2 * This file is part of the Vamsas Client version 0.2.
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3 * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
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4 * Andrew Waterhouse and Dominik Lindner.
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6 * Earlier versions have also been incorporated into Jalview version 2.4
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7 * since 2008, and TOPALi version 2 since 2007.
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9 * The Vamsas Client is free software: you can redistribute it and/or modify
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10 * it under the terms of the GNU Lesser General Public License as published by
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11 * the Free Software Foundation, either version 3 of the License, or
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12 * (at your option) any later version.
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14 * The Vamsas Client is distributed in the hope that it will be useful,
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15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 * GNU Lesser General Public License for more details.
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19 * You should have received a copy of the GNU Lesser General Public License
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20 * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
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22 package uk.ac.vamsas.objects.utils;
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24 import java.io.IOException;
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26 import uk.ac.vamsas.objects.core.Tree;
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27 import uk.ac.vamsas.objects.utils.trees.NewickFile;
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29 public class Trees {
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32 * TODO: implement helper functions based on NewickFile tree parser
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34 * 1. create a newickfile object from a newick string. 2. let user map a
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35 * vamsas object to each node by setting that node's
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36 * ((SequenceNode)node).setElement(VorbaId) 3. generate Tree object with
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37 * newickString as a newick string, and added treenodes to record mapping to
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