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 * @(#)Partition.java
022 */
023
024 package edu.upenn.crimson;
025
026 import edu.upenn.crimson.io.*;
027
028 /**
029 * Partition header info.
030 *
031 * @author Stephen Fisher
032 * @version $Id: Partition.java,v 1.16 2007/05/16 18:55:58 fisher Exp $
033 */
034
035 public class Partition {
036
037 /** This is a unique name for the partition object. */
038 private String id = "";
039
040 /** This is the tree structure for this partition. */
041 private String treeID = "";
042
043 /** Model specific to this partition object. */
044 private String modelID = "";
045
046 /** Notes specific to this partition object. */
047 private String notes = "";
048
049 /**
050 * Total length of the partition's sequence. This shouldn't be
051 * changed after the partition is created.
052 */
053 private int length = 0;
054
055 public Partition(String id, Tree tree) {
056 this(id, tree, null, 0, "");
057 }
058
059 public Partition(String id, Tree tree, Model model, int length, String notes) throws InvalidIDException {
060 // if no ID, then error
061 if (CrimsonUtils.isEmpty(id)) {
062 CrimsonUtils.printError("Invalid partition ID.");
063 throw new InvalidIDException("Partition ID can not be empty.");
064 } else if (ObjectHandles.containsPartition(id)) {
065 CrimsonUtils.printError("Partition ID already exists, much specify a different ID:" + id);
066 throw new InvalidIDException("Partition ID already exists.");
067
068 }
069
070 this.id = id.trim().toUpperCase();
071 this.length = length;
072 this.notes = notes;
073
074 // we require a model object rather than an ID, to make sure
075 // that the model really exists.
076 if (model != null) this.modelID = model.getID();
077
078 // by protecting against null trees, we are effectively
079 // allowing for the creation of partitions that are not
080 // attached to trees. These will need to be attached to a
081 // tree manually.
082 if (tree != null) tree.addPartition(this);
083
084 // add the tree to the relevant lists
085 ObjectHandles.addPartition(this);
086 }
087
088 //--------------------------------------------------------------------------
089 // Setters and Getters
090
091 public String getID() { return id; }
092
093 /** Get the ID for the tree containing this partition. */
094 public String getTreeID() { return treeID; }
095
096 /**
097 * Sets the ID for the model underlying this partition. We require
098 * a model object rather than an ID, to make sure that the model
099 * really exists.
100 */
101 public void setModelID(Model model) {
102 if (model == null) return;
103
104 this.modelID = model.getID();
105
106 // update the PARTITIONS database
107 if (! Partitions.dbContains(id)) {
108 CrimsonUtils.printError("Partition (" + id + ") not in database, model ID not saved to database.");
109 return;
110 }
111
112 // UPDATE partitions SET model_id = modelID WHERE id = id
113 String sql = "UPDATE partitions SET model_id = '" + modelID.toUpperCase();
114 sql += "' WHERE id = '" + id.toUpperCase() + "' AND tree_id = '" + treeID.toUpperCase() + "'";
115 if (! Database.execUpdate(sql))
116 CrimsonUtils.printError("Error updating model_id in partition " + id + ".");
117 }
118
119 /** Returns the ID for the model underlying this partition. */
120 public String getModelID() { return modelID; }
121
122 /**
123 * Updates the notes field in the partition object and the
124 * PARTITIONS table.
125 */
126 public void setNotes(String notes) {
127 this.notes = notes;
128
129 // update the TREES database
130 if (! Partitions.dbContains(id)) {
131 CrimsonUtils.printError("Partition (" + id + ") not in database, partition notes not updated.");
132 return;
133 }
134
135 // UPDATE partitions SET notes = notes WHERE id = id
136 String sql = "UPDATE partitions SET notes = '" + notes;
137 sql += "' WHERE id = '" + id.toUpperCase() + "' AND tree_id = '" + treeID.toUpperCase() + "'";
138 if (! Database.execUpdate(sql))
139 CrimsonUtils.printError("Error updating notes in partition " + id + ".");
140 }
141
142 public String getNotes() { return notes; }
143
144 public int getLength() { return length; }
145
146 //--------------------------------------------------------------------------
147 // Miscellaneous Methods
148
149 /** Returns Partition information. */
150 public String toString() {
151 if (CrimsonUtils.isEmpty(modelID)) {
152 return id + " (" + length + " bp)";
153 } else {
154 return id + " (" + length + " bp, " + modelID + ")";
155 }
156 }
157
158 } // Partition.java