trunk/proteinstructure/EdgeNbh.java

package proteinstructure;

import java.util.TreeMap;
import java.util.Collections;

public class EdgeNbh extends TreeMap<Integer,String> {
        

        private static final long serialVersionUID = 1L;

        // central edge residues
        public int i_resser;
        public String i_resType;
        public int j_resser;
        public String j_resType;
        
        public EdgeNbh(int i_resser, String i_resType, int j_resser, String j_resType){
                super();
                this.i_resser=i_resser;
                this.i_resType=i_resType;
                this.j_resser=j_resser;
                this.j_resType=j_resType;               
        }
        
        public String getMotif(){
                String motif="";
                int min=Math.min(Math.min(i_resser,j_resser), Collections.min(this.keySet()));
                int max=Math.max(Math.max(i_resser,j_resser), Collections.max(this.keySet()));
                int gapSize=0;
                String gap="";
                for (int i=min;i<=max;i++){
                        if (this.containsKey(i)){
                                motif+=gap;
                                motif+=AA.threeletter2oneletter(this.get(i));
                                gapSize=0;
                                gap="";
                        } else if (i==i_resser){
                                motif+=gap;
                                motif+="x";
                                gapSize=0;
                                gap="";
                        } else if (i==j_resser){
                                motif+=gap;
                                motif+="y";
                                gapSize=0;
                                gap="";
                        } else {
                                gapSize++;
                                gap="_{"+gapSize+"}";
                        }
                }
                return motif;
        }

        public String getMotifFullGaps(){
                String motif="";
                int min=Math.min(Math.min(i_resser,j_resser), Collections.min(this.keySet()));
                int max=Math.max(Math.max(i_resser,j_resser), Collections.max(this.keySet()));
                for (int i=min;i<=max;i++){
                        if (this.containsKey(i)){
                                motif+=AA.threeletter2oneletter(this.get(i));   
                        } else if (i==i_resser){
                                motif+="x";
                        } else if (i==j_resser){
                                motif+="y";                             
                        } else {
                                motif+="_";
                        }
                }
                return motif;
        }
        
        public String toString(){
                if (this.isEmpty()) return "";
                else return this.getMotif();
        }
}
Revision:	196
Committed:	Wed Jun 13 15:05:31 2007 UTC (17 years, 3 months ago) by duarte
File size:	1746 byte(s)
Log Message:	Added toString and getMotifFullGaps missing in EdgeNbh
Line	User	Rev	File contents
1	duarte	179	package proteinstructure;
2
3			import java.util.TreeMap;
4			import java.util.Collections;
5
6			public class EdgeNbh extends TreeMap<Integer,String> {
7
8
9			private static final long serialVersionUID = 1L;
10
11			// central edge residues
12			public int i_resser;
13			public String i_resType;
14			public int j_resser;
15			public String j_resType;
16
17			public EdgeNbh(int i_resser, String i_resType, int j_resser, String j_resType){
18			super();
19			this.i_resser=i_resser;
20			this.i_resType=i_resType;
21			this.j_resser=j_resser;
22			this.j_resType=j_resType;
23			}
24
25			public String getMotif(){
26			String motif="";
27			int min=Math.min(Math.min(i_resser,j_resser), Collections.min(this.keySet()));
28			int max=Math.max(Math.max(i_resser,j_resser), Collections.max(this.keySet()));
29	duarte	196	int gapSize=0;
30			String gap="";
31	duarte	179	for (int i=min;i<=max;i++){
32			if (this.containsKey(i)){
33	duarte	196	motif+=gap;
34			motif+=AA.threeletter2oneletter(this.get(i));
35			gapSize=0;
36			gap="";
37			} else if (i==i_resser){
38			motif+=gap;
39			motif+="x";
40			gapSize=0;
41			gap="";
42			} else if (i==j_resser){
43			motif+=gap;
44			motif+="y";
45			gapSize=0;
46			gap="";
47			} else {
48			gapSize++;
49			gap="_{"+gapSize+"}";
50			}
51			}
52			return motif;
53			}
54
55			public String getMotifFullGaps(){
56			String motif="";
57			int min=Math.min(Math.min(i_resser,j_resser), Collections.min(this.keySet()));
58			int max=Math.max(Math.max(i_resser,j_resser), Collections.max(this.keySet()));
59			for (int i=min;i<=max;i++){
60			if (this.containsKey(i)){
61	duarte	179	motif+=AA.threeletter2oneletter(this.get(i));
62			} else if (i==i_resser){
63			motif+="x";
64			} else if (i==j_resser){
65			motif+="y";
66			} else {
67			motif+="_";
68			}
69			}
70			return motif;
71			}
72
73	duarte	196	public String toString(){
74			if (this.isEmpty()) return "";
75			else return this.getMotif();
76			}
77	duarte	179	}