import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.bin.BuildDetails;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
import jalview.json.binding.biojson.v1.AnnotationPojo;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.ColorUtils;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
private String application = "Jalview";
- public static final String FILE_EXT = "json";
-
- public static final String FILE_DESC = "JSON";
-
private String globalColourScheme;
private boolean showSeqFeatures;
private FeatureRenderer fr;
- private List<int[]> hiddenColumns;
-
- private ColumnSelection columnSelection;
+ private HiddenColumns hiddenColumns;
private List<String> hiddenSeqRefs;
private ArrayList<SequenceI> hiddenSequences;
+ private final static String TCOFFEE_SCORE = "TCoffeeScore";
+
public JSONFile()
{
super();
super(source);
}
- public JSONFile(String inFile, String type) throws IOException
+ public JSONFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
@Override
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
String jsonOutput = null;
try
}
int count = 0;
- for (SequenceI seq : seqs)
+ for (SequenceI seq : sqs)
{
StringBuilder name = new StringBuilder();
name.append(seq.getName()).append("/").append(seq.getStart())
}
else
{
- if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+ // These color schemes require annotation, disable them if annotations
+ // are not exported
+ if (globalColourScheme
+ .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
+ || globalColourScheme.equalsIgnoreCase(
+ JalviewColourScheme.TCoffee.toString()))
{
- jsonAlignmentPojo.setGlobalColorScheme("None");
+ jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
}
}
if (exportSettings.isExportFeatures())
{
jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+ .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
}
if (exportSettings.isExportGroups() && seqGroups != null
SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
seqGrpPojo.setGroupName(seqGrp.getName());
seqGrpPojo.setColourScheme(ColourSchemeProperty
- .getColourName(seqGrp.cs));
+ .getColourName(seqGrp.getColourScheme()));
seqGrpPojo.setColourText(seqGrp.getColourText());
seqGrpPojo.setDescription(seqGrp.getDescription());
seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
// hidden column business
if (getViewport().hasHiddenColumns())
{
- List<int[]> hiddenCols = getViewport().getColumnSelection()
- .getHiddenColumns();
- StringBuilder hiddenColsBuilder = new StringBuilder();
- for (int[] range : hiddenCols)
- {
- hiddenColsBuilder.append(";").append(range[0]).append("-")
- .append(range[1]);
- }
-
- hiddenColsBuilder.deleteCharAt(0);
- hiddenSections[0] = hiddenColsBuilder.toString();
+ hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
+ .regionsToString(";", "-");
}
// hidden rows/seqs business
}
public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- List<SequenceI> seqs, FeatureRenderer fr)
+ SequenceI[] sqs, FeatureRenderer fr)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
- List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
- for (SequenceI seq : seqs)
+ List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
+ if (sqs == null)
+ {
+ return sequenceFeaturesPojo;
+ }
+
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
+ for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
String.valueOf(seq.hashCode()));
- String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr.findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
+ 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());
public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
Vector<AlignmentAnnotation> annotations)
{
- List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+ List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
if (annotations == null)
{
return jsonAnnotations;
AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
alignAnnotPojo.setDescription(annot.description);
alignAnnotPojo.setLabel(annot.label);
+ if (!Double.isNaN(annot.score))
+ {
+ alignAnnotPojo.setScore(annot.score);
+ }
+ alignAnnotPojo.setCalcId(annot.getCalcId());
+ alignAnnotPojo.setGraphType(annot.graph);
+
+ AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
+ annotSetting.setBelowAlignment(annot.belowAlignment);
+ annotSetting.setCentreColLabels(annot.centreColLabels);
+ annotSetting.setScaleColLabel(annot.scaleColLabel);
+ annotSetting.setShowAllColLabels(annot.showAllColLabels);
+ annotSetting.setVisible(annot.visible);
+ annotSetting.setHasIcon(annot.hasIcons);
+ alignAnnotPojo.setAnnotationSettings(annotSetting);
+ SequenceI refSeq = annot.sequenceRef;
+ if (refSeq != null)
+ {
+ alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
+ }
for (Annotation annotation : annot.annotations)
{
AnnotationPojo annotationPojo = new AnnotationPojo();
annotationPojo.setValue(annotation.value);
annotationPojo
.setSecondaryStructure(annotation.secondaryStructure);
- annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+ String displayChar = annotation.displayCharacter == null ? null
+ : annotation.displayCharacter;
+ // System.out.println("--------------------->[" + displayChar + "]");
+ annotationPojo.setDisplayCharacter(displayChar);
+ if (annotation.colour != null)
+ {
+ annotationPojo.setColour(
+ jalview.util.Format.getHexString(annotation.colour));
+ }
alignAnnotPojo.getAnnotations().add(annotationPojo);
}
else
{
- alignAnnotPojo.getAnnotations().add(annotationPojo);
+ if (annot.getCalcId() != null
+ && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
+ {
+ // do nothing
+ }
+ else
+ {
+ alignAnnotPojo.getAnnotations().add(annotationPojo);
+ }
}
}
jsonAnnotations.add(alignAnnotPojo);
{
globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
- Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
- "showSeqFeatures").toString());
+ Boolean showFeatures = Boolean.valueOf(
+ jvSettingsJsonObj.get("showSeqFeatures").toString());
setShowSeqFeatures(showFeatures);
parseHiddenSeqRefsAsList(jvSettingsJsonObj);
parseHiddenCols(jvSettingsJsonObj);
}
- hiddenSequences = new ArrayList<SequenceI>();
- seqMap = new Hashtable<String, Sequence>();
- for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
- .hasNext();)
+ hiddenSequences = new ArrayList<>();
+ seqMap = new Hashtable<>();
+ for (Iterator<JSONObject> sequenceIter = seqJsonArray
+ .iterator(); sequenceIter.hasNext();)
{
JSONObject sequence = sequenceIter.next();
String sequcenceString = sequence.get("seq").toString();
seqMap.put(seqUniqueId, seq);
}
-
parseFeatures(jsonSeqArray);
- for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
- .hasNext();)
+ for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
+ .iterator(); seqGrpIter.hasNext();)
{
JSONObject seqGrpObj = seqGrpIter.next();
String grpName = seqGrpObj.get("groupName").toString();
String colourScheme = seqGrpObj.get("colourScheme").toString();
String description = (seqGrpObj.get("description") == null) ? null
: seqGrpObj.get("description").toString();
- boolean displayBoxes = Boolean.valueOf(seqGrpObj
- .get("displayBoxes").toString());
- boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
- .toString());
- boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
- .toString());
- boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
- "showNonconserved").toString());
+ boolean displayBoxes = Boolean
+ .valueOf(seqGrpObj.get("displayBoxes").toString());
+ boolean displayText = Boolean
+ .valueOf(seqGrpObj.get("displayText").toString());
+ boolean colourText = Boolean
+ .valueOf(seqGrpObj.get("colourText").toString());
+ boolean showNonconserved = Boolean
+ .valueOf(seqGrpObj.get("showNonconserved").toString());
int startRes = Integer
.valueOf(seqGrpObj.get("startRes").toString());
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
- ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ ArrayList<SequenceI> grpSeqs = new ArrayList<>();
if (sequenceRefs.size() > 0)
{
Iterator<String> seqHashIter = sequenceRefs.iterator();
}
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
- displayBoxes, displayText, colourText,
- startRes, endRes);
- seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
- seqGrp);
+ displayBoxes, displayText, colourText, startRes, endRes);
+ seqGrp.setColourScheme(ColourSchemeMapper
+ .getJalviewColourScheme(colourScheme, seqGrp));
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
}
- for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
- .hasNext();)
+ for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
+ .iterator(); alAnnotIter.hasNext();)
{
JSONObject alAnnot = alAnnotIter.next();
JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
Annotation[] annotations = new Annotation[annotJsonArray.size()];
int count = 0;
- for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
- .hasNext();)
+ for (Iterator<JSONObject> annotIter = annotJsonArray
+ .iterator(); annotIter.hasNext();)
{
JSONObject annot = annotIter.next();
if (annot == null)
}
else
{
- float val = annot.get("value") == null ? null : Float
- .valueOf(annot.get("value").toString());
- String desc = annot.get("description") == null ? null : annot
- .get("description").toString();
+ float val = annot.get("value") == null ? null
+ : Float.valueOf(annot.get("value").toString());
+ String desc = annot.get("description") == null ? null
+ : annot.get("description").toString();
char ss = annot.get("secondaryStructure") == null
|| annot.get("secondaryStructure").toString()
- .equalsIgnoreCase("u0000") ? ' ' : annot
- .get("secondaryStructure").toString().charAt(0);
+ .equalsIgnoreCase("u0000") ? ' '
+ : annot.get("secondaryStructure")
+ .toString().charAt(0);
String displayChar = annot.get("displayCharacter") == null ? ""
: annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
+ if (annot.get("colour") != null)
+ {
+ Color color = ColorUtils
+ .parseColourString(annot.get("colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
- AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
- .get("label").toString(), alAnnot.get("description")
- .toString(), annotations);
+ AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
+ alAnnot.get("label").toString(),
+ alAnnot.get("description").toString(), annotations);
+ alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
+ : Integer.valueOf(alAnnot.get("graphType").toString());
+
+ JSONObject diplaySettings = (JSONObject) alAnnot
+ .get("annotationSettings");
+ if (diplaySettings != null)
+ {
+
+ alignAnnot.scaleColLabel = (diplaySettings
+ .get("scaleColLabel") == null) ? false
+ : Boolean.valueOf(diplaySettings
+ .get("scaleColLabel").toString());
+ alignAnnot.showAllColLabels = (diplaySettings
+ .get("showAllColLabels") == null) ? true
+ : Boolean.valueOf(diplaySettings
+ .get("showAllColLabels").toString());
+ alignAnnot.centreColLabels = (diplaySettings
+ .get("centreColLabels") == null) ? true
+ : Boolean.valueOf(diplaySettings
+ .get("centreColLabels").toString());
+ alignAnnot.belowAlignment = (diplaySettings
+ .get("belowAlignment") == null) ? false
+ : Boolean.valueOf(diplaySettings
+ .get("belowAlignment").toString());
+ alignAnnot.visible = (diplaySettings.get("visible") == null)
+ ? true
+ : Boolean.valueOf(
+ diplaySettings.get("visible").toString());
+ alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
+ ? true
+ : Boolean.valueOf(
+ diplaySettings.get("hasIcon").toString());
+
+ }
+ if (alAnnot.get("score") != null)
+ {
+ alignAnnot.score = Double
+ .valueOf(alAnnot.get("score").toString());
+ }
+
+ String calcId = (alAnnot.get("calcId") == null) ? ""
+ : alAnnot.get("calcId").toString();
+ alignAnnot.setCalcId(calcId);
+ String seqHash = (alAnnot.get("sequenceRef") != null)
+ ? alAnnot.get("sequenceRef").toString()
+ : null;
+
+ Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
+ if (sequence != null)
+ {
+ alignAnnot.sequenceRef = sequence;
+ sequence.addAlignmentAnnotation(alignAnnot);
+ if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
+ {
+ alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
+ false);
+ sequence.addAlignmentAnnotation(alignAnnot);
+ alignAnnot.adjustForAlignment();
+ }
+ }
+ alignAnnot.validateRangeAndDisplay();
this.annotations.add(alignAnnot);
+
}
} catch (Exception e)
{
public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
{
- hiddenSeqRefs = new ArrayList<String>();
+ hiddenSeqRefs = new ArrayList<>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
if (hiddenCols != null && !hiddenCols.isEmpty())
{
- columnSelection = new ColumnSelection();
+ hiddenColumns = new HiddenColumns();
String[] rangeStrings = hiddenCols.split(";");
for (String rangeString : rangeStrings)
{
String[] range = rangeString.split("-");
- columnSelection.hideColumns(Integer.valueOf(range[0]),
+ hiddenColumns.hideColumns(Integer.valueOf(range[0]),
Integer.valueOf(range[1]));
}
}
if (jsonSeqFeatures != null)
{
displayedFeatures = new FeaturesDisplayed();
- for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
- .hasNext();)
+ for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures
+ .iterator(); seqFeatureItr.hasNext();)
{
JSONObject jsonFeature = seqFeatureItr.next();
Long begin = (Long) jsonFeature.get("xStart");
}
}
+ @Override
public String getGlobalColourScheme()
{
return globalColourScheme;
this.displayedFeatures = displayedFeatures;
}
+ @Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ if (avpanel == null)
+ {
+ return;
+ }
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
fr = avpanel.cloneFeatureRenderer();
// Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : annots)
+ if (annots != null)
{
- if (annot != null && !annot.autoCalculated)
+ for (AlignmentAnnotation annot : annots)
{
- if (!annot.visible)
+ if (annot != null && !annot.autoCalculated)
{
- continue;
+ annotations.add(annot);
}
- annotations.add(annot);
}
}
- globalColourScheme = ColourSchemeProperty.getColourName(viewport
- .getGlobalColourScheme());
+ globalColourScheme = ColourSchemeProperty
+ .getColourName(viewport.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
}
+ @Override
public boolean isShowSeqFeatures()
{
return showSeqFeatures;
return annotations;
}
- public List<int[]> getHiddenColumns()
+ @Override
+ public HiddenColumns getHiddenColumns()
{
return hiddenColumns;
}
- public ColumnSelection getColumnSelection()
+ public void setHiddenColumns(HiddenColumns hidden)
{
- return columnSelection;
- }
-
- public void setColumnSelection(ColumnSelection columnSelection)
- {
- this.columnSelection = columnSelection;
+ this.hiddenColumns = hidden;
}
+ @Override
public SequenceI[] getHiddenSequences()
{
if (hiddenSequences == null || hiddenSequences.isEmpty())
this.exportJalviewSettings = exportJalviewSettings;
}
}
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
}
git://source.jalview.org / jalview.git / blobdiff