001 /*
002 * CRIMSON
003 * Copyright (c) 2006, Stephen Fisher, Susan Davidson, and Junhyong Kim,
004 * University of Pennsylvania.
005 *
006 * This program is free software; you can redistribute it and/or
007 * modify it under the terms of the GNU General Public License as
008 * published by the Free Software Foundation; either version 2 of the
009 * License, or (at your option) any later version.
010 *
011 * This program is distributed in the hope that it will be useful, but
012 * WITHOUT ANY WARRANTY; without even the implied warranty of
013 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
014 * General Public License for more details.
015 *
016 * You should have received a copy of the GNU General Public License
017 * along with this program; if not, write to the Free Software
018 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
019 * 02110-1301 USA.
020 *
021 * @(#)Trees.java
022 */
023
024 package edu.upenn.crimson.io;
025
026 import edu.upenn.crimson.*;
027 import java.util.ArrayList;
028 import java.util.Iterator;
029
030 /**
031 * Functions related to the TREES table.
032 *
033 * @author Stephen Fisher
034 * @version $Id: Trees.java,v 1.28 2009/07/16 16:19:52 fisher Exp $
035 */
036
037 public class Trees {
038
039 //--------------------------------------------------------------------------
040 // Miscellaneous Methods
041
042 /** This will load all trees from the TREES table. */
043 public static void loadAll() {
044 // make sure a database is open. We don't need to check for
045 // the existance of the TREES database because this was done
046 // when the database was opened.
047 if (! Database.isOpen()) {
048 CrimsonUtils.printError("Unable to build tree list, no open database.");
049 return;
050 }
051
052 // clear the lists before we start
053 ObjectHandles.clearTreeLists();
054
055 CrimsonUtils.printMsg("Loading tree info...");
056
057 // get the list of trees in the TREES table.
058 String sql = "SELECT id, model_id, notes, num_species, num_leaves, ";
059 sql += "is_binary, is_ultrametric, min_level, max_level, min_temp_depth, max_temp_depth, ";
060 sql += "min_stem_length, max_stem_length FROM TREES";
061 ArrayList results = Database.sqlToArray(sql);
062
063 // if the query failed then exit
064 if (results == null) {
065 CrimsonUtils.printError("Unable to build tree lists, error accessing TREES table.");
066 return;
067 }
068
069 // convert each row in the results to a Tree
070 for (Iterator rows = results.iterator(); rows.hasNext();) {
071 ArrayList row = (ArrayList) rows.next();
072
073 // we load the stats from the table so we don't need
074 // to build the tree and compute the stats.
075 new Tree(String.valueOf(row.get(0)), null,
076 ObjectHandles.getModel(String.valueOf(row.get(1))),
077 String.valueOf(row.get(2)),
078 Integer.parseInt(String.valueOf(row.get(3))),
079 Integer.parseInt(String.valueOf(row.get(4))),
080 (String.valueOf(row.get(5)).equals("1") ? true : false),
081 (String.valueOf(row.get(6)).equals("1") ? true : false),
082 Integer.parseInt(String.valueOf(row.get(7))),
083 Integer.parseInt(String.valueOf(row.get(8))),
084 Double.parseDouble(String.valueOf(row.get(9))),
085 Double.parseDouble(String.valueOf(row.get(10))),
086 Double.parseDouble(String.valueOf(row.get(11))),
087 Double.parseDouble(String.valueOf(row.get(12))));
088 }
089 }
090
091 /**
092 * Removes a tree from the database. When trees are deleted, the
093 * database will automatically remove the related entries in the
094 * PARTITIONS and PART_DATA table. If delQueries is true then
095 * remove any queries that reference this tree. If delQueries is
096 * false, then quit on error if any queries reference this tree.
097 * @XXX We aren't relying on the database sutomatic cascade
098 * deleting of records because the version of MySQL prior to 5.1
099 * do not support this fuction for MyISAM tables, which are the
100 * tables we are using.
101 */
102 public static boolean delete(String id, boolean delQueries) {
103 if (! ObjectHandles.containsTree(id)) {
104 CrimsonUtils.printWarning("Tree '" + id + "' doesn't exist and thus can't be deleted.");
105 return false;
106 }
107
108 id = id.toUpperCase();
109 String queries = "";
110 ArrayList qToDelete = new ArrayList();
111 for (Iterator i = ObjectHandles.queryIterator(); i.hasNext();) {
112 Query query = (Query) i.next();
113 if (id.equals(query.getTreeID())) {
114 if (delQueries) {
115 CrimsonUtils.printWarning("Query '" + query.getID() + "' being deleted.");
116 qToDelete.add(query.getID());
117 } else {
118 queries += " Query: " + query.getID() + "\n";
119 }
120 }
121 }
122
123 if (! CrimsonUtils.isEmpty(queries)) {
124 CrimsonUtils.printError("Queries exist that reference the tree '" + id + "'.");
125 CrimsonUtils.printError("These queries must be changed to reference other trees before this tree can be deleted.");
126 CrimsonUtils.printError("If these queries are in the database, then the changes must be published to the database.\n" + queries);
127 return false;
128 } else if (qToDelete.size() > 0) {
129 for (Iterator i = qToDelete.iterator(); i.hasNext();) {
130 Queries.delete((String) i.next());
131 }
132 }
133
134 Tree tree = ObjectHandles.getTree(id);
135 for (Iterator i = tree.getPartitions().iterator(); i.hasNext();) {
136 Partition partition = (Partition) i.next();
137 if (! Partitions.delete(partition.getID())) return false;
138 }
139
140 // if successfully delete all partitions, then delete the tree
141 if (! Database.delete("TREES", id)) return false;
142
143 // rebuild tree and partition list
144 loadAll();
145 Partitions.loadAll();
146
147 return true;
148 }
149
150 /**
151 * This will return true if a tree exists in TREES with an id
152 * equal to 'id'.
153 */
154 public static boolean dbContains(String id) {
155 ArrayList out = Database.sqlToArray("SELECT id FROM TREES WHERE id = '" + id.toUpperCase() + "'");
156 if ((out == null) || (out.size() == 0)) return false;
157 else return true;
158 }
159
160 /**
161 * Returns the non-Blob columns in the TREES table. Each table
162 * record will be separated by a '\n' in the output.
163 */
164 public String toString() {
165 // SELECT id, species, max_temp_depth, notes FROM trees;
166 String sql = "SELECT ID, MODEL_ID, NOTES FROM TREES";
167 ArrayList results = Database.sqlToArray(sql);
168
169 if (results == null) {
170 CrimsonUtils.printError("Error printing TREES table.");
171 return "";
172 }
173
174 StringBuffer out = new StringBuffer("");
175 out.append("ID \t MODEL_ID \t NOTES\n");
176 for (Iterator rows = results.iterator(); rows.hasNext();) {
177 ArrayList row = (ArrayList) rows.next();
178 for (int i = 0; i < 2; i++) out.append(String.valueOf(row.get(i)) + " \t ");
179 out.append(String.valueOf(row.get(2)) + "\n");
180 }
181
182 return out.toString().trim();
183 }
184
185 } // Trees.java