org.biojavax.utils.StringTools Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojavax.utils;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Utility class for formatting strings into regular-sized blocks.
* @author Richard Holland
* @since 1.5
*/
public class StringTools {
// Static methods so should never be instantiated.
private StringTools() {}
/**
* Takes an input string and appends spaces to the left. Ignores
* any existing leading whitespace when counting the indent size.
* @param input the input string
* @param leftIndent the number of spaces to indent it by.
* @return the indented string.
*/
public static String leftIndent(String input, int leftIndent) {
StringBuffer b = new StringBuffer();
for (int i = 0; i < leftIndent; i++) b.append(" "); // yuck!
b.append(input);
return b.toString();
}
/**
* Pads a string to be a certain width by prepending spaces.
* @param input the string to pad.
* @param totalWidth the final width required including padded space.
*/
public static String leftPad(String input, int totalWidth) {
return leftPad(input, ' ', totalWidth);
}
/**
* Pads a string to be a certain width by prepending given symbols.
* @param input the string to pad.
* @param padChar the symbol to pad with.
* @param totalWidth the final width required including padded symbols.
*/
public static String leftPad(String input, char padChar, int totalWidth) {
StringBuffer b = new StringBuffer();
b.append(input);
while(b.length()=start && newline= input.length()) splitPoint=input.length();
//hard case, have to split it!
else {
//if not match sep, find first point that does
while (splitPoint>=start) {
char c = input.charAt(splitPoint);
Matcher m = p.matcher(""+c);
if (m.matches()) {
splitPoint+=1;// splitpoint is index of separator - include on this line - assumes a single character separator
break;
}
splitPoint--;
}
//if ended up at splitPoint=start, splitPoint=start+width
//in order to break word mid-way through
if (splitPoint<=start) splitPoint = start+width;
}
//trailing blanks - which may include the separator - are not in genbank lines - so they are removed
//output chunk from start to splitPoint - do not include trailing newline - it will be added by writeKeyValueLine
lines.add(trimTrailingBlanks(newline==splitPoint-1?input.substring(start, splitPoint-1):input.substring(start, splitPoint)));
start=splitPoint;// start right after the separator
}
return (String[])lines.toArray(new String[0]);
}
private final static String trimTrailingBlanks(final String theString) {
if (theString.length() ==0 || theString.charAt(theString.length()-1) != ' ') return theString;
int len = theString.length();
final char[] val = theString.toCharArray();
while (len > 0 && (val[len - 1] <= ' ')) len--;
return ((len < theString.length())) ? theString.substring(0, len) : theString;
}
/**
* Writes some text to the output stream in the following format:
* key text
* continuation of text
* where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
* and the text is split over multiple lines at the nearest occurrence of whitespace.
* @param key the key to write on the first line only
* @param text the text to write out
* @param keyWidth the width to indent the text by (in which the key will be printed)
* @param os the stream to write the formatted output to
*/
public static void writeKeyValueLine(String key, String text, int keyWidth, int lineWidth, PrintStream os) {
writeKeyValueLine(key,text,keyWidth,lineWidth,null,null,os);
}
/**
* Writes some text to the output stream in the following format:
* key text
* continuation of text
* where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
* and the text is split over multiple lines at the nearest occurrence of separator sep.
* @param key the key to write on the first line only
* @param text the text to write out
* @param keyWidth the width to indent the text by (in which the key will be printed)
* @param sep the separator to split the text on if it exceeds the line width
* @param os the stream to write the formatted output to
*/
public static void writeKeyValueLine(String key, String text, int keyWidth, int lineWidth, String sep, PrintStream os) {
writeKeyValueLine(key,text,keyWidth,lineWidth,sep,null,os);
}
/**
* Writes some text to the output stream in the following format:
* key text
* wrappedKey continuation of text
* where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth,
* and the text is split over multiple lines at the nearest occurrence of separator sep.
* @param key the key to write on the first line only
* @param text the text to write out
* @param keyWidth the width to indent the text by (in which the key will be printed)
* @param sep the separator to split the text on if it exceeds the line width
* @param wrappedKey the key to print on second and subsequent lines
* @param os the stream to write the formatted output to
*/
public static void writeKeyValueLine(String key, String text, int keyWidth, int lineWidth, String sep, String wrappedKey, PrintStream os) {
if (key==null || text==null) return; // skip blank lines
if (wrappedKey==null) wrappedKey=""; // stop null pointer exceptions on wrapped keys
if (sep==null) sep="\\s+"; // stop null pointer exceptions on the separator
// text = text.trim(); // trim leading/trailing whitespace from text - this deletes leading blank lines from comments: e.g. AC140936
String[] lines = StringTools.wordWrap(text, sep, lineWidth-keyWidth);
if (lines.length==0) os.println(StringTools.rightPad(key,keyWidth));
else {
lines[0] = StringTools.rightPad(key,keyWidth)+
lines[0];
os.println(lines[0]);
for (int i = 1; i < lines.length; i++) os.println(StringTools.rightPad(wrappedKey,keyWidth)+lines[i]);
}
}
}
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