/*
* 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.
*/
package org.broad.igv.feature;
public class Cytoband implements NamedFeature {
String chromosome;
String name;
String longName;
int end;
int start;
char type; // p, n, or c
short stain;
public Cytoband(String chromosome) {
this.chromosome = chromosome;
this.name = "";
}
public void trim() {
// @todo -- trim arrays
}
@Override
public String getContig() {
return chromosome;
}
public String getChr() {
return chromosome;
}
public void setName(String name) {
this.name = name;
}
public String getName() {
return name;
}
public String getLongName() {
if(longName == null) {
longName = chromosome.replace("chr", "") + name;
}
return longName;
}
public void setEnd(int end) {
this.end = end;
}
public int getEnd() {
return end;
}
public void setStart(int start) {
this.start = start;
}
public int getStart() {
return start;
}
public void setType(char type) {
this.type = type;
}
public char getType() {
return type;
}
public void setStain(short stain) {
this.stain = stain;
}
public short getStain() {
return stain;
}
}