-{"seqs":[{"name":"FER_CAPAN/3-34","start":3,"svid":"1.0","end":34,"id":"1665704504","seq":"SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF","order":1},{"name":"FER1_SOLLC/3-34","start":3,"svid":"1.0","end":34,"id":"1003594867","seq":"SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF","order":2},{"name":"Q93XJ9_SOLTU/3-34","start":3,"svid":"1.0","end":34,"id":"1332961135","seq":"SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF","order":3},{"name":"FER1_PEA/6-37","start":6,"svid":"1.0","end":37,"id":"1335040546","seq":"ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL","order":4},{"name":"Q7XA98_TRIPR/6-39","start":6,"svid":"1.0","end":39,"id":"1777084554","seq":"ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF","order":5},{"name":"FER_TOCH/3-34","start":3,"svid":"1.0","end":34,"id":"823528539","seq":"FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF","order":6}],"appSettings":{"globalColorScheme":"zappo","webStartUrl":"www.jalview.org/services/launchApp","application":"Jalview","hiddenSeqs":"823528539","showSeqFeatures":"true","version":"2.9","hiddenCols":"32-33;34-34"},"seqGroups":[{"displayText":true,"startRes":21,"groupName":"JGroup:1883305585","endRes":29,"colourText":false,"sequenceRefs":["1003594867","1332961135","1335040546","1777084554"],"svid":"1.0","showNonconserved":false,"colourScheme":"Zappo","displayBoxes":true}],"alignAnnotation":[{"svid":"1.0","annotations":[{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"}],"description":"New description","label":"Secondary Structure"}],"svid":"1.0","seqFeatures":[{"fillColor":"#7d1633","score":0,"sequenceRef":"1332961135","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1335040546","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1777084554","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"}]}
\ No newline at end of file
+{"seqs":[{"name":"FER_CAPAN/3-34","start":3,"svid":"1.0","end":34,"id":"1665704504","seq":"SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF","order":1},{"name":"FER1_SOLLC/3-34","start":3,"svid":"1.0","end":34,"id":"1003594867","seq":"SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF","order":2},{"name":"Q93XJ9_SOLTU/3-34","start":3,"svid":"1.0","end":34,"id":"1332961135","seq":"SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF","order":3},{"name":"FER1_PEA/6-37","start":6,"svid":"1.0","end":37,"id":"1335040546","seq":"ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL","order":4},{"name":"Q7XA98_TRIPR/6-39","start":6,"svid":"1.0","end":39,"id":"1777084554","seq":"ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF","order":5},{"name":"FER_TOCH/3-34","start":3,"svid":"1.0","end":34,"id":"823528539","seq":"FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF","order":6}],"appSettings":{"globalColorScheme":"zappo","webStartUrl":"www.jalview.org/services/launchApp","application":"Jalview","hiddenSeqs":"823528539","showSeqFeatures":"true","version":"2.9","hiddenCols":"32-33;34-34"},"seqGroups":[{"displayText":true,"startRes":21,"groupName":"JGroup:1883305585","endRes":29,"colourText":false,"sequenceRefs":["1003594867","1332961135","1335040546","1777084554"],"svid":"1.0","showNonconserved":false,"colourScheme":"Zappo","displayBoxes":true}],"alignAnnotation":[{"svid":"1.0","annotations":[{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"β","value":0,"secondaryStructure":"E"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"α","value":0,"secondaryStructure":"H"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"},{"displayCharacter":"","value":0,"secondaryStructure":"\u0000"}],"description":"New description","label":"Secondary Structure"}],"svid":"1.0","seqFeatures":[{"fillColor":"#7d1633","score":0,"sequenceRef":"1332961135","featureGroup":"Pfam","svid":"1.0","description":"My description","xStart":0,"xEnd":0,"type":"Domain"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1332961135","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1335040546","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"},{"fillColor":"#7d1633","score":0,"sequenceRef":"1777084554","featureGroup":"Jalview","svid":"1.0","description":"desciption","xStart":3,"xEnd":13,"type":"feature_x"}]}
\ No newline at end of file
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
+import jalview.util.Format;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
if (exportSettings.isExportFeatures())
{
- jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
+ jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
}
if (exportSettings.isExportGroups() && seqGroups != null
return hiddenSections;
}
- public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- SequenceI[] sqs, FeatureRenderer fr)
+ protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ SequenceI[] sqs)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
FeatureColourFinder finder = new FeatureColourFinder(fr);
+ String[] visibleFeatureTypes = displayedFeatures == null ? null
+ : displayedFeatures.getVisibleFeatures().toArray(
+ new String[displayedFeatures.getVisibleFeatureCount()]);
+
for (SequenceI seq : sqs)
{
- SequenceI dataSetSequence = seq.getDatasetSequence();
- SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
- : seq.getDatasetSequence().getSequenceFeatures();
-
- seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
- : seqFeatures;
- if (seqFeatures == null)
- {
- continue;
- }
-
+ /*
+ * get all features currently visible (and any non-positional features)
+ */
+ List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
+ visibleFeatureTypes);
for (SequenceFeature sf : seqFeatures)
{
- if (displayedFeatures != null
- && displayedFeatures.isVisible(sf.getType()))
- {
- SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
- String.valueOf(seq.hashCode()));
-
- String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(finder.findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
- jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
- jsonFeature.setXend(seq.findIndex(sf.getEnd()));
- jsonFeature.setType(sf.getType());
- jsonFeature.setDescription(sf.getDescription());
- jsonFeature.setLinks(sf.links);
- jsonFeature.setOtherDetails(sf.otherDetails);
- jsonFeature.setScore(sf.getScore());
- jsonFeature.setFillColor(featureColour);
- jsonFeature.setFeatureGroup(sf.getFeatureGroup());
- sequenceFeaturesPojo.add(jsonFeature);
- }
+ SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
+ String.valueOf(seq.hashCode()));
+
+ String featureColour = (fr == null) ? null : Format
+ .getHexString(finder.findFeatureColour(Color.white, seq,
+ seq.findIndex(sf.getBegin())));
+ int xStart = sf.getBegin() == 0 ? 0
+ : seq.findIndex(sf.getBegin()) - 1;
+ int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
+ jsonFeature.setXstart(xStart);
+ jsonFeature.setXend(xEnd);
+ jsonFeature.setType(sf.getType());
+ jsonFeature.setDescription(sf.getDescription());
+ jsonFeature.setLinks(sf.links);
+ jsonFeature.setOtherDetails(sf.otherDetails);
+ jsonFeature.setScore(sf.getScore());
+ jsonFeature.setFillColor(featureColour);
+ jsonFeature.setFeatureGroup(sf.getFeatureGroup());
+ sequenceFeaturesPojo.add(jsonFeature);
}
}
return sequenceFeaturesPojo;
Float score = Float.valueOf(jsonFeature.get("score").toString());
Sequence seq = seqMap.get(seqRef);
- int featureBegin = seq.findPosition(begin.intValue());
- int featureEnd = seq.findPosition(end.intValue()) - 1;
+
+ /*
+ * begin/end of 0 is for a non-positional feature
+ */
+ int featureBegin = begin.intValue() == 0 ? 0 : seq
+ .findPosition(begin.intValue());
+ int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
+ .intValue()) - 1;
SequenceFeature sequenceFeature = new SequenceFeature(type,
description, featureBegin, featureEnd, score, featureGrp);
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
@BeforeTest(alwaysRun = true)
public void setup() throws Exception
{
+ /*
+ * construct expected values
+ * nb this have to match the data in examples/example.json
+ */
// create and add sequences
Sequence[] seqs = new Sequence[5];
seqs[0] = new Sequence("FER_CAPAN",
// create and add sequence features
SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
- "desciption", "status", 6, 15, "Jalview");
+ "description", "status", 6, 15, "Jalview");
SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
- "desciption", "status", 9, 18, "Jalview");
+ "description", "status", 9, 18, "Jalview");
SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
- "desciption", "status", 9, 18, "Jalview");
+ "description", "status", 9, 18, "Jalview");
+ // non-positional feature:
+ SequenceFeature seqFeature5 = new SequenceFeature("Domain",
+ "My description", "status", 0, 0, "Pfam");
seqs[2].addSequenceFeature(seqFeature2);
seqs[3].addSequenceFeature(seqFeature3);
seqs[4].addSequenceFeature(seqFeature4);
+ seqs[2].addSequenceFeature(seqFeature5);
for (Sequence seq : seqs)
{
return true;
}
- public boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
+ boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
{
System.out.println("Testing >>> " + actualSeq.getName());
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
- System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
+ System.out.println(expectedGrp.cs.getColourScheme() + " | "
+ + actualGrp.cs.getColourScheme());
+ boolean colourSchemeMatches = (expectedGrp.cs.getColourScheme() == null && actualGrp.cs
+ .getColourScheme() == null)
+ || expectedGrp.cs.getColourScheme().getClass()
+ .equals(actualGrp.cs.getColourScheme().getClass());
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
- && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
+ && colourSchemeMatches
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
private boolean featuresMatched(SequenceI seq1, SequenceI seq2)
{
- boolean matched = false;
try
{
if (seq1 == null && seq2 == null)
return true;
}
- SequenceFeature[] inFeature = seq1.getSequenceFeatures();
- SequenceFeature[] outFeature = seq2.getSequenceFeatures();
+ List<SequenceFeature> inFeature = seq1.getFeatures().getAllFeatures();
+ List<SequenceFeature> outFeature = seq2.getFeatures()
+ .getAllFeatures();
- if (inFeature == null && outFeature == null)
- {
- return true;
- }
- else if ((inFeature == null && outFeature != null)
- || (inFeature != null && outFeature == null))
+ if (inFeature.size() != outFeature.size())
{
+ System.err.println("Feature count in: " + inFeature.size()
+ + ", out: " + outFeature.size());
return false;
}
- int testSize = inFeature.length;
- int matchedCount = 0;
+ SequenceFeatures.sortFeatures(inFeature, true);
+ SequenceFeatures.sortFeatures(outFeature, true);
+ int i = 0;
for (SequenceFeature in : inFeature)
{
- for (SequenceFeature out : outFeature)
+ SequenceFeature out = outFeature.get(i);
+ System.out.println(out.getType() + " | " + in.getType());
+ System.out.println(out.getBegin() + " | " + in.getBegin());
+ System.out.println(out.getEnd() + " | " + in.getEnd());
+
+ if (in.getBegin() == out.getBegin() && in.getEnd() == out.getEnd()
+ && in.getScore() == out.getScore()
+ && in.getFeatureGroup().equals(out.getFeatureGroup())
+ && in.getType().equals(out.getType()))
{
- System.out.println(out.getType() + " | " + in.getType());
- System.out.println(out.getBegin() + " | " + in.getBegin());
- System.out.println(out.getEnd() + " | " + in.getEnd());
-
- if (inFeature.length == outFeature.length
- && in.getBegin() == out.getBegin()
- && in.getEnd() == out.getEnd()
- && in.getScore() == out.getScore()
- && in.getFeatureGroup().equals(out.getFeatureGroup())
- && in.getType().equals(out.getType()))
- {
-
- ++matchedCount;
- }
}
- }
- System.out.println("matched count >>>>>> " + matchedCount);
- if (testSize == matchedCount)
- {
- matched = true;
+ else
+ {
+ System.err.println("Feature[" + i + "] mismatch, in: "
+ + in.toString() + ", out: "
+ + outFeature.get(i).toString());
+ return false;
+ }
+ i++;
}
} catch (Exception e)
{
e.printStackTrace();
}
// System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
- return matched;
+ return true;
}
/**
Assert.assertNotNull(newAlignment.getGroups());
for (SequenceGroup seqGrp : newAlignment.getGroups())
{
- SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName());
+ SequenceGroup expectedGrp = copySg;
AssertJUnit.assertTrue(
"Failed SequenceGroup Test for >>> " + seqGrp.getName(),
isGroupMatched(expectedGrp, seqGrp));
git://source.jalview.org / jalview.git / commitdiff