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1 package datastructures;
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2
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3 import java.util.Vector;
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4
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5 /**
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6 * @author Ali Abdallah
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7 * @version 01.2011
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8 * @since jdk 1.6.0
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9 */
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10
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11 public class GenomeFrame extends Frame{
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12
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13 int limit;
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14 Vector<Integer> hits;
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15
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16 public GenomeFrame(int start, int length) {
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17 super(start, length);
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18 limit = end;
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19 hits = new Vector<Integer>(length);
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20 hits.setSize(length);
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21 for(int i = 0; i < length; i++){
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22 hits.set(i, 0);
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23 }
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24 }
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25
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26 public int getHit(int base){
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27 if(base-start < hits.size())
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28 return hits.get(base-start);
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29 else
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30 return -1;
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31 }
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32
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33 public void setHit(int base, int bhits){
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34 if(base-start < hits.size()){
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35 hits.set(base-start, bhits);
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36 }
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37 }
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38
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39 public boolean contains(ReadFrame r){
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40 return (start <= r.start() && end >= r.end());
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41 }
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42
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43 public boolean overlaps(ReadFrame r){
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44 return (end >= r.start() && end < r.end());
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45 }
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46
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47
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48
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49 public void addBases(int nr){
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50 for(int i = 0; i < nr; i++){
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51 hits.add(1);
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52 }
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53 }
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54
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55 public String toString(){
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56 return start+":"+end+" ("+limit+")";
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57 }
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58
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59
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60 public void updateHits(ReadFrame read) {
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61 for(int base = read.start(); base <= read.end(); base++){
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62 setHit(base, getHit(base)+1);
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63 }
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64 }
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65
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66 public void updateFrameFromRightEnd(ReadFrame readF) {
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67 // TODO Auto-generated method stub
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68 for(int i = end+1; i <= readF.end(); i++)
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69 hits.add(0);
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70 end = readF.end();
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71 }
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72
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73 public boolean limitExceeded(ReadFrame readF) {
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74 return readF.start() > limit;
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75 }
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76
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77 public void updateFrameFromBothEnds(ReadFrame readF, int length) {
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78 for(int i = end-readF.start()+1; i < length; i++ )
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79 hits.add(0);
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80 for(int i = 0; i < readF.start()-start; i++)
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81 hits.remove(0);
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82 start = readF.start();
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83 end = start+length-1;
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84 limit = end;
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85 }
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86
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87 }
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