+++ /dev/null
-package fr.orsay.lri.varna.models.templates;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-import fr.orsay.lri.varna.applications.templateEditor.Couple;
-import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.RNA;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement;
-import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
-
-/**
- * A RNATemplateMapping is a mapping between bases in an RNA sequence
- * and elements in a RNA template.
- * A base is mapped to only one template element
- * but a template element can be mapped to several bases.
- * This class is designed to be similar to the Mapping class.
- *
- * @author Raphael Champeimont
- */
-public class RNATemplateMapping {
- private Map<Integer, RNATemplateElement> map = new HashMap<Integer, RNATemplateElement>();
- private Map<RNATemplateElement, ArrayList<Integer>> invmap = new HashMap<RNATemplateElement, ArrayList<Integer>>();
-
- /**
- * Alignment distance.
- */
- private double distance;
-
-
- public double getDistance() {
- return distance;
- }
-
- public void setDistance(double distance) {
- this.distance = distance;
- }
-
- /**
- * Tell this mapping object that this base index and this element are
- * mapped with each other. This will throw RNATemplateMappingException
- * and do nothing if the base index is already in the mapping.
- */
- public void addCouple(int baseIndex, RNATemplateElement templateElement) throws RNATemplateMappingException {
- if (map.containsKey(baseIndex)) {
- throw (new RNATemplateMappingException("Base index already in mapping: " + baseIndex));
- }
- if (baseIndex < 0) {
- throw (new RNATemplateMappingException("Invalid base index: " + baseIndex));
- }
- map.put(baseIndex, templateElement);
- if (!invmap.containsKey(templateElement)) {
- invmap.put(templateElement, new ArrayList<Integer>());
- }
- invmap.get(templateElement).add(baseIndex);
- }
-
-
- public String showCompact(RNA r)
- {
- HashMap<String,Couple<Integer,Integer> > ranges = new HashMap<String,Couple<Integer,Integer> >();
- for(int i:map.keySet())
- {
- RNATemplateElement t = map.get(i);
- String k = t.getName();
- if (t instanceof RNATemplate.RNATemplateHelix)
- {
- k += " (" + ((RNATemplateHelix) t).getCaption() + ")";
- ModeleBase mb = r.getBaseAt(i);
- if (mb.getElementStructure()>i)
- k = k+":5'";
- else
- k = k+":3'";
- }
- if (!ranges.containsKey(k))
- { ranges.put(k, new Couple<Integer,Integer>(Integer.MAX_VALUE,Integer.MIN_VALUE)); }
- Couple<Integer,Integer> c = ranges.get(k);
- c.first = Math.min(c.first, i);
- c.second = Math.max(c.second, i);
- }
- String result = "";
- for(String k:ranges.keySet())
- {
- Couple<Integer,Integer> c = ranges.get(k);
- RNATemplateElement t = map.get(c.first);
- String type = ((t instanceof RNATemplate.RNATemplateHelix)?"strand":"loop");
- if (t instanceof RNATemplate.RNATemplateHelix)
- {
- if (k.endsWith("5'"))
- {
- Couple<Integer,Integer> c3 = ranges.get(k.replace("5'", "3'"));
- result += "dummyID\t1\t"+k.replace(":5'", "")+"\t"+type+"\t"+c.first+"-"+c.second+":"+c3.first+"-"+c3.second+"\n";
- }
- }
- else if (t instanceof RNATemplate.RNATemplateUnpairedSequence)
- {
- result += "dummyID\t1\t"+k+"\t"+type+"\t"+c.first+"-"+c.second+"\n";
- }
- }
- result += "alignment distance = " + distance;
- return result;
- }
-
-
- /**
- * If the given base index is in the mapping, return the
- * corresponding template element, otherwise return null.
- */
- public RNATemplateElement getPartner(int baseIndex) {
- if (map.containsKey(baseIndex)) {
- return map.get(baseIndex);
- } else {
- return null;
- }
- }
-
-
-
- /**
- * If the given template element is in the mapping, return an ArrayList
- * containing the corresponding base indexes, otherwise return null.
- * Note that you should not modify the returned ArrayList because
- * no copy is made, so if you modify it this mapping object will
- * contain inconsistent data.
- */
- public ArrayList<Integer> getAncestor(RNATemplateElement templateElement) {
- if (invmap.containsKey(templateElement)) {
- return invmap.get(templateElement);
- } else {
- return null;
- }
- }
-
-
-
- /**
- * Return a set containing all the base indexes in the mapping.
- * You should not modify the returned set.
- */
- public Set<Integer> getSourceElemsAsSet() {
- return map.keySet();
- }
-
-
-
- /**
- * Return a set containing all the template elements in the mapping.
- * You should not modify the return set.
- */
- public Set<RNATemplateElement> getTargetElemsAsSet() {
- return invmap.keySet();
- }
-
-
-
-}
git://source.jalview.org / jalview.git / blobdiff