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Client library for the URI-based RESTful service for the gl project.
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/*
gl-client Client library for the URI-based RESTful service for the gl project.
Copyright (c) 2012-2015 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
*/
package org.nmdp.gl.client;
import com.google.common.base.CharMatcher;
/**
* Fluent builder-style client API for creating GL String-formatted representations of gl resources.
*/
public final class GlstringBuilder {
// todo: replace this hack with antlr grammar
private String locus;
private Tree tree = new Tree();
private static final CharMatcher operators = CharMatcher.anyOf("/~+|^");
/**
* Return this GL String builder configured with the specified locus. If an allele has already been added
* to this builder, this call provides the locus operator ('^' character). The locus
* operator combines two or more genotype lists into a multilocus unphased genotype.
*
* As an operator, calls to this method must be interspersed by calls to {@link #allele(String)}.
*
* @param glstring locus in GL String format, must not be null
* @return this GL String builder configured with the specified locus
* @throws IllegalStateException if successive calls to any operator methods ({@link #allelicAmbiguity()},
* {@link #inPhase()}, {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)}) are
* made without an interspersed call to {@link #allele(String)}
*/
public GlstringBuilder locus(final String glstring) {
if (tree.isEmpty()) {
locus = glstring;
}
else if (tree.root.isOperator() && tree.root.right == null) {
throw new IllegalStateException("must call allele(String) between successive calls to any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
else {
Node root = new Node();
root.value = "^";
root.left = tree.root;
tree.root = root;
}
return this;
}
/**
* Return this GL String builder configured with the specified allele. Calls to this method must
* be interspersed by calls to operator methods ({@link #allelicAmbiguity()}, {@link #inPhase()},
* {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)}).
*
* @param glstring allele in GL String format, must not be null
* @return this GL String builder configured with the specified allele
* @throws IllegalStateException if successive calls to this method are made without an interspersed
* call to an operator method ({@link #allelicAmbiguity()}, {@link #inPhase()}, {@link #plus()},
* {@link #genotypicAmbiguity()}, and {@link #locus(String)})
*/
public GlstringBuilder allele(final String glstring) {
Node node = new Node();
node.value = glstring;
if (tree.isEmpty()) {
tree.root = node;
}
else {
if (!tree.root.isOperator()) {
throw new IllegalStateException("must provide an operator(allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus) between successive calls to allele(glstring)");
}
if (tree.root.left == null) {
tree.root.left = node;
}
else if (tree.root.right == null) {
tree.root.right = node;
}
else {
// todo: is this ever reached?
throw new IllegalStateException("must provide an operator(allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus) between successive calls to allele(glstring)");
}
}
return this;
}
/**
* Return this GL String builder configured with an allelic ambiguity operator ('/' character).
* The allelic ambiguity operator combines two or more alleles into an allele list.
*
* As an operator, calls to this method must be interspersed by calls to {@link #allele(String)}.
*
* @return this GL String builder configured with an allelic ambiguity operator ('/' character)
* @throws IllegalStateException if successive calls to any operator methods ({@link #allelicAmbiguity()},
* {@link #inPhase()}, {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)}) are
* made without an interspersed call to {@link #allele(String)}
*/
public GlstringBuilder allelicAmbiguity() {
if (tree.isEmpty()) {
throw new IllegalStateException("must call allele(String) before any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
if (tree.root.isOperator() && tree.root.right == null) {
throw new IllegalStateException("must call allele(String) between successive calls to any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
Node root = new Node();
root.value = "/";
root.left = tree.root;
tree.root = root;
return this;
}
/**
* Return this GL String builder configured with an in phase operator ('~' character).
* The in phase operator combines two or more allele lists into a haplotype.
*
* As an operator, calls to this method must be interspersed by calls to {@link #allele(String)}.
*
* @return this GL String builder configured with an in phase operator ('~' character)
* @throws IllegalStateException if successive calls to any operator methods ({@link #allelicAmbiguity()},
* {@link #inPhase()}, {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)}) are
* made without an interspersed call to {@link #allele(String)}
*/
public GlstringBuilder inPhase() {
if (tree.isEmpty()) {
throw new IllegalStateException("must call allele(String) before any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
if (tree.root.isOperator() && tree.root.right == null) {
throw new IllegalStateException("must call allele(String) between successive calls to any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
Node root = new Node();
root.value = "~";
root.left = tree.root;
tree.root = root;
return this;
}
/**
* Return this GL String builder configured with an plus operator ('+' character). The
* plus operator combines two or more haplotypes into a genotype.
*
* As an operator, calls to this method must be interspersed by calls to {@link #allele(String)}.
*
* @return this GL String builder configured with an plus operator ('+' character)
* @throws IllegalStateException if this operator method is called before a call to {@link #allele(String)}
* @throws IllegalStateException if successive calls to any operator methods ({@link #allelicAmbiguity()},
* {@link #inPhase()}, {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)}) are
* made without an interspersed call to {@link #allele(String)}
*/
public GlstringBuilder plus() {
if (tree.isEmpty()) {
throw new IllegalStateException("must call allele(String) before any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
if (tree.root.isOperator() && tree.root.right == null) {
throw new IllegalStateException("must call allele(String) between successive calls to any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
Node root = new Node();
root.value = "+";
root.left = tree.root;
tree.root = root;
return this;
}
/**
* Return this GL String builder configured with a genotypic ambiguity operator ('|' character).
* The genotypic ambiguity operator combines two or more genotypes into a genotype list.
*
* As an operator, calls to this method must be interspersed by calls to {@link #allele(String)}.
*
* @return this GL String builder configured with a genotypic ambiguity operator ('|' character)
* @throws IllegalStateException if this operator method is called before a call to {@link #allele(String)}
* @throws IllegalStateException if successive calls to any operator methods ({@link #allelicAmbiguity()},
* {@link #inPhase()}, {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)}) are
* made without an interspersed call to {@link #allele(String)}
*/
public GlstringBuilder genotypicAmbiguity() {
if (tree.isEmpty()) {
throw new IllegalStateException("must call allele(String) before any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
if (tree.root.isOperator() && tree.root.right == null) {
throw new IllegalStateException("must call allele(String) between successive calls to any operator (allelicAmbiguity, inPhase, plus, genotypicAmbiguity, locus)");
}
Node root = new Node();
root.value = "|";
root.left = tree.root;
tree.root = root;
return this;
}
/**
* Return this GL String builder with its configuration reset.
*
* @return this GL String builder with its configuration reset
*/
public GlstringBuilder reset() {
tree.root = null;
return this;
}
/**
* Build and return a new GL String configured from the properties of this GL String builder.
*
* @return a new GL String configured from the properties of this GL String builder
* @throws IllegalStateException if {@link #locus(String)} or {@link #allele(String)} has not been called at least once
* @throws IllegalStateException if the last call was an operator ({@link #allelicAmbiguity()}, {@link #inPhase()},
* {@link #plus()}, {@link #genotypicAmbiguity()}, and {@link #locus(String)})
*/
public String build() {
if (locus == null && tree.isEmpty()) {
throw new IllegalStateException("must call locus(String) or allele(String) at least once");
}
if (tree.isEmpty()) {
return locus;
}
String glstring = tree.toString();
char last = glstring.charAt(glstring.length() - 1);
if (operators.matches(last)) {
throw new IllegalStateException("last element of a glstring must not be an operator, was " + last);
}
return glstring;
}
private final class Tree {
Node root;
boolean isEmpty() {
return root == null;
}
private void dfs(final Node node, final StringBuilder sb) {
if (node.left != null) {
dfs(node.left, sb);
}
sb.append(node.value);
if (node.right != null) {
dfs(node.right, sb);
}
}
@Override
public String toString() {
if (root == null) {
return "";
}
if (root.isLeaf()) {
return root.value;
}
StringBuilder sb = new StringBuilder();
dfs(root, sb);
return sb.toString();
}
}
private final class Node {
Node left;
Node right;
String value;
boolean isLeaf() {
return left == null && right == null;
}
boolean isOperator() {
return operators.matchesAnyOf(value);
}
}
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