/*
* 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.lists;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
/**
* @author jrobinso
* @date Sep 26, 2010
*/
public class GeneList {
private String group;
private boolean editable = true;
private String name;
private String description;
private List<String> loci;
private boolean showName = true;
private static Comparator<String> POSITION_COMPARATOR;
public GeneList(String name, String description, String group, List<String> loci) {
init(name, description, group, loci);
}
public GeneList(String name, List<String> loci) {
this(name, null, GeneListManager.USER_GROUP, loci);
}
public GeneList(String name, List<String> loci, boolean showName) {
this(name, null, GeneListManager.USER_GROUP, loci);
this.showName = showName;
}
public GeneList() {
this.group = GeneListManager.USER_GROUP;
}
private void init(String name, String description, String group, List<String> loci) {
this.group = group;
this.description = description;
this.name = name;
//We do this to guarantee that certain operations will be supported
this.loci = loci;
}
public String getName() {
return name;
}
public String getDisplayName() {
return showName ? name : "";
}
public List<String> getLoci() {
return loci;
}
public int size() {
return loci == null ? 0 : loci.size();
}
public void add(String gene) {
if (loci == null) {
loci = new ArrayList<String>(1);
}
try {
//Can't guarantee that list will support this operation
loci.add(gene);
} catch (Exception e) {
loci = new ArrayList<String>(loci);
loci.add(gene);
}
}
public GeneList copy() {
return new GeneList(name + " copy", loci);
}
public void setLoci(List<String> strings) {
loci = strings;
}
public void setName(String name) {
this.name = name;
}
public boolean isEditable() {
return editable;
}
public String getGroup() {
return group;
}
public void setEditable(boolean editable) {
this.editable = editable;
}
public void setGroup(String group) {
this.group = group;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
/**
* Sort loci by "position". This only sorts loci of the form chr1:100-200.
*/
// public static void sortByPosition(List<String> loci) {
// if (POSITION_COMPARATOR == null) initComparator();
//
// Collections.sort(loci, POSITION_COMPARATOR);
// }
//
// private static synchronized void initComparator() {
// POSITION_COMPARATOR = new Comparator<String>() {
// public int compare(String s1, String s2) {
// Locus l1 = Locus.fromString(s1);
// Locus l2 = Locus.fromString(s2);
// boolean l1Valid = l1 != null;
// boolean l2Valid = l2 != null;
// if (l1Valid && l2Valid) {
// return 0;
// } else if (!l1Valid) {
// return -1;
// } else if (!l2Valid) {
// return 1;
// } else if (!l1.getChr().equals(l2.getChr())) {
// return l1.getChr().compareTo(l2.getChr());
// } else {
// return l1.getStart() - l2.getStart();
// }
// }
//
// };
// }
public void sort(Comparator<String> comparator) {
Collections.sort(this.loci, comparator);
}
}