private AlignmentViewport av;
- private jalview.api.FeatureRenderer fr;
+ private JSONExportSettings jsonExportSettings;
public JSONFile()
{
{
try
{
- JSONExportSettings exportSettings = new JSONExportSettings();
- exportSettings.setExportAnnotations(true);
- exportSettings.setExportGroups(true);
- exportSettings.setExportJalviewSettings(true);
- exportSettings.setExportSequenceFeatures(true);
+ if (getJsonExportSettings() == null)
+ {
+ jsonExportSettings = new JSONExportSettings();
+ jsonExportSettings.setExportAnnotations(true);
+ jsonExportSettings.setExportGroups(true);
+ jsonExportSettings.setExportJalviewSettings(true);
+ jsonExportSettings.setExportSequenceFeatures(true);
+ }
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
if (Desktop.getCurrentAlignFrame() != null)
.getCurrentAlignFrame().getViewport()
.getGlobalColourScheme());
this.av = Desktop.getCurrentAlignFrame().getCurrentView();
- this.fr = Desktop.getCurrentAlignFrame().alignPanel
- .cloneFeatureRenderer();
- displayedFeatures = av.getFeaturesDisplayed();
+ setDisplayedFeatures(av.getFeaturesDisplayed());
showSeqFeatures = Desktop.getCurrentAlignFrame().showSeqFeatures
.isSelected();
}
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- if (exportSettings.isExportJalviewSettings())
+ if (jsonExportSettings.isExportJalviewSettings())
{
JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
jvSettings.setGlobalColorScheme(globalColorScheme);
jsonAlignmentPojo.setJalviewSettings(jvSettings);
}
- if (exportSettings.isExportAnnotations())
+ if (jsonExportSettings.isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (exportSettings.isExportSequenceFeatures())
+ if (jsonExportSettings.isExportSequenceFeatures())
{
jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(seqs,
- displayedFeatures));
+ getDisplayedFeatures()));
}
- if (exportSettings.isExportGroups() && seqGroups.size() > 0)
+ if (jsonExportSettings.isExportGroups() && seqGroups != null
+ && seqGroups.size() > 0)
{
- ArrayList<SequenceGrpPojo> sequenceGroupsPojo = new ArrayList<SequenceGrpPojo>();
for (SequenceGroup seqGrp : seqGroups)
{
SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
SequenceI dataSetSequence = seq.getDatasetSequence();
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
: seq.getDatasetSequence().getSequenceFeatures();
+
+ if (seqFeatures == null)
+ {
+ continue;
+ }
+
for (SequenceFeature sf : seqFeatures)
{
if (displayedFeatures != null
&& displayedFeatures.isVisible(sf.getType()))
{
- // String fillColor = ((fr != null) ? jalview.util.Format
- // .getHexString(fr.findFeatureColour(Color.white, seq,
- // seq.findIndex(sf.getBegin()))) : null);
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
seq.getName() + "_" + seq.hashCode());
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setLinks(sf.links);
jsonFeature.setOtherDetails(sf.otherDetails);
jsonFeature.setScore(sf.getScore());
- // jsonFeature.setFillColor(fillColor);
jsonFeature.setFeatureGroup(sf.getFeatureGroup());
sequenceFeaturesPojo.add(jsonFeature);
}
Vector<AlignmentAnnotation> annotations)
{
List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+ if (annotations == null)
+ {
+ return jsonAnnotations;
+ }
for (AlignmentAnnotation annot : annotations)
{
AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
return jsonAnnotations;
}
- public void parse(String jsonAlignmentString)
+ @SuppressWarnings("unchecked")
+ public JSONFile parse(String jsonAlignmentString)
{
try
{
"showSeqFeatures").toString());
setColourScheme(getJalviewColorScheme(jsColourScheme));
JSONFile.setSeqFeaturesEnabled(showFeatures);
- // Desktop.setCurrentSeqFeaturesVisible(showFeatures);
}
seqMap = new Hashtable<String, Sequence>();
- // Desktop.setCurrentGlobalColourScheme(cs);
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
{
{
e.printStackTrace();
}
+ return this;
}
+ @SuppressWarnings("unchecked")
private void parseFeatures(JSONArray jsonSeqFeatures)
{
if (jsonSeqFeatures != null)
{
- for (@SuppressWarnings("unchecked")
- Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
+ for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
.hasNext();)
{
JSONObject jsonFeature = seqFeatureItr.next();
Long begin = (Long) jsonFeature.get("xStart");
Long end = (Long) jsonFeature.get("xEnd");
String type = (String) jsonFeature.get("type");
- String color = (String) jsonFeature.get("fillColor");
String featureGrp = (String) jsonFeature.get("featureGroup");
String descripiton = (String) jsonFeature.get("description");
String seqRef = (String) jsonFeature.get("sequenceRef");
}
}
- private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+ public ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
{
ColourSchemeI jalviewColor = null;
for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
JSONFile.seqFeaturesEnabled = seqFeaturesEnabled;
}
+ public FeaturesDisplayedI getDisplayedFeatures()
+ {
+ return displayedFeatures;
+ }
+
+ public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
+ {
+ this.displayedFeatures = displayedFeatures;
+ }
+
+ public JSONExportSettings getJsonExportSettings()
+ {
+ return jsonExportSettings;
+ }
+
+ public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+ {
+ this.jsonExportSettings = jsonExportSettings;
+ }
+
public class JSONExportSettings
{
private boolean exportSequence;
--- /dev/null
+package jalview.io;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+
+import java.util.ArrayList;
+
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+public class JSONFileTest
+{
+ private JSONFile jsonFile;
+
+ private int TEST_SEQ_HEIGHT = 0;
+
+ private int TEST_GRP_HEIGHT = 0;
+
+ @Before
+ public void setUp() throws Exception
+ {
+ jsonFile = new JSONFile();
+
+ // create and add sequences
+ Sequence[] seqs = new Sequence[5];
+ seqs[0] = new Sequence("FER_CAPAN",
+ "SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF", 3, 34);
+ seqs[1] = new Sequence("FER1_SOLLC",
+ "SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF", 3, 34);
+ seqs[2] = new Sequence("Q93XJ9_SOLTU",
+ "SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF", 3, 34);
+ seqs[3] = new Sequence("FER1_PEA",
+ "ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL", 6, 37);
+ seqs[4] = new Sequence("Q7XA98_TRIPR",
+ "ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF", 6, 39);
+
+ // create and add sequence features
+ SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
+ "desciption", "status", 22, 29, "jalview");
+ SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
+ "desciption", "status", 25, 32, "jalview");
+ SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
+ "desciption", "status", 25, 32, "jalview");
+ seqs[2].addSequenceFeature(seqFeature2);
+ seqs[3].addSequenceFeature(seqFeature3);
+ seqs[4].addSequenceFeature(seqFeature4);
+
+ // add created features to features displayed
+ FeaturesDisplayed fDis = new FeaturesDisplayed();
+ fDis.setVisible("feature_x");
+ jsonFile.setDisplayedFeatures(fDis);
+ JSONFile.setSeqFeaturesEnabled(true);
+
+ for (Sequence seq : seqs)
+ {
+ seq.setDatasetSequence(seq);
+ jsonFile.seqs.add(seq);
+ }
+
+ // create and add sequence groups
+ ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ grpSeqs.add(seqs[0]);
+ grpSeqs.add(seqs[1]);
+ grpSeqs.add(seqs[2]);
+ ColourSchemeI scheme = jsonFile.getJalviewColorScheme("zappo");
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1114606272",
+ scheme, true, true, false, 2, 9);
+ seqGrp.setShowNonconserved(false);
+ seqGrp.setDescription(null);
+ jsonFile.seqGroups.add(seqGrp);
+
+ // create and add annotation
+ Annotation[] annot = new Annotation[35];
+ annot[0] = new Annotation("", "", '\u0000', 0);
+ annot[1] = new Annotation("", "", '\u0000', 0);
+ annot[2] = new Annotation("α", "", 'H', 0);
+ annot[3] = new Annotation("α", "", 'H', 0);
+ annot[4] = new Annotation("α", "", 'H', 0);
+ annot[5] = new Annotation("α", "", 'H', 0);
+ annot[6] = new Annotation("", "", '\u0000', 0);
+ annot[7] = new Annotation("", "", '\u0000', 0);
+ annot[8] = new Annotation("", "", '\u0000', 0);
+ annot[9] = new Annotation("", "", '\u0000', 0);
+ annot[10] = new Annotation("β", "", 'E', 0);
+ annot[11] = new Annotation("β", "", 'E', 0);
+ annot[12] = new Annotation("", "", '\u0000', 0);
+ annot[13] = new Annotation("", "", '\u0000', 0);
+ annot[14] = new Annotation("", "", '\u0000', 0);
+ annot[15] = new Annotation("", "", '\u0000', 0);
+ annot[16] = new Annotation("α", "", 'H', 0);
+ annot[17] = new Annotation("α", "", 'H', 0);
+ annot[18] = new Annotation("α", "", 'H', 0);
+ annot[19] = new Annotation("α", "", 'H', 0);
+ annot[20] = new Annotation("α", "", 'H', 0);
+
+ annot[21] = new Annotation("", "", '\u0000', 0);
+ annot[22] = new Annotation("", "", '\u0000', 0);
+ annot[23] = new Annotation("", "", '\u0000', 0);
+ annot[24] = new Annotation("", "", '\u0000', 0);
+ annot[25] = new Annotation("", "", '\u0000', 0);
+ annot[26] = new Annotation("", "", '\u0000', 0);
+ annot[27] = new Annotation("", "", '\u0000', 0);
+ annot[28] = new Annotation("", "", '\u0000', 0);
+ annot[29] = new Annotation("", "", '\u0000', 0);
+ annot[30] = new Annotation("", "", '\u0000', 0);
+ annot[31] = new Annotation("", "", '\u0000', 0);
+ annot[32] = new Annotation("β", "", 'E', 0);
+ annot[33] = new Annotation("β", "", 'E', 0);
+ annot[34] = new Annotation("β", "", 'E', 0);
+
+ AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
+ "Secondary Structure", "New description", annot);
+ jsonFile.annotations.add(alignAnnot);
+
+ // Alignment al = new Alignment(seqs);
+ TEST_SEQ_HEIGHT = jsonFile.seqs.size();
+ TEST_GRP_HEIGHT = jsonFile.seqGroups.size();
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test
+ public void test()
+ {
+ String jsonOuput = jsonFile.print();
+ // System.out.println(">>>>>>>>>>>>>> " + jsonOuput);
+ JSONFile output = new JSONFile().parse(jsonOuput);
+
+ int matchedCounter = 0;
+ for (SequenceI in : jsonFile.getSeqs())
+ {
+ for (SequenceI out : output.getSeqs())
+ {
+ if (in.getName().equals(out.getName())
+ && in.getSequenceAsString().equals(
+ out.getSequenceAsString())
+ && in.getStart() == out.getStart()
+ && in.getEnd() == out.getEnd() && featuresMatched(in, out))
+ {
+ // System.out.println(">>>> Seq Match Detected");
+ ++matchedCounter;
+ }
+ }
+ }
+ Assert.assertTrue(matchedCounter == TEST_SEQ_HEIGHT);
+
+ matchedCounter = 0;
+ for (SequenceGroup in : jsonFile.getSeqGroups())
+ {
+ for (SequenceGroup out : output.getSeqGroups())
+ {
+ if (in.getName().equals(out.getName())
+ && in.getColourText() == out.getColourText()
+ && in.getDisplayBoxes() == out.getDisplayBoxes()
+ && in.getIgnoreGapsConsensus() == out
+ .getIgnoreGapsConsensus() && in.cs.equals(out.cs)
+ && in.getSequences().size() == out.getSequences().size())
+ {
+ // System.out.println(">>>> Grp Match Detected");
+ ++matchedCounter;
+ }
+ }
+ Assert.assertTrue(matchedCounter == TEST_GRP_HEIGHT);
+ }
+
+ }
+
+ 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();
+
+ if (inFeature == null && outFeature == null)
+ {
+ return true;
+ }
+ else if ((inFeature == null && outFeature != null)
+ || (inFeature != null && outFeature == null))
+ {
+ return false;
+ }
+
+ int testSize = inFeature.length;
+ int matchedCount = 0;
+ // System.out.println(">>>>>>>>>>>>> 1");
+ for (SequenceFeature in : inFeature)
+ {
+ for (SequenceFeature out : inFeature)
+ {
+ if (inFeature.length == outFeature.length
+ && in.getBegin() == out.getBegin()
+ && in.getEnd() == out.getEnd()
+ && in.getScore() == out.getScore()
+ && in.getFeatureGroup().equals(out.getFeatureGroup()))
+ {
+
+ ++matchedCount;
+ }
+ }
+ }
+ if (testSize == matchedCount)
+ {
+ matched = true;
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ // System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
+ return matched;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff