/*
* the sequence the mapped features are on
*/
- private final SequenceI linkedSeq;
+ private final SequenceI featureSequence;
/*
* the mapping between sequences;
- * NB this could be in either sense
+ * NB this could be in either sense (from or to featureSequence)
*/
private final Mapping mapping;
/*
- * if true, mapping is from the linked sequence, else to the linked sequence
- */
- private boolean mappingIsFromLinkedSequence;
-
- /*
- * features on linkedSeq that overlap the mapped positions
+ * features on featureSequence that overlap the mapped positions
*/
public final List<SequenceFeature> features;
* Constructor
*
* @param theMapping
- * @param from
- * the sequence mapped from (e.g. CDS)
+ * sequence mapping (which may be either to, or from, the sequence
+ * holding the linked features)
+ * @param featureSeq
+ * the sequence hosting the virtual features
* @param pos
- * the residue position in the sequence mapped to
+ * the residue position in the sequence mapped to
* @param res
- * the residue character at position pos
+ * the residue character at position pos
* @param theFeatures
- * list of mapped features found in the 'from' sequence at
- * the mapped position(s)
+ * list of mapped features found in the 'featureSeq' sequence at the
+ * mapped position(s)
*/
- public MappedFeatures(Mapping theMapping, SequenceI from, int pos,
+ public MappedFeatures(Mapping theMapping, SequenceI featureSeq, int pos,
char res, List<SequenceFeature> theFeatures)
{
mapping = theMapping;
- linkedSeq = from;
- mappingIsFromLinkedSequence = mapping.to != linkedSeq;
+ featureSequence = featureSeq;
toPosition = pos;
toResidue = res;
features = theFeatures;
{
codonPos = codonPositions;
baseCodon = new char[3];
- int cdsStart = linkedSeq.getStart();
+ int cdsStart = featureSequence.getStart();
baseCodon[0] = Character
- .toUpperCase(linkedSeq.getCharAt(codonPos[0] - cdsStart));
+ .toUpperCase(featureSequence.getCharAt(codonPos[0] - cdsStart));
baseCodon[1] = Character
- .toUpperCase(linkedSeq.getCharAt(codonPos[1] - cdsStart));
+ .toUpperCase(featureSequence.getCharAt(codonPos[1] - cdsStart));
baseCodon[2] = Character
- .toUpperCase(linkedSeq.getCharAt(codonPos[2] - cdsStart));
+ .toUpperCase(featureSequence.getCharAt(codonPos[2] - cdsStart));
}
else
{
*/
public String getLinkedSequenceName()
{
- return linkedSeq == null ? null : linkedSeq.getName();
+ return featureSequence == null ? null : featureSequence.getName();
}
/**
public int[] getMappedPositions(int begin, int end)
{
MapList map = mapping.getMap();
- return mappingIsFromLinkedSequence ? map.locateInTo(begin, end)
- : map.locateInFrom(begin, end);
+ return mapping.to == featureSequence ? map.locateInFrom(begin, end)
+ : map.locateInTo(begin, end);
}
+ /**
+ * Answers true if the linked features are on coding sequence, false if on
+ * peptide
+ *
+ * @return
+ */
public boolean isFromCds()
{
if (mapping.getMap().getFromRatio() == 3)
{
- return mappingIsFromLinkedSequence;
+ return mapping.to != featureSequence;
}
- return !mappingIsFromLinkedSequence;
+ return mapping.to == featureSequence;
}
}
{
beginRange = mf.getMappedPositions(begin, begin);
endRange = mf.getMappedPositions(end, end);
+ if (beginRange == null || endRange == null)
+ {
+ // something went wrong
+ return false;
+ }
begin = beginRange[0];
end = endRange[endRange.length - 1];
}
SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
3, 1);
- Mapping mapping = new Mapping(seq.getDatasetSequence(), map);
+ Mapping mapping = new Mapping(seq, map);
List<SequenceFeature> features = new ArrayList<>();
// vary ttg (Leu) to ttc (Phe)
SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.GffConstants;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
+import jalview.util.MapList;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import junit.extensions.PA;
.endsWith(
"<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
}
+
+ /**
+ * Test adding a linked feature to the tooltip
+ */
+ @Test(groups = "Functional")
+ public void testAppendFeature_virtualFeature()
+ {
+ /*
+ * map CDS to peptide sequence
+ */
+ SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+ SequenceI peptide = new Sequence("Peptide/8-14", "PLRFQMD");
+ MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+ 3, 1);
+ Mapping mapping = new Mapping(peptide, map);
+
+ /*
+ * assume variant feature found at CDS position 106 G>C
+ */
+ List<SequenceFeature> features = new ArrayList<>();
+ // vary ttg (Leu) to ttc (Phe)
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+ Float.NaN, null);
+ features.add(sf);
+ MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+ StringBuilder sb = new StringBuilder();
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+ sar.appendFeature(sb, 1, null, sf, mf, 0);
+
+ /*
+ * linked feature shown in tooltip in protein coordinates
+ */
+ assertEquals("variant 9; G,C", sb.toString());
+
+ /*
+ * adding "alleles" attribute to variant allows peptide consequence
+ * to be calculated and added to the tooltip
+ */
+ sf.setValue("alleles", "G,C");
+ sb = new StringBuilder();
+ sar.appendFeature(sb, 1, null, sf, mf, 0);
+ assertEquals("variant 9; G,C p.Leu9Phe", sb.toString());
+
+ /*
+ * now a virtual peptide feature on CDS
+ * feature at 11-12 on peptide maps to 110-115 on CDS
+ * here we test for tooltip at 113 (t)
+ */
+ SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12,
+ 2.3f, "Uniprot");
+ features.clear();
+ features.add(sf2);
+ mapping = new Mapping(peptide, map);
+ mf = new MappedFeatures(mapping, peptide, 113, 't', features);
+ sb = new StringBuilder();
+ sar.appendFeature(sb, 1, null, sf2, mf, 0);
+ assertEquals("metal 110 115; Fe Score=2.3", sb.toString());
+ }
}
git://source.jalview.org / jalview.git / commitdiff