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package proteinstructure; |
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import java.lang.Comparable; |
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import java.util.TreeSet; |
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import java.util.regex.Matcher; |
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import java.util.regex.Pattern; |
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|
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/** |
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* Class representing an integer interval with a beginning |
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* and an end integers |
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* |
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*/ |
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public class Interval implements Comparable { |
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|
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public int beg; |
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public int end; |
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|
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public Interval(int beg,int end){ |
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this.beg=beg; |
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this.end=end; |
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} |
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|
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public int compareTo(Object o) { |
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Interval other = (Interval) o; |
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if (this.beg>other.beg){ |
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return 1; |
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} |
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else if (this.beg<other.beg){ |
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return -1; |
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} |
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else if (this.beg==other.beg){ |
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if (this.end>other.end){ |
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return 1; |
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} |
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else if (this.end<other.end){ |
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return -1; |
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} |
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} |
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return 0; // if none of the conditions before returned, then both beg and end are equal |
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} |
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|
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public int getLength(){ |
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return (end - beg); |
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} |
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|
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public boolean equals(Object o){ |
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Interval other = (Interval) o; |
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if (this.beg==other.beg && this.end==other.end){ |
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return true; |
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} |
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return false; |
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} |
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|
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public String toString() { |
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return this.beg+" "+this.end; |
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} |
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|
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|
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/*----------------------------- static methods --------------------------------*/ |
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|
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/** |
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* Returns true if selStr is a valid selection string in 'comma-hyphen' syntax, e.g. 1-3,5,7-8. |
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* @return true if selStr is a syntactically correct selection string, false otherwise |
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*/ |
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public static boolean isValidSelectionString(String selStr) { |
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Pattern p = Pattern.compile("\\d+(-\\d+)?(,\\d+(-\\d+)?)*"); |
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Matcher m = p.matcher(selStr); |
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return m.matches(); |
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} |
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|
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/** |
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* Create a new TreeSet of integers from a selection string in 'comma-hyphen' nomenclature, e.g. 1-3,5,7-8. |
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* The validity of a selection string can be checked by isValidSelectionString(). |
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* @return A TreeSet of integers corresponding to the given selection string or null of string is invalid. |
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*/ |
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public static TreeSet<Integer> parseSelectionString(String selStr) { |
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if(!isValidSelectionString(selStr)) return null; |
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TreeSet<Integer> newSet = new TreeSet<Integer>(); |
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String[] tokens = selStr.split(","); |
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for(String t:tokens) { |
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if(t.contains("-")) { |
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String[] range = t.split("-"); |
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int from = Integer.parseInt(range[0]); |
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int to = Integer.parseInt(range[1]); |
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for(int i=from; i <= to; i++) { |
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newSet.add(i); |
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} |
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|
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} else { |
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int num = Integer.parseInt(t); |
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newSet.add(num); |
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} |
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} |
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return newSet; |
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} |
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|
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/** |
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* Returns the set as a vector of intervals of consecutive elements. |
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* @return |
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*/ |
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public static IntervalSet getIntervals(TreeSet<Integer> intSet) { |
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IntervalSet intervals = new IntervalSet(); |
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if(intSet.size() == 0) return intervals; |
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// intSet is sorted becaus it's a TreeSet |
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int last = intSet.first(); // previous element |
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int start = last; // start if current interval |
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for(int n:intSet) { |
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int i = n; |
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if(i > last+1) { |
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// output interval and start new one |
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intervals.add(new Interval(start, last)); |
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start = i; |
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last = i; |
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} else |
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if(i == last) { |
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// can that even happen? |
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} else |
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if(i == last+1) { |
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last = i; |
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} |
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} |
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// output last interval |
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intervals.add(new Interval(start, last)); |
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return intervals; |
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} |
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} |
