Java Regex String Matching
0
I am using the Regex matcher for approximate string matching. I have a question regarding how to make it allow for overlapping matches. Currently, it finds a match then skips to the end of that hit and searches starting there.
Current Code
import java.util.Scanner;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
public class BNDM2 {
public static void main(String args){
Scanner sc = new Scanner(System.in);
String nucleotides,pattern;
System.out.print("Enter sequence:");
pattern = sc.nextLine();
System.out.print("Enter nucleotides:");
nucleotides= sc.nextLine();
// first convert the pattern into a proper regex
// i.e. replacing any N with [ATCG]
Pattern regex = Pattern.compile(pattern.replaceAll("N", "[ATCG]"));
// create a Matcher to find everywhere that the pattern matches
Matcher m = regex.matcher(nucleotides);
// find all the matches
while (m.find()) {
System.out.println("Match found:");
System.out.println("start:" + m.start());
System.out.println("end:" + (m.end() - 1)); // minus 1 here because the end of a regex match is always off by 1
System.out.println();
System.out.println("|" + nucleotides.substring(m.start(),m.end())+"|......");
}
}
}
java regex
asked Nov 13 '18 at 23:25
STRSTR
164
add a comment |
0
I am using the Regex matcher for approximate string matching. I have a question regarding how to make it allow for overlapping matches. Currently, it finds a match then skips to the end of that hit and searches starting there.
Current Code
import java.util.Scanner;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
public class BNDM2 {
public static void main(String args){
Scanner sc = new Scanner(System.in);
String nucleotides,pattern;
System.out.print("Enter sequence:");
pattern = sc.nextLine();
System.out.print("Enter nucleotides:");
nucleotides= sc.nextLine();
// first convert the pattern into a proper regex
// i.e. replacing any N with [ATCG]
Pattern regex = Pattern.compile(pattern.replaceAll("N", "[ATCG]"));
// create a Matcher to find everywhere that the pattern matches
Matcher m = regex.matcher(nucleotides);
// find all the matches
while (m.find()) {
System.out.println("Match found:");
System.out.println("start:" + m.start());
System.out.println("end:" + (m.end() - 1)); // minus 1 here because the end of a regex match is always off by 1
System.out.println();
System.out.println("|" + nucleotides.substring(m.start(),m.end())+"|......");
}
}
}
java regex
asked Nov 13 '18 at 23:25
STRSTR
164
Can you show us a sample of your input data, the results you're getting, and the how they differ from your expected results?
– mypetlion
Nov 13 '18 at 23:29
You're probably going to need quantifiers but as mypetlion says, hard to help you without input + current output vs desired output...
– Mena
Nov 13 '18 at 23:33
add a comment |
0
0
0
I am using the Regex matcher for approximate string matching. I have a question regarding how to make it allow for overlapping matches. Currently, it finds a match then skips to the end of that hit and searches starting there.
Current Code
import java.util.Scanner;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
public class BNDM2 {
public static void main(String args){
Scanner sc = new Scanner(System.in);
String nucleotides,pattern;
System.out.print("Enter sequence:");
pattern = sc.nextLine();
System.out.print("Enter nucleotides:");
nucleotides= sc.nextLine();
// first convert the pattern into a proper regex
// i.e. replacing any N with [ATCG]
Pattern regex = Pattern.compile(pattern.replaceAll("N", "[ATCG]"));
// create a Matcher to find everywhere that the pattern matches
Matcher m = regex.matcher(nucleotides);
// find all the matches
while (m.find()) {
System.out.println("Match found:");
System.out.println("start:" + m.start());
System.out.println("end:" + (m.end() - 1)); // minus 1 here because the end of a regex match is always off by 1
System.out.println();
System.out.println("|" + nucleotides.substring(m.start(),m.end())+"|......");
}
}
}
java regex
asked Nov 13 '18 at 23:25
STRSTR
164
I am using the Regex matcher for approximate string matching. I have a question regarding how to make it allow for overlapping matches. Currently, it finds a match then skips to the end of that hit and searches starting there.
Current Code
import java.util.Scanner;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
public class BNDM2 {
public static void main(String args){
Scanner sc = new Scanner(System.in);
String nucleotides,pattern;
System.out.print("Enter sequence:");
pattern = sc.nextLine();
System.out.print("Enter nucleotides:");
nucleotides= sc.nextLine();
// first convert the pattern into a proper regex
// i.e. replacing any N with [ATCG]
Pattern regex = Pattern.compile(pattern.replaceAll("N", "[ATCG]"));
// create a Matcher to find everywhere that the pattern matches
Matcher m = regex.matcher(nucleotides);
// find all the matches
while (m.find()) {
System.out.println("Match found:");
System.out.println("start:" + m.start());
System.out.println("end:" + (m.end() - 1)); // minus 1 here because the end of a regex match is always off by 1
System.out.println();
System.out.println("|" + nucleotides.substring(m.start(),m.end())+"|......");
}
}
}
java regex
java regex
asked Nov 13 '18 at 23:25
STRSTR
164
asked Nov 13 '18 at 23:25
STRSTR
164
asked Nov 13 '18 at 23:25
STRSTR
164
asked Nov 13 '18 at 23:25
STRSTR
164
asked Nov 13 '18 at 23:25
STRSTR
164
164
Can you show us a sample of your input data, the results you're getting, and the how they differ from your expected results?
– mypetlion
Nov 13 '18 at 23:29
You're probably going to need quantifiers but as mypetlion says, hard to help you without input + current output vs desired output...
– Mena
Nov 13 '18 at 23:33
add a comment |
Can you show us a sample of your input data, the results you're getting, and the how they differ from your expected results?
– mypetlion
Nov 13 '18 at 23:29
You're probably going to need quantifiers but as mypetlion says, hard to help you without input + current output vs desired output...
– Mena
Nov 13 '18 at 23:33
Can you show us a sample of your input data, the results you're getting, and the how they differ from your expected results?
– mypetlion
Nov 13 '18 at 23:29
Can you show us a sample of your input data, the results you're getting, and the how they differ from your expected results?
– mypetlion
Nov 13 '18 at 23:29
You're probably going to need quantifiers but as mypetlion says, hard to help you without input + current output vs desired output...
– Mena
Nov 13 '18 at 23:33
You're probably going to need quantifiers but as mypetlion says, hard to help you without input + current output vs desired output...
– Mena
Nov 13 '18 at 23:33
add a comment |
1 Answer
1
active
oldest
votes
0
You could use public boolean find(int start) and loop through your entire String
int index = 0;
while (index < nucleotides.length() && m.find(index)) {
//your code here
index=m.start()+1;
}
answered Nov 13 '18 at 23:38
JustinJustin
9781511
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
0
You could use public boolean find(int start) and loop through your entire String
int index = 0;
while (index < nucleotides.length() && m.find(index)) {
//your code here
index=m.start()+1;
}
answered Nov 13 '18 at 23:38
JustinJustin
9781511
add a comment |
0
You could use public boolean find(int start) and loop through your entire String
int index = 0;
while (index < nucleotides.length() && m.find(index)) {
//your code here
index=m.start()+1;
}
answered Nov 13 '18 at 23:38
JustinJustin
9781511
add a comment |
0
0
0
You could use public boolean find(int start) and loop through your entire String
int index = 0;
while (index < nucleotides.length() && m.find(index)) {
//your code here
index=m.start()+1;
}
answered Nov 13 '18 at 23:38
JustinJustin
9781511
You could use public boolean find(int start) and loop through your entire String
int index = 0;
while (index < nucleotides.length() && m.find(index)) {
//your code here
index=m.start()+1;
}
answered Nov 13 '18 at 23:38
JustinJustin
9781511
answered Nov 13 '18 at 23:38
JustinJustin
9781511
answered Nov 13 '18 at 23:38
JustinJustin
9781511
answered Nov 13 '18 at 23:38
JustinJustin
9781511
9781511
add a comment |
add a comment |
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Can you show us a sample of your input data, the results you're getting, and the how they differ from your expected results?
– mypetlion
Nov 13 '18 at 23:29
You're probably going to need quantifiers but as mypetlion says, hard to help you without input + current output vs desired output...
– Mena
Nov 13 '18 at 23:33