trunk/proteinstructure/EC.java

package proteinstructure;

import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Vector;

/** This class encapsulates the EC annotation of a single protein chain. */
public class EC {

        /*--------------------------- member variables --------------------------*/
        
        private HashMap<Integer,HashSet<ECRegion>> resser2ecregion;     // residue serials to set of ec regions
        private Vector<ECRegion> ecRegions;                                                             // the actual collection of ec regions
        
        /*----------------------------- constructors ----------------------------*/
        
        /** Create an empty ec object */
        public EC() {
                this.ecRegions = new Vector<ECRegion>();
                this.resser2ecregion = new HashMap<Integer,HashSet<ECRegion>>();
        }
        
        /*---------------------------- public methods ---------------------------*/
        
        /**
         * Add the given ec region to this ec object.
         */
        public void add(ECRegion e) {
                this.ecRegions.add(e);
                Interval intv = e.getInterval();
                for(int i = intv.beg; i <= intv.end; i++) {
                        HashSet<ECRegion> values = resser2ecregion.get(i);
                        if (values == null) {
                                values = new HashSet<ECRegion>();
                                resser2ecregion.put(i,values);
                        }
                        values.add(e);
                }
        }
        
        /**
         * Returns true iff this ec object contains no scop regions.
         */
        public boolean isEmpty() {
                return this.ecRegions.isEmpty();
        }
        
        /** 
         * Returns an iterator over all assigned ec regions in this object.
         */
        public Iterator<ECRegion> getIterator() {
                return ecRegions.iterator();
        }
        
        /** 
         * For a given residue returns the ec regions this residue participates in,
         * or null if the residue is not in an assigned ec region.
         */
        public HashSet<ECRegion> getECRegion(int resser){
                if(resser2ecregion.containsKey(resser)) {
                        return this.resser2ecregion.get(resser);
                } else {
                        return null;
                }
        }
        
        public String getECNum(int resser) {
                String ecNums = null;
                if (resser2ecregion.containsKey(resser)) {
                        ecNums = "";
                        HashSet<ECRegion> ecs = getECRegion(resser);
                        Iterator<ECRegion> it = ecs.iterator();
                        while (it.hasNext()) {
                                ECRegion er = (ECRegion)it.next();
                                ecNums += er.getECNum();
                                if (it.hasNext()) {
                                        ecNums += ",";
                                }
                        }
                }
                return ecNums;
        }
        
        /** Return a deep copy of this ec object */
        public EC copy() {
                EC newS = new EC();
                for(ECRegion e:ecRegions) {
                        newS.add(e.copy());
                }
                return newS;
        }
                
        /** Returns the number of ec regions in this ec object */
        public int getNumRegions() {
                return this.ecRegions.size();
        }
}
Revision:	502
Committed:	Tue Jan 8 11:00:15 2008 UTC (16 years, 9 months ago) by stehr
File size:	2497 byte(s)
Log Message:	EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning Interval: added typing to Comparator to avoid eclipse warning
Line	User	Rev	File contents
1	filippis	382	package proteinstructure;
2
3			import java.util.HashMap;
4			import java.util.HashSet;
5			import java.util.Iterator;
6			import java.util.Vector;
7
8			/** This class encapsulates the EC annotation of a single protein chain. */
9			public class EC {
10
11			/--------------------------- member variables --------------------------/
12
13			private HashMap<Integer,HashSet<ECRegion>> resser2ecregion; // residue serials to set of ec regions
14			private Vector<ECRegion> ecRegions; // the actual collection of ec regions
15
16			/----------------------------- constructors ----------------------------/
17
18			/** Create an empty ec object */
19			public EC() {
20			this.ecRegions = new Vector<ECRegion>();
21			this.resser2ecregion = new HashMap<Integer,HashSet<ECRegion>>();
22			}
23
24			/---------------------------- public methods ---------------------------/
25
26			/**
27			* Add the given ec region to this ec object.
28			*/
29			public void add(ECRegion e) {
30			this.ecRegions.add(e);
31			Interval intv = e.getInterval();
32			for(int i = intv.beg; i <= intv.end; i++) {
33			HashSet<ECRegion> values = resser2ecregion.get(i);
34			if (values == null) {
35			values = new HashSet<ECRegion>();
36			resser2ecregion.put(i,values);
37			}
38			values.add(e);
39			}
40			}
41
42			/**
43			* Returns true iff this ec object contains no scop regions.
44			*/
45			public boolean isEmpty() {
46			return this.ecRegions.isEmpty();
47			}
48
49			/**
50			* Returns an iterator over all assigned ec regions in this object.
51			*/
52			public Iterator<ECRegion> getIterator() {
53			return ecRegions.iterator();
54			}
55
56			/**
57			* For a given residue returns the ec regions this residue participates in,
58			* or null if the residue is not in an assigned ec region.
59			*/
60			public HashSet<ECRegion> getECRegion(int resser){
61			if(resser2ecregion.containsKey(resser)) {
62			return this.resser2ecregion.get(resser);
63			} else {
64			return null;
65			}
66			}
67
68			public String getECNum(int resser) {
69			String ecNums = null;
70			if (resser2ecregion.containsKey(resser)) {
71			ecNums = "";
72			HashSet<ECRegion> ecs = getECRegion(resser);
73	stehr	502	Iterator<ECRegion> it = ecs.iterator();
74	filippis	382	while (it.hasNext()) {
75			ECRegion er = (ECRegion)it.next();
76			ecNums += er.getECNum();
77			if (it.hasNext()) {
78			ecNums += ",";
79			}
80			}
81			}
82			return ecNums;
83			}
84
85			/** Return a deep copy of this ec object */
86			public EC copy() {
87			EC newS = new EC();
88			for(ECRegion e:ecRegions) {
89			newS.add(e.copy());
90			}
91			return newS;
92			}
93
94			/** Returns the number of ec regions in this ec object */
95			public int getNumRegions() {
96			return this.ecRegions.size();
97			}
98			}