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filippis |
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package proteinstructure; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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import java.util.Iterator; |
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import java.util.Vector; |
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/** This class encapsulates the EC annotation of a single protein chain. */ |
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public class EC { |
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/*--------------------------- member variables --------------------------*/ |
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private HashMap<Integer,HashSet<ECRegion>> resser2ecregion; // residue serials to set of ec regions |
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private Vector<ECRegion> ecRegions; // the actual collection of ec regions |
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/*----------------------------- constructors ----------------------------*/ |
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/** Create an empty ec object */ |
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public EC() { |
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this.ecRegions = new Vector<ECRegion>(); |
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this.resser2ecregion = new HashMap<Integer,HashSet<ECRegion>>(); |
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} |
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/*---------------------------- public methods ---------------------------*/ |
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/** |
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* Add the given ec region to this ec object. |
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*/ |
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public void add(ECRegion e) { |
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this.ecRegions.add(e); |
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Interval intv = e.getInterval(); |
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for(int i = intv.beg; i <= intv.end; i++) { |
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HashSet<ECRegion> values = resser2ecregion.get(i); |
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if (values == null) { |
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values = new HashSet<ECRegion>(); |
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resser2ecregion.put(i,values); |
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} |
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values.add(e); |
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} |
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} |
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/** |
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* Returns true iff this ec object contains no scop regions. |
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*/ |
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public boolean isEmpty() { |
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return this.ecRegions.isEmpty(); |
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} |
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/** |
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* Returns an iterator over all assigned ec regions in this object. |
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*/ |
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public Iterator<ECRegion> getIterator() { |
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return ecRegions.iterator(); |
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} |
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/** |
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* For a given residue returns the ec regions this residue participates in, |
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* or null if the residue is not in an assigned ec region. |
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*/ |
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public HashSet<ECRegion> getECRegion(int resser){ |
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if(resser2ecregion.containsKey(resser)) { |
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return this.resser2ecregion.get(resser); |
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} else { |
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return null; |
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} |
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} |
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public String getECNum(int resser) { |
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String ecNums = null; |
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if (resser2ecregion.containsKey(resser)) { |
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ecNums = ""; |
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HashSet<ECRegion> ecs = getECRegion(resser); |
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Iterator it = ecs.iterator(); |
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while (it.hasNext()) { |
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ECRegion er = (ECRegion)it.next(); |
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ecNums += er.getECNum(); |
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if (it.hasNext()) { |
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ecNums += ","; |
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} |
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} |
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} |
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return ecNums; |
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} |
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/** Return a deep copy of this ec object */ |
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public EC copy() { |
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EC newS = new EC(); |
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for(ECRegion e:ecRegions) { |
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newS.add(e.copy()); |
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} |
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return newS; |
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} |
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/** Returns the number of ec regions in this ec object */ |
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public int getNumRegions() { |
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return this.ecRegions.size(); |
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} |
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} |