import jalview.util.MessageManager;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Stack;
-import java.util.Vector;
public class Rna
{
* @return
* @throw {@link WUSSParseException}
*/
- public static Vector<SimpleBP> getSimpleBPs(CharSequence line)
+ protected static List<SimpleBP> getSimpleBPs(CharSequence line)
throws WUSSParseException
{
Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
- Vector<SimpleBP> pairs = new Vector<SimpleBP>();
+ List<SimpleBP> pairs = new ArrayList<SimpleBP>();
int i = 0;
while (i < line.length())
{
return pairs;
}
- public static SequenceFeature[] getBasePairs(List<SimpleBP> bps)
- throws WUSSParseException
- {
- SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
- for (int p = 0; p < bps.size(); p++)
- {
- SimpleBP bp = bps.get(p);
- outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
- bp.getBP3(), "");
- }
- return outPairs;
- }
+
- public static List<SimpleBP> getModeleBP(CharSequence line)
- throws WUSSParseException
- {
- Vector<SimpleBP> bps = getSimpleBPs(line);
- return new ArrayList<SimpleBP>(bps);
- }
+
/**
* Function to get the end position corresponding to a given start position
* @param pairs
* Array of SequenceFeature (output from Rna.GetBasePairs)
*/
- public static void HelixMap(SequenceFeature[] pairs)
+ protected static void computeHelixMap(SequenceFeature[] pairs)
{
int helix = 0; // Number of helices/current helix
int lastopen = 0; // Position of last open bracket reviewed
int lastclose = 9999999; // Position of last close bracket reviewed
- int i = pairs.length; // Number of pairs
int open; // Position of an open bracket under review
int close; // Position of a close bracket under review
int j; // Counter
- Hashtable<Integer, Integer> helices = new Hashtable<Integer, Integer>();
+ Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
// Keep track of helix number for each position
// Go through each base pair and assign positions a helix
- for (i = 0; i < pairs.length; i++)
+ for (int i = 0; i < pairs.length; i++)
{
open = pairs[i].getBegin();
lastopen = open;
lastclose = close;
-
}
}
return c;
}
}
+
+ public static SequenceFeature[] getHelixMap(CharSequence rnaAnnotation)
+ throws WUSSParseException
+ {
+ List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+
+ int helix = 0; // Number of helices/current helix
+ int lastopen = 0; // Position of last open bracket reviewed
+ int lastclose = 9999999; // Position of last close bracket reviewed
+
+ Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
+ // Keep track of helix number for each position
+
+ // Go through each base pair and assign positions a helix
+ List<SimpleBP> bps = getSimpleBPs(rnaAnnotation);
+ for (SimpleBP basePair : bps)
+ {
+ final int open = basePair.getBP5();
+ final int close = basePair.getBP3();
+
+ // System.out.println("open " + open + " close " + close);
+ // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
+
+ // we're moving from right to left based on closing pair
+ /*
+ * catch things like <<..>>..<<..>> |
+ */
+ if (open > lastclose)
+ {
+ helix++;
+ }
+
+ /*
+ * catch things like <<..<<..>>..<<..>>>> |
+ */
+ int j = bps.size() - 1;
+ while (j >= 0)
+ {
+ int popen = bps.get(j).getBP5();
+
+ // System.out.println("j " + j + " popen " + popen + " lastopen "
+ // +lastopen + " open " + open);
+ if ((popen < lastopen) && (popen > open))
+ {
+ if (helices.containsValue(popen)
+ && ((helices.get(popen)) == helix))
+ {
+ continue;
+ }
+ else
+ {
+ helix++;
+ break;
+ }
+ }
+ j -= 1;
+ }
+
+ // Put positions and helix information into the hashtable
+ helices.put(open, helix);
+ helices.put(close, helix);
+
+ // Record helix as featuregroup
+ result.add(new SequenceFeature("RNA helix", "", "", open, close,
+ String.valueOf(helix)));
+
+ lastopen = open;
+ lastclose = close;
+ }
+
+ return result.toArray(new SequenceFeature[result.size()]);
+ }
}
import static org.testng.AssertJUnit.fail;
import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.SequenceFeature;
import jalview.gui.JvOptionPane;
-import java.util.Vector;
+import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public void testGetSimpleBPs() throws WUSSParseException
{
String rna = "([{})]"; // JAL-1081 example
- Vector<SimpleBP> bps = Rna.getSimpleBPs(rna);
+ List<SimpleBP> bps = Rna.getSimpleBPs(rna);
assertEquals(3, bps.size());
/*
.valueOf((char) i) + " "));
}
}
+
+ @Test(groups = "Functional")
+ public void testGetHelixMap_oneHelix() throws WUSSParseException
+ {
+ String rna = ".(..[{.<..>}..].)";
+ SequenceFeature[] sfs = Rna.getHelixMap(rna);
+ assertEquals(4, sfs.length);
+
+ /*
+ * pairs are added in the order in which the closing bracket is found
+ * (see testGetSimpleBPs)
+ */
+ assertEquals(7, sfs[0].getBegin());
+ assertEquals(10, sfs[0].getEnd());
+ assertEquals("0", sfs[0].getFeatureGroup());
+ assertEquals(5, sfs[1].getBegin());
+ assertEquals(11, sfs[1].getEnd());
+ assertEquals("0", sfs[1].getFeatureGroup());
+ assertEquals(4, sfs[2].getBegin());
+ assertEquals(14, sfs[2].getEnd());
+ assertEquals("0", sfs[2].getFeatureGroup());
+ assertEquals(1, sfs[3].getBegin());
+ assertEquals(16, sfs[3].getEnd());
+ assertEquals("0", sfs[3].getFeatureGroup());
+ }
+
+ @Test(groups = "Functional")
+ public void testGetHelixMap_twoHelices() throws WUSSParseException
+ {
+ String rna = ".([.)]..{.<}.>";
+ SequenceFeature[] sfs = Rna.getHelixMap(rna);
+ assertEquals(4, sfs.length);
+
+ /*
+ * pairs are added in the order in which the closing bracket is found
+ * (see testGetSimpleBPs)
+ */
+ assertEquals(1, sfs[0].getBegin());
+ assertEquals(4, sfs[0].getEnd());
+ assertEquals("0", sfs[0].getFeatureGroup());
+ assertEquals(2, sfs[1].getBegin());
+ assertEquals(5, sfs[1].getEnd());
+ assertEquals("0", sfs[1].getFeatureGroup());
+ assertEquals(8, sfs[2].getBegin());
+ assertEquals(11, sfs[2].getEnd());
+ assertEquals("1", sfs[2].getFeatureGroup());
+ assertEquals(10, sfs[3].getBegin());
+ assertEquals(13, sfs[3].getEnd());
+ assertEquals("1", sfs[3].getFeatureGroup());
+ }
}
git://source.jalview.org / jalview.git / commitdiff