package org.biojava.bio.program.tagvalue; import java.util.regex.Matcher; import java.util.regex.Pattern; import org.biojava.utils.ParserException; /** *
* A TagValueParser that splits a line based upon a regular expression. There * are configuration parameters analgous to those in LineSplitParser for * configuring parsing details. *
* * @author Matthew Pocock * @author Keith James (enabled empty line EOR) * @since 1.3 */ public class RegexParser implements TagValueParser { private Pattern pattern = null; private int tagGroup = -1; private int valueGroup = -1; private String endOfRecord = null; private boolean trimTag = false; private boolean trimValue = false; private boolean continueOnEmptyTag = false; private boolean mergeSameTag = false; private String tag; /** * Create a new RegexParser with all boolean values set to false. */ public RegexParser() {} /** * Set the Pattern used to split lines. * * @param pattern the Pattern used to split lines */ public void setPattern(Pattern pattern) { this.pattern = pattern; } /** * Get the Pattern currently used to split lines. * * @return the current Pattern */ public Pattern getPattern() { return pattern; } /** * Set the group number that will match the tag. * * @param group the tag group number */ public void setTagGroup(int group) { this.tagGroup = group; } /** * Get the group number that matches the tag. * * @return the tag group number */ public int getTagGroup() { return tagGroup; } /** * Set the group number that will match the value. * * @param group the value group number */ public void setValueGroup(int group) { this.valueGroup = group; } /** * Get the group number that matches the value. * * @return the value group number */ public int getValueGroup() { return valueGroup; } /** * Set the explicit end-of-record string. * * @param endOfRecord the new endOfRecord String */ public void setEndOfRecord(String endOfRecord) { this.endOfRecord = endOfRecord; } /** * Get the explicit end-of-record string. * * @return the current endOfRecord String */ public String getEndOfRecord() { return endOfRecord; } /** * Enable trimming of the tag using String.trim(). * * @param trimTag true if tags should be trimmed, false otherwise */ public void setTrimTag(boolean trimTag) { this.trimTag = trimTag; } /** * See if trimming of tags is enabled. * * @return true if tag trimming is enabled, false otherwise */ public boolean getTrimTag() { return trimTag; } /** * Enable trimming of the value using String.trim(). * * @param trimValue true if values should be trimmed, false otherwise */ public void setTrimValue(boolean trimValue) { this.trimValue = trimValue; } /** * See if trimming of values is enabled. * * @return true if value trimming is enabled, false otherwise */ public boolean getTrimValue() { return trimValue; } /** * Decide whether to treat empty tags as continuations of the previous non * -empty tag. * * @param continueOnEmptyTag true if empty tags should be replaced, false * otherwise */ public void setContinueOnEmptyTag(boolean continueOnEmptyTag) { this.continueOnEmptyTag = continueOnEmptyTag; } /** * Report whether empty tags will be treated as continuations of the last non * -empty tag. * * @return true if empty tags will be replaced, false otherwise */ public boolean getContinueOnEmptyTag() { return continueOnEmptyTag; } /** * Decide if multiple examples of a single tag should be merged into a single * start/endTag pair with multiple values, or multiple start/endTag pairs each * with a single value. * * @param mergeSameTag true if tags will be merged, false otherwise */ public void setMergeSameTag(boolean mergeSameTag) { this.mergeSameTag = mergeSameTag; } /** * Report whether empty tags will be treated as continuations of the last non * -empty tag. * * @return true if tags will be merged, false otherwise */ public boolean getMergeSameTag() { return mergeSameTag; } public TagValue parse(Object o) throws ParserException { String line = o.toString(); // Use of the special value for the EOR marker allows a blank line // to be used to delimit records. Many file formats are like this. if (endOfRecord != null) { if (endOfRecord == TagValueParser.EMPTY_LINE_EOR) { if (line.equals(TagValueParser.EMPTY_LINE_EOR)) { return null; } } else { if (line.startsWith(endOfRecord)) { return null; } } } Matcher matcher = pattern.matcher(line); if(!matcher.find()) { throw new ParserException("Could not match " + pattern.pattern() + " to " + line); } String tag = matcher.group(tagGroup); if(trimTag) { tag = tag.trim(); } String value = matcher.group(valueGroup); if(trimValue) { value = value.trim(); } if(continueOnEmptyTag && (tag.length() == 0)) { return new TagValue(this.tag, value, false); } else if(mergeSameTag && tag.equals(this.tag)) { return new TagValue(tag, value, false); } else { return new TagValue(this.tag = tag, value, true); } } }