/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.tools.parsers;
import org.broad.igv.track.TrackType;
import java.util.Hashtable;
/**
* @author jrobinso
*/
public abstract class AbstractParser {
private static Hashtable<String, String> chromosomeNames = new Hashtable();
private DataConsumer dataConsumer;
String trackLine = null;
private TrackType trackType = TrackType.COPY_NUMBER;
private String[] headings;
public AbstractParser(DataConsumer dataConsumer) {
this.dataConsumer = dataConsumer;
}
/**
* @return the dataConsumer
*/
public DataConsumer getDataConsumer() {
return dataConsumer;
}
protected void setTrackParameters() {
dataConsumer.setTrackParameters(trackType, trackLine, headings);
}
/**
* Note: This is an exact copy of the method in ExpressionFileParser. Refactor to merge these
* two parsers, or share a common base class.
*
* @param comment
*/
void parseComment(String comment) {
String tmp = comment.substring(1, comment.length());
if (tmp.startsWith("track")) {
trackLine = tmp;
} else {
String[] tokens = tmp.split("=");
if (tokens.length != 2) {
return;
}
String key = tokens[0].trim().toLowerCase();
if (key.equals("type")) {
try {
setTrackType(TrackType.valueOf(tokens[1].trim().toUpperCase()));
} catch (Exception exception) {
}
}
}
}
/**
* @param headings the headings to set
*/
public void setHeadings(String[] headings) {
this.headings = headings;
}
/**
* @return the headings
*/
public String[] getHeadings() {
return headings;
}
/**
* @return the trackType
*/
public TrackType getTrackType() {
return trackType;
}
/**
* @param trackType the trackType to set
*/
public void setTrackType(TrackType trackType) {
this.trackType = trackType;
}
}