baseCode - 0.2.5

Clover coverage report - baseCode - 0.2.5

Coverage timestamp: Tue Apr 12 2005 11:31:58 EDT

FRAMES NO FRAMES

file stats:	LOC:	182		Methods:	12
	NCLOC:	89		Classes:	1

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Source file

Conditionals

Statements

Methods

TOTAL

GONames.java

 package baseCode.bio.geneset;
 
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
 
 import org.xml.sax.SAXException;
 
 import baseCode.bio.GOEntry;
 import baseCode.dataStructure.graph.DirectedGraph;
 import baseCode.dataStructure.graph.DirectedGraphNode;
 import baseCode.xml.GOParser;
 
 /**
  * Rea data from GO XML file, store in easy-to-use data structure.
  * <p>
  * Copyright (c) 2004 Columbia University
  * 
  * @author Paul Pavlidis
  * @author Homin Lee
  * @version $Id: GONames.java,v 1.3 2004/12/28 22:07:27 pavlidis Exp $
  */
 public class GONames {
 
    private static Map goNameMap;
    private Set newGeneSets = new HashSet();
    private GOParser parser;
 
    /**
     * @param filename <code>String</code> The XML file containing class to name mappings. First column is the class
     *        id, second is a description that will be used int program output.
     * @throws IOException
     * @throws SAXException
     */
    public GONames( String filename ) throws SAXException, IOException {
       if ( filename == null || filename.length() == 0 ) {
          throw new IllegalArgumentException(
                "Invalid filename " + filename + " or no filename was given" );
       }
 
       InputStream i = new FileInputStream( filename );
       parser = new GOParser( i );
       goNameMap = parser.getGONameMap();
    }
 
    /**
     * @param inputStream
     * @throws IOException
     * @throws SAXException
     */
    public GONames( InputStream inputStream ) throws IOException, SAXException {
       if ( inputStream == null ) {
          throw new IOException( "Input stream was null" );
       }
 
       parser = new GOParser( inputStream );
       goNameMap = parser.getGONameMap();
    }
 
    /**
     * Get the graph representation of the GO hierarchy. This can be used to support JTree representations.
     * 
     * @return
     */
    public DirectedGraph getGraph() {
       return parser.getGraph();
    }
 
    /**
     * @param id
     * @return a Set containing the ids of geneSets which are immediately below the selected one in the hierarchy.
     */
    public Set getChildren( String id ) {
       Set returnVal = new HashSet();
       Set children = ( ( DirectedGraphNode ) getGraph().get( id ) )
             .getChildNodes();
       for ( Iterator it = children.iterator(); it.hasNext(); ) {
          DirectedGraphNode child = ( DirectedGraphNode ) it.next();
          String childKey = ( ( GOEntry ) child.getItem() ).getId()
                .intern();
          returnVal.add( childKey.intern() );
       }
       return returnVal;
    }
 
    /**
     * @param id
     * @return a Set containing the ids of geneSets which are immediately above the selected one in the hierarchy.
     */
    public Set getParents( String id ) {
       Set returnVal = new HashSet();
       Set parents = ( ( DirectedGraphNode ) getGraph().get( id ) )
             .getParentNodes();
       for ( Iterator it = parents.iterator(); it.hasNext(); ) {
          DirectedGraphNode parent = ( DirectedGraphNode ) it.next();
          String parentKey = ( ( GOEntry ) parent.getItem() ).getId()
                .intern();
          returnVal.add( parentKey.intern() );
       }
       return returnVal;
    }
 
    /**
     * Get the Map representation of the GO id - name associations.
     * 
     * @return Map
     */
    public Map getMap() {
       return goNameMap;
    }
 
    /**
     * @param go_ID String
     * @return String
     */
    public String getNameForId( String go_ID ) {
 
       if ( !goNameMap.containsKey( go_ID ) ) {
          return "<no description available>";
       }
 
       return ( ( String ) ( goNameMap.get( go_ID ) ) ).intern();
    }
    
    
    /**
     * Get the aspect (molecular_function etc) for an id.
     * @param go_ID
     * @return
     */
    public String getAspectForId( String go_ID ) {
       if ( !goNameMap.containsKey( go_ID ) ) {
          return "<no aspect available>";
       }
       return ((GOEntry)getGraph().getNodeContents(go_ID)).getAspect();
    }
    
 
    /**
     * @param id String
     * @param name String
     * @todo this should modify the tree representation too.
     */
    public void addClass( String id, String name ) {
       goNameMap.put( id, name );
       newGeneSets.add( id );
    }
 
    /**
     * @param id String
     * @param name String
     * @todo this should modify the tree representation too.
     */
    public void modifyClass( String id, String name ) {
       goNameMap.put( id, name );
       newGeneSets.add( id );
    }
 
    /**
     * Check if a gene set is already defined.
     * 
     * @param id
     * @return
     */
    public boolean newSet( String id ) {
       return newGeneSets.contains( id );
    }
 
    /**
     * Return the Set of all new gene sets (ones which were added after loading the file)
     * 
     * @return
     */
    public Set getNewGeneSets() {
       return newGeneSets;
    }
 
 }

1		package baseCode.bio.geneset;
2
3		import java.io.FileInputStream;
4		import java.io.IOException;
5		import java.io.InputStream;
6		import java.util.HashSet;
7		import java.util.Iterator;
8		import java.util.Map;
9		import java.util.Set;
10
11		import org.xml.sax.SAXException;
12
13		import baseCode.bio.GOEntry;
14		import baseCode.dataStructure.graph.DirectedGraph;
15		import baseCode.dataStructure.graph.DirectedGraphNode;
16		import baseCode.xml.GOParser;
17
18		/**
19		* Rea data from GO XML file, store in easy-to-use data structure.
20		* <p>
21		* Copyright (c) 2004 Columbia University
22		*
23		* @author Paul Pavlidis
24		* @author Homin Lee
25		* @version $Id: GONames.java,v 1.3 2004/12/28 22:07:27 pavlidis Exp $
26		*/
27		public class GONames {
28
29		private static Map goNameMap;
30		private Set newGeneSets = new HashSet();
31		private GOParser parser;
32
33		/**
34		* @param filename <code>String</code> The XML file containing class to name mappings. First column is the class
35		* id, second is a description that will be used int program output.
36		* @throws IOException
37		* @throws SAXException
38		*/
39	0	public GONames( String filename ) throws SAXException, IOException {
40	0	if ( filename == null \|\| filename.length() == 0 ) {
41	0	throw new IllegalArgumentException(
42		"Invalid filename " + filename + " or no filename was given" );
43		}
44
45	0	InputStream i = new FileInputStream( filename );
46	0	parser = new GOParser( i );
47	0	goNameMap = parser.getGONameMap();
48		}
49
50		/**
51		* @param inputStream
52		* @throws IOException
53		* @throws SAXException
54		*/
55	0	public GONames( InputStream inputStream ) throws IOException, SAXException {
56	0	if ( inputStream == null ) {
57	0	throw new IOException( "Input stream was null" );
58		}
59
60	0	parser = new GOParser( inputStream );
61	0	goNameMap = parser.getGONameMap();
62		}
63
64		/**
65		* Get the graph representation of the GO hierarchy. This can be used to support JTree representations.
66		*
67		* @return
68		*/
69	0	public DirectedGraph getGraph() {
70	0	return parser.getGraph();
71		}
72
73		/**
74		* @param id
75		* @return a Set containing the ids of geneSets which are immediately below the selected one in the hierarchy.
76		*/
77	0	public Set getChildren( String id ) {
78	0	Set returnVal = new HashSet();
79	0	Set children = ( ( DirectedGraphNode ) getGraph().get( id ) )
80		.getChildNodes();
81	0	for ( Iterator it = children.iterator(); it.hasNext(); ) {
82	0	DirectedGraphNode child = ( DirectedGraphNode ) it.next();
83	0	String childKey = ( ( GOEntry ) child.getItem() ).getId()
84		.intern();
85	0	returnVal.add( childKey.intern() );
86		}
87	0	return returnVal;
88		}
89
90		/**
91		* @param id
92		* @return a Set containing the ids of geneSets which are immediately above the selected one in the hierarchy.
93		*/
94	0	public Set getParents( String id ) {
95	0	Set returnVal = new HashSet();
96	0	Set parents = ( ( DirectedGraphNode ) getGraph().get( id ) )
97		.getParentNodes();
98	0	for ( Iterator it = parents.iterator(); it.hasNext(); ) {
99	0	DirectedGraphNode parent = ( DirectedGraphNode ) it.next();
100	0	String parentKey = ( ( GOEntry ) parent.getItem() ).getId()
101		.intern();
102	0	returnVal.add( parentKey.intern() );
103		}
104	0	return returnVal;
105		}
106
107		/**
108		* Get the Map representation of the GO id - name associations.
109		*
110		* @return Map
111		*/
112	0	public Map getMap() {
113	0	return goNameMap;
114		}
115
116		/**
117		* @param go_ID String
118		* @return String
119		*/
120	0	public String getNameForId( String go_ID ) {
121
122	0	if ( !goNameMap.containsKey( go_ID ) ) {
123	0	return "<no description available>";
124		}
125
126	0	return ( ( String ) ( goNameMap.get( go_ID ) ) ).intern();
127		}
128
129
130		/**
131		* Get the aspect (molecular_function etc) for an id.
132		* @param go_ID
133		* @return
134		*/
135	0	public String getAspectForId( String go_ID ) {
136	0	if ( !goNameMap.containsKey( go_ID ) ) {
137	0	return "<no aspect available>";
138		}
139	0	return ((GOEntry)getGraph().getNodeContents(go_ID)).getAspect();
140		}
141
142
143		/**
144		* @param id String
145		* @param name String
146		* @todo this should modify the tree representation too.
147		*/
148	0	public void addClass( String id, String name ) {
149	0	goNameMap.put( id, name );
150	0	newGeneSets.add( id );
151		}
152
153		/**
154		* @param id String
155		* @param name String
156		* @todo this should modify the tree representation too.
157		*/
158	0	public void modifyClass( String id, String name ) {
159	0	goNameMap.put( id, name );
160	0	newGeneSets.add( id );
161		}
162
163		/**
164		* Check if a gene set is already defined.
165		*
166		* @param id
167		* @return
168		*/
169	0	public boolean newSet( String id ) {
170	0	return newGeneSets.contains( id );
171		}
172
173		/**
174		* Return the Set of all new gene sets (ones which were added after loading the file)
175		*
176		* @return
177		*/
178	0	public Set getNewGeneSets() {
179	0	return newGeneSets;
180		}
181
182		}