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:	149		Methods:	4
	NCLOC:	81		Classes:	1

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Source file

Conditionals

Statements

Methods

TOTAL

GroupMap.java

 package baseCode.misc;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed;
 import baseCode.io.reader.MapReader;
 
 /**
  * A data structure representing a map between items and a single set of keys. For example, a set of probes and the
  * genes they map to. Probes that point to the same gene are in the same "group".
  * <p>
  * Copyright (c) 2004
  * </p>
  * <p>
  * Institution: Columbia University
  * </p>
  * 
  * @author Paul Pavlidis
  * @version $Id: GroupMap.java,v 1.3 2004/07/27 03:18:58 pavlidis Exp $
  */
 
 public class GroupMap {
 
    private int uniqueItems;
    private Map duplicateMap;
    private static Log log = LogFactory.getLog( GroupMap.class );
 
    /**
     * @return int The number of unique items in the GroupMap.
     */
    public int getUniqueItems() {
       return uniqueItems;
    }
 
    /**
     * For a given key, return true if it has duplicates.
     * 
     * @param k String
     * @return boolean
     */
    public boolean hasDuplicates( String k ) {
       return numDuplicates( k ) > 0;
    }
 
    /**
     * For a given key, return the number of duplicates it has (not counting itself).
     * 
     * @param k String
     * @return int
     */
    public int numDuplicates( String k ) {
       return ( ( HashSet ) duplicateMap.get( k ) ).size();
    }
 
    /**
     * The input file format is that used by {@link baseCode.io.reader.MapReader}.
     * 
     * @param filename Duplicate map file name to be read by a MapReader.
     * @param dataMatrix Data file this the map refers to.
     * @return Map
     * @throws IOException
     */
    public Map read( String filename, DenseDoubleMatrix2DNamed dataMatrix )
          throws IOException {
 
       if ( filename == null || dataMatrix == null ) {
          throw new IllegalArgumentException(
                "You must give a valid file name and data matrix." );
       }
 
       MapReader m = new MapReader();
       Map initialMap = m.read( filename );
       Map insideOutMap = new HashMap();
 
       // first we turn the map inside-out so we have gene --> probeA, probeB,
       // probeC.
       Set keys = initialMap.keySet();
       for ( Iterator it = keys.iterator(); it.hasNext(); ) {
          String p = ( String ) it.next();
 
          if ( !dataMatrix.hasRow( p ) ) {
             continue;
          }
 
          String v = ( String ) initialMap.get( p );
 
          if ( insideOutMap.get( v ) == null ) {
             insideOutMap.put( v, new ArrayList() );
          }
          ( ( ArrayList ) insideOutMap.get( v ) ).add( p );
       }
 
       uniqueItems = insideOutMap.size();
       log.info( uniqueItems + " unique items read from duplicate map" );
 
       // turn that map into a map of probeA --> probe1, probe2, where probes1
       // and probes2 are in the same 'group' as probeA
       this.duplicateMap = new HashMap();
       keys = insideOutMap.keySet();
       for ( Iterator it = keys.iterator(); it.hasNext(); ) {
          String g = ( String ) it.next();
          ArrayList v = ( ArrayList ) insideOutMap.get( g );
 
          for ( Iterator vit = v.iterator(); vit.hasNext(); ) {
             String p = ( String ) vit.next();
             if ( duplicateMap.get( p ) == null ) {
                duplicateMap.put( p, new HashSet() );
             }
 
             for ( Iterator kit = v.iterator(); kit.hasNext(); ) {
                String pp = ( String ) kit.next();
                if ( p.equals( pp ) ) {
                   continue;
                }
 
                ( ( Set ) duplicateMap.get( p ) ).add( pp );
             }
          }
       }
 
       // now a sanity check. Make sure every item in our data is also in the
       // duplicate map.
       for ( Iterator it = dataMatrix.getRowNameMapIterator(); it.hasNext(); ) {
          boolean foundProblem = false;
          String rowName = ( String ) it.next();
          if ( !duplicateMap.containsKey( rowName ) ) {
             duplicateMap.put( rowName, new HashSet() );
             foundProblem = true;
          }
          if ( foundProblem ) {
             throw new IllegalStateException(
                   "The data has item(s) that aren't in the duplicate map." );
          }
       }
 
       return this.duplicateMap;
 
    }
 
 }

1		package baseCode.misc;
2
3		import java.io.IOException;
4		import java.util.ArrayList;
5		import java.util.HashMap;
6		import java.util.HashSet;
7		import java.util.Iterator;
8		import java.util.Map;
9		import java.util.Set;
10
11		import org.apache.commons.logging.Log;
12		import org.apache.commons.logging.LogFactory;
13
14		import baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed;
15		import baseCode.io.reader.MapReader;
16
17		/**
18		* A data structure representing a map between items and a single set of keys. For example, a set of probes and the
19		* genes they map to. Probes that point to the same gene are in the same "group".
20		* <p>
21		* Copyright (c) 2004
22		* </p>
23		* <p>
24		* Institution: Columbia University
25		* </p>
26		*
27		* @author Paul Pavlidis
28		* @version $Id: GroupMap.java,v 1.3 2004/07/27 03:18:58 pavlidis Exp $
29		*/
30
31		public class GroupMap {
32
33		private int uniqueItems;
34		private Map duplicateMap;
35		private static Log log = LogFactory.getLog( GroupMap.class );
36
37		/**
38		* @return int The number of unique items in the GroupMap.
39		*/
40	0	public int getUniqueItems() {
41	0	return uniqueItems;
42		}
43
44		/**
45		* For a given key, return true if it has duplicates.
46		*
47		* @param k String
48		* @return boolean
49		*/
50	0	public boolean hasDuplicates( String k ) {
51	0	return numDuplicates( k ) > 0;
52		}
53
54		/**
55		* For a given key, return the number of duplicates it has (not counting itself).
56		*
57		* @param k String
58		* @return int
59		*/
60	0	public int numDuplicates( String k ) {
61	0	return ( ( HashSet ) duplicateMap.get( k ) ).size();
62		}
63
64		/**
65		* The input file format is that used by {@link baseCode.io.reader.MapReader}.
66		*
67		* @param filename Duplicate map file name to be read by a MapReader.
68		* @param dataMatrix Data file this the map refers to.
69		* @return Map
70		* @throws IOException
71		*/
72	0	public Map read( String filename, DenseDoubleMatrix2DNamed dataMatrix )
73		throws IOException {
74
75	0	if ( filename == null \|\| dataMatrix == null ) {
76	0	throw new IllegalArgumentException(
77		"You must give a valid file name and data matrix." );
78		}
79
80	0	MapReader m = new MapReader();
81	0	Map initialMap = m.read( filename );
82	0	Map insideOutMap = new HashMap();
83
84		// first we turn the map inside-out so we have gene --> probeA, probeB,
85		// probeC.
86	0	Set keys = initialMap.keySet();
87	0	for ( Iterator it = keys.iterator(); it.hasNext(); ) {
88	0	String p = ( String ) it.next();
89
90	0	if ( !dataMatrix.hasRow( p ) ) {
91	0	continue;
92		}
93
94	0	String v = ( String ) initialMap.get( p );
95
96	0	if ( insideOutMap.get( v ) == null ) {
97	0	insideOutMap.put( v, new ArrayList() );
98		}
99	0	( ( ArrayList ) insideOutMap.get( v ) ).add( p );
100		}
101
102	0	uniqueItems = insideOutMap.size();
103	0	log.info( uniqueItems + " unique items read from duplicate map" );
104
105		// turn that map into a map of probeA --> probe1, probe2, where probes1
106		// and probes2 are in the same 'group' as probeA
107	0	this.duplicateMap = new HashMap();
108	0	keys = insideOutMap.keySet();
109	0	for ( Iterator it = keys.iterator(); it.hasNext(); ) {
110	0	String g = ( String ) it.next();
111	0	ArrayList v = ( ArrayList ) insideOutMap.get( g );
112
113	0	for ( Iterator vit = v.iterator(); vit.hasNext(); ) {
114	0	String p = ( String ) vit.next();
115	0	if ( duplicateMap.get( p ) == null ) {
116	0	duplicateMap.put( p, new HashSet() );
117		}
118
119	0	for ( Iterator kit = v.iterator(); kit.hasNext(); ) {
120	0	String pp = ( String ) kit.next();
121	0	if ( p.equals( pp ) ) {
122	0	continue;
123		}
124
125	0	( ( Set ) duplicateMap.get( p ) ).add( pp );
126		}
127		}
128		}
129
130		// now a sanity check. Make sure every item in our data is also in the
131		// duplicate map.
132	0	for ( Iterator it = dataMatrix.getRowNameMapIterator(); it.hasNext(); ) {
133	0	boolean foundProblem = false;
134	0	String rowName = ( String ) it.next();
135	0	if ( !duplicateMap.containsKey( rowName ) ) {
136	0	duplicateMap.put( rowName, new HashSet() );
137	0	foundProblem = true;
138		}
139	0	if ( foundProblem ) {
140	0	throw new IllegalStateException(
141		"The data has item(s) that aren't in the duplicate map." );
142		}
143		}
144
145	0	return this.duplicateMap;
146
147		}
148
149		}