Matcher and Substring what's wrong?

Question

I'm trying to read in a large file. I have decided to do regular expressions and use the Pattern and Matcher.
It works great but for some reason it doesn't get all the text between the REB.
                         while ((line = bdr.readLine()) != null) {
                    lineLength = line.length();
                    lineNumber =  i;
                    pat = Pattern.compile("REB");
                    mat = pat.matcher(line);
                    while(mat.find()) {
                         System.out.println("  ");
                         if(checkIndex(line, mat.start()) && checkIndex(line, mat.end()+4))
                              bookName = line.substring(mat.start() + 4, mat.end() + 4);     
                         System.out.println("Book:" + bookName);
                         if(intEnd != mat.end()) {
                              intStart = intEnd;
                              intEnd = mat.end();
                         System.out.println("Start Index:" + intStart);
                         System.out.println("End Index:" + intEnd);
                         System.out.println("Line Number:" + lineNumber);
                         System.out.println("Last Index in Line:" + line.lastIndexOf(line.charAt(intEnd)));
                         System.out.println("Line Length:" + line.length());
                         if(intEnd > intStart) {
                              text = line.substring(intStart, intEnd);
                         } else {
                              text = line.substring(mat.start(), line.length());
                         System.out.println("Text:" + text);
                    i++;
               }My problem is it seems to skip 1.5, it will get 1.4 and 1.6. Is there something I'm missing? or doing wrong?
The output I get from doing this is this:
Book:Gen
Start Index:0
End Index:3
Line Number:11
Last Index in Line:11
Line Length:15
Text:REB
Book:Gen
Start Index:3
End Index:10
Line Number:12
Last Index in Line:676
Line Length:681
Text: �1�REB
Book:Gen
Start Index:10
End Index:184
Line Number:12
Last Index in Line:676
Line Length:681
Text: Genesis 1.1�IN the beginning God created the heavens and the earth.1:1�2 In . . . earth was: or When God began to create the heavens and the earth, 2the earth was.���1.2 REB
Book:Gen
Start Index:184
End Index:400
Line Number:12
Last Index in Line:676
Line Length:681
Text: Genesis 1.2�The earth was a vast waste, darkness covered the deep, and the spirit of God hovered over the surface of the water.1:2 the spirit . . . hovered: or a great wind swept; or a wind from God swept.���1.3 REB
Book:Gen
Start Index:400
End Index:473
Line Number:12
Last Index in Line:676
Line Length:681
Text: Genesis 1.3�God said, �Let there be light,� and there was light; 1.4 REB
Book:Gen
Start Index:473
End Index:563
Line Number:12
Last Index in Line:676
Line Length:681
Text: Genesis 1.4�and God saw the light was good, and he separated light from darkness. 1.5 REB
Book:Gen
Start Index:563
End Index:3
Line Number:13
Last Index in Line:11
Line Length:15
Text:REB Genesis 1.6
Book:Gen
Start Index:3
End Index:7
Line Number:14
Last Index in Line:326
Line Length:331
Text: REB
Book:Gen
Start Index:7
End Index:110
Line Number:14
Last Index in Line:326
Line Length:331
Text: Genesis 1.6     God said, �Let there be a vault between the waters, to separate water from water.� 1.7 REBThe text file looks like this.
My problem is what happend to 1.5 in the output? It's like it got skipped some how.
Revised English Bible
Revised English Bible
Old Testament
Law
Genesis
Copyright � 1989 by Oxford University Press and Cambridge University Press.
Used by permission.
GENESIS
1.1     The creation of the universe
The creation of the universe
REB Genesis 1.1
1.1 �1�REB Genesis 1.1�IN the beginning God created the heavens and the earth.1:1�2 In . . . earth was: or When God began to create the heavens and the earth, 2the earth was.���1.2 REB Genesis 1.2�The earth was a vast waste, darkness covered the deep, and the spirit of God hovered over the surface of the water.1:2 the spirit . . . hovered: or a great wind swept; or a wind from God swept.���1.3 REB Genesis 1.3�God said, �Let there be light,� and there was light; 1.4 REB Genesis 1.4�and God saw the light was good, and he separated light from darkness. 1.5 REB Genesis 1.5�He called the light day, and the darkness night. So evening came, and morning came; it was the first day.
REB Genesis 1.6
1.6 REB Genesis 1.6     God said, �Let there be a vault between the waters, to separate water from water.� 1.7 REB Genesis 1.7�So God made the vault, and separated the water under the vault from the water above it, and so it was;

Answer 1

You are also missing 1.7
"So God made the vault, and separated the water under the vault from the water above it, and so it was;"
What happens is that the line
while(mat.find()) {
steps down the line looking for the pattern "REB". But you are always taking the line upto the last match of "REB". Note that the output lines always end in "REB".
Text: Genesis 1.4�and God saw the light was good, and he separated light from darkness. 1.5 REB
So after you match this "REB" and print out the text up to it there are no more "REB" s on the line to
match so you drop out if the while loop without processing the end of the line.
A quick way to check this is to add "REB" at the end of the line and see if it picks it up.