import java.util.ListIterator;
import java.util.Vector;
- import com.stevesoft.pat.Regex;
-
import fr.orsay.lri.varna.models.rna.RNA;
/**
*/
public class Sequence extends ASequence implements SequenceI
{
- private static final Regex limitrx = new Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
-
- private static final Regex endrx = new Regex("[0-9]{1,}$");
-
SequenceI datasetSequence;
String name;
*/
int index = -1;
- private SequenceFeatures sequenceFeatureStore;
+ private SequenceFeaturesI sequenceFeatureStore;
/*
* A cursor holding the approximate current view position to the sequence,
checkValidRange();
}
+ /**
+ * If 'name' ends in /i-j, where i >= j > 0 are integers, extracts i and j as
+ * start and end respectively and removes the suffix from the name
+ */
void parseId()
{
if (name == null)
"POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signature?
- if (limitrx.search(name))
+ int slashPos = name.lastIndexOf('/');
+ if (slashPos > -1 && slashPos < name.length() - 1)
{
- name = limitrx.left();
- endrx.search(limitrx.stringMatched());
- setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
- endrx.matchedFrom() - 1)));
- setEnd(Integer.parseInt(endrx.stringMatched()));
+ String suffix = name.substring(slashPos + 1);
+ String[] range = suffix.split("-");
+ if (range.length == 2)
+ {
+ try
+ {
+ int from = Integer.valueOf(range[0]);
+ int to = Integer.valueOf(range[1]);
+ if (from > 0 && to >= from)
+ {
+ name = name.substring(0, slashPos);
+ setStart(from);
+ setEnd(to);
+ checkValidRange();
+ }
+ } catch (NumberFormatException e)
+ {
+ // leave name unchanged if suffix is invalid
+ }
+ }
}
}
+ /**
+ * Ensures that 'end' is not before the end of the sequence, that is,
+ * (end-start+1) is at least as long as the count of ungapped positions. Note
+ * that end is permitted to be beyond the end of the sequence data.
+ */
void checkValidRange()
{
// Note: JAL-774 :
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
endRes++;
}
}
/**
- * DOCUMENT ME!
+ * Sets the sequence name. If the name ends in /start-end, then the start-end
+ * values are parsed out and set, and the suffix is removed from the name.
*
- * @param name
- * DOCUMENT ME!
+ * @param theName
*/
@Override
- public void setName(String name)
+ public void setName(String theName)
{
- this.name = name;
+ this.name = theName;
this.parseId();
}
* and we may have included adjacent or enclosing features;
* remove any that are not enclosing, non-contact features
*/
- if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
+ boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+ && Comparison.isGap(sequence[toColumn - 1]);
+ if (endPos > this.end || endColumnIsGapped)
{
ListIterator<SequenceFeature> it = result.listIterator();
while (it.hasNext())
SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
"desc", 13, 14, 2f, null);
sq.addSequenceFeature(sfContactFG);
+ // add single position feature at [I]
+ SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
+ "desc", 16, 16, null);
+ sq.addSequenceFeature(sfI);
// no features in columns 1-2 (-A)
List<SequenceFeature> found = sq.findFeatures(1, 2);
// columns 10-11 (--) should find nothing
found = sq.findFeatures(10, 11);
assertEquals(0, found.size());
+
+ // columns 14-14 (I) should find variant feature
+ found = sq.findFeatures(14, 14);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sfI));
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
+ public void testFindFeatures_largeEndPos()
+ {
+ /*
+ * imitate a PDB sequence where end is larger than end position
+ */
+ SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
+ sq.createDatasetSequence();
+
+ assertTrue(sq.findFeatures(1, 9).isEmpty());
+ // should be no array bounds exception - JAL-2772
+ assertTrue(sq.findFeatures(1, 15).isEmpty());
+
+ // add feature on BCD
+ SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+ null);
+ sq.addSequenceFeature(sfBCD);
+
+ // no features in columns 1-2 (-A)
+ List<SequenceFeature> found = sq.findFeatures(1, 2);
+ assertTrue(found.isEmpty());
+
+ // columns 1-6 (-ABC--) includes BCD
+ found = sq.findFeatures(1, 6);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sfBCD));
+
+ // columns 10-11 (--) should find nothing
+ found = sq.findFeatures(10, 11);
+ assertEquals(0, found.size());
+ }
++
++ @Test(groups = { "Functional" })
+ public void testSetName()
+ {
+ SequenceI sq = new Sequence("test", "-ABC---DE-F--");
+ assertEquals("test", sq.getName());
+ assertEquals(1, sq.getStart());
+ assertEquals(6, sq.getEnd());
+
+ sq.setName("testing");
+ assertEquals("testing", sq.getName());
+
+ sq.setName("test/8-10");
+ assertEquals("test", sq.getName());
+ assertEquals(8, sq.getStart());
+ assertEquals(13, sq.getEnd()); // note end is recomputed
+
+ sq.setName("testing/7-99");
+ assertEquals("testing", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd()); // end may be beyond physical end
+
+ sq.setName("/2-3");
+ assertEquals("", sq.getName());
+ assertEquals(2, sq.getStart());
+ assertEquals(7, sq.getEnd());
+
+ sq.setName("test/"); // invalid
+ assertEquals("test/", sq.getName());
+ assertEquals(2, sq.getStart());
+ assertEquals(7, sq.getEnd());
+
+ sq.setName("test/6-13/7-99");
+ assertEquals("test/6-13", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/0-5"); // 0 is invalid - ignored
+ assertEquals("test/0-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/a-5"); // a is invalid - ignored
+ assertEquals("test/a-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/6-5"); // start > end is invalid - ignored
+ assertEquals("test/6-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/5"); // invalid - ignored
+ assertEquals("test/5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/-5"); // invalid - ignored
+ assertEquals("test/-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/5-"); // invalid - ignored
+ assertEquals("test/5-", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/5-6-7"); // invalid - ignored
+ assertEquals("test/5-6-7", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName(null); // invalid, gets converted to space
+ assertEquals("", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCheckValidRange()
+ {
+ Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
+ assertEquals(7, sq.getStart());
+ assertEquals(12, sq.getEnd());
+
+ /*
+ * checkValidRange ensures end is at least the last residue position
+ */
+ PA.setValue(sq, "end", 2);
+ sq.checkValidRange();
+ assertEquals(12, sq.getEnd());
+
+ /*
+ * end may be beyond the last residue position
+ */
+ PA.setValue(sq, "end", 22);
+ sq.checkValidRange();
+ assertEquals(22, sq.getEnd());
+ }
}
git://source.jalview.org / jalview.git / commitdiff