform.win32.WinDef.HMODULE;
import com.sun.jna.platform.win32.WinNT;
import com.sun.jna.platform.win32.WinNT.HANDLE;
import com.sun.jna.ptr.IntByReference;
import com.sun.jna.win32.W32APIOptions;
import java.io.File;
//////////////////////////////////////////////////
// Extracted from: https://github.com/warmuuh/AndroidCtx/tree/master/HotContext/src/luz/winapi
import inject.luz.winapi.constants.DwDesiredAccess;
import inject.luz.winapi.tools.Advapi32Tools;
import inject.luz.winapi.tools.Kernel32Tools;
import luz.winapi.api.exception.Kernel32Exception;
//////////////////////////////////////////////////////////////////////////////////////////////
public class Inject {
private static int GetPid(String proc){
int id = 0;
Kernel32 kernel32 = (Kernel32) Native.loadLibrary(Kernel32.class, W32APIOptions.UNICODE_OPTIONS);
Tlhelp32.PROCESSENTRY32.ByReference processEntry = new Tlhelp32.PROCESSENTRY32.ByReference();
WinNT.HANDLE snapshot = kernel32.CreateToolhelp32Snapshot(Tlhelp32.TH32CS_SNAPPROCESS, new WinDef.DWORD(0));
try {
while (kernel32.Process32Next(snapshot, processEntry)) {
if (Native.toString(processEntry.szExeFile).equalsIgnoreCase(proc)) {
id = processEntry.th32ProcessID.intValue();
}
}
}
finally {
kernel32.CloseHandle(snapshot);
}
return id;
}
private static String findProcessByPID(int pid){
String name = "";
Kernel32 kernel32 = (Kernel32) Native.loadLibrary(Kernel32.class, W32APIOptions.UNICODE_OPTIONS);
Tlhelp32.PROCESSENTRY32.ByReference processEntry = new Tlhelp32.PROCESSENTRY32.ByReference();
WinNT.HANDLE snapshot = kernel32.CreateToolhelp32Snapshot(Tlhelp32.TH32CS_SNAPPROCESS, new WinDef.DWORD(0));
try {
while (kernel32.Process32Next(snapshot, processEntry)) {
if (pid == processEntry.th32ProcessID.intValue()) {
name = processEntry.szExeFile.toString();
}
}
}
finally {
kernel32.CloseHandle(snapshot);
}
return name;
}
public static void inject(File dll, Integer pId) throws Kernel32Exception {
if(null == dll || !dll.exists() || !dll.isFile() || !dll.getName().endsWith(".dll"))
return;
String p = findProcessByPID(pId);
if(null == p) return;
Kernel32 kernel = Kernel32.INSTANCE;
HMODULE kernel32Pointer = kernel.GetModuleHandle("Kernel32");
// Cannot find "GetProcAddress"
Pointer loadLibraryAddress = kernel.GetProcAddress(kernel32Pointer, "LoadLibraryA");
HANDLE process = null;
DwDesiredAccess access = new DwDesiredAccess();
access.setPROCESS_ALL_ACCESS();
try {
Advapi32Tools.getInstance().enableDebugPrivilege(Kernel32Tools.getInstance().GetCurrentProcess());
} catch (Exception e) {
}
// Incompatible types "Pointer" and "HANDLE"
process = Kernel32Tools.getInstance().OpenProcess(access, false, pId);
String path = dll.getPath() + '\0';
byte[] bytes = path.getBytes();
int pathLength = bytes.length;
// Cannot find "VirtualAllocEx"
Pointer memoryDllPath = kernel.VirtualAllocEx(process, null, pathLength, Kernel32Tools.MEM_COMMIT, Kernel32Tools.PAGE_READWRITE);
Memory dllPathContent = new Memory(pathLength);
for(int i=0;i<pathLength;i++)
dllPathContent.setByte(i, bytes[i]);
IntByReference writeResult = new IntByReference();
boolean successWritting = kernel.WriteProcessMemory(process, memoryDllPath, dllPathContent, pathLength, writeResult);
if(!successWritting) {
kernel.CloseHandle(process);
return;
}
IntByReference threadId = new IntByReference();
// Pointer cannot be converted to "FOREIGN_THREAD_START_ROUTINE"
Pointer thread = kernel.CreateRemoteThread(process, null, 0, loadLibraryAddress, memoryDllPath, 0, threadId);
boolean res = false;
// Incompatible types "Pointer" and "HANDLE" //Cannot find "WAIT_TIMEOUT"
res = kernel.WaitForSingleObject(thread, Integer.MAX_VALUE) != Kernel32Tools.WAIT_TIMEOUT;
// Cannot find "VirtualFreeEx" method // Cannot find "MEM_RELEASE"
kernel.VirtualFreeEx(process, memoryDllPath, pathLength, Kernel32Tools.MEM_RELEASE);
kernel.CloseHandle(process);
}
/**
* #param args the command line arguments
*/
public static void main(String[] args) {
System.out.println(GetPid("notepad.exe"));
}
}
Thank in advance by any suggestion or help :-)

JNA missing methods? It ain't so!
You just need to extend the library and add your own (and, ideally, also contribute the "missing" methods back to the JNA library so others can benefit.
Here is an example of how someone has mapped GetProcAddress.
Someone has mapped VirtualAllocEx here (although they should properly have extended Kernel32 rather than copied it entirely and edited portions)
I couldn't find an example of VirtualFreeEx within the same 15 seconds I found the others... doesn't mean it's not out there but after writing the others you shouldn't have much trouble writing it as well.

How to overwrite file in Java with one changed value

I am trying to make a program that uses JFrames and JPanels to construct a voting program. There is a file called voters.txt that is formatted like so:
1234:Herb Weaselman:false
9876:Marge Magnificent:false
4444:Ingmar Inglenook:false
8888:Hector Heroman:false
5678:Agnes Angular:false
In the beginning of my program, I have to ask the user for their voter ID and if their input does not match one of the IDs from the text file, then the program ends. I have managed to achieve this but now I need to overwrite this voters.txt file by changing the false element of whoever voted to true. For instance, if the user entered an ID of 1234, then I would need to change the word after Herb Weaselman to true instead of false. I am not sure how to do this. I know how to write to a file but am not sure how to change that one specific element. Here is the code I have currently:
import java.awt.*;
import javax.swing.*;
import java.awt.event.*;
import java.util.Scanner;
import java.io.*;
import java.util.ArrayList;
public class Assig5 extends JFrame
{
public Assig5()
{
}
public static void main(String[] args) throws IOException
{
LoginWindow loginWindow = new LoginWindow();
loginWindow.fileReader();
if(!loginWindow.checkResult(loginWindow.result))
{
System.out.println("Invalid Voter ID");
System.exit(0);
}
System.out.println("Continue");
}
}
import java.awt.*;
import javax.swing.*;
import java.awt.event.*;
import java.util.Scanner;
import java.io.*;
import java.util.ArrayList;
public class LoginWindow extends JFrame
{
static ArrayList<String> list = new ArrayList<String>();
public String result;
public LoginWindow()
{
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
result = JOptionPane.showInputDialog(frame, "Enter voter ID:");
}
public static void fileReader() throws FileNotFoundException
{
Scanner s = new Scanner(new File("voters.txt"));
while (s.hasNextLine())
{
list.add(s.nextLine());
}
s.close();
}
public static boolean checkResult(String result)
{
for(int i = 0; i < list.size(); i++)
{
String[] retval = list.get(i).split(":");
if(retval[0].equals(result))
{
return true;
}
}
return false;
}
}
Any help would be appreciated. Thanks in advance.

Just change your array index from false to true when there is a match. Then rewrite the file with the data from the array. If there is not match, the file does not change.
Solution
if(retval[0].equals(result)){
retval[2] = true;
return true;
}