package jalview.io;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
-import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
+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.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.json.binding.v1.AlignmentAnnotationPojo;
-import jalview.json.binding.v1.AlignmentPojo;
-import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
-import jalview.json.binding.v1.AnnotationPojo;
-import jalview.json.binding.v1.SequenceFeaturesPojo;
-import jalview.json.binding.v1.SequenceGrpPojo;
-import jalview.json.binding.v1.SequencePojo;
-import jalview.schemes.ColourSchemeI;
+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.util.Format;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
-public class JSONFile extends AlignFile
-{
- private ColourSchemeI colourScheme;
-
- private String version = "2.9";
+import java.awt.Color;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
- private String webstartUrl = "www.jalview.org/services/launchApp";
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
- private String application = "Jalview";
+public class JSONFile extends AlignFile implements ComplexAlignFile
+{
+ private static String version = new BuildDetails().getVersion();
- public static final String FILE_EXT = "json";
+ private String webstartUrl = "https://www.jalview.org/services/launchApp";
- public static final String FILE_DESC = "JSON";
+ private String application = "Jalview";
- private String globalColorScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
private FeatureRenderer fr;
- private JSONExportSettings jsonExportSettings;
-
- private List<int[]> hiddenColumns;
+ 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
public void parse() throws IOException
{
- StringBuilder jsonStringBuilder = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- jsonStringBuilder.append(currentLine);
- }
- parse(jsonStringBuilder.toString());
+ parse(getReader());
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
String jsonOutput = null;
try
{
- if (getJsonExportSettings() == null)
- {
- jsonExportSettings = new JSONExportSettings();
- jsonExportSettings.setExportAnnotations(true);
- jsonExportSettings.setExportGroups(true);
- jsonExportSettings.setExportJalviewSettings(true);
- jsonExportSettings.setExportSequenceFeatures(true);
- }
-
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- if (getViewport() != null)
+ AlignExportSettingI exportSettings = getExportSettings();
+
+ // if no export settings were supplied use the following with all values
+ // defaulting to true
+ if (exportSettings == null)
{
- globalColorScheme = ColourSchemeProperty
- .getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
- fr = getViewport().getFeatureRenderer();
+ exportSettings = new AlignExportSettingI()
+ {
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
}
int count = 0;
- for (SequenceI seq : seqs)
+ for (SequenceI seq : sqs)
{
StringBuilder name = new StringBuilder();
name.append(seq.getName()).append("/").append(seq.getStart())
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
-
- if (jsonExportSettings.isExportJalviewSettings())
+ jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
+ jsonAlignmentPojo.getAppSettings().put("application", application);
+ jsonAlignmentPojo.getAppSettings().put("version", version);
+ jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+ jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+ String.valueOf(showSeqFeatures));
+
+ String[] hiddenSections = getHiddenSections();
+ if (hiddenSections != null)
{
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
- jsonAlignmentPojo.getAppSettings().put("application", application);
- jsonAlignmentPojo.getAppSettings().put("version", version);
- jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
- jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
- String.valueOf(showSeqFeatures));
-
- String[] hiddenSections = exportHiddenSections();
- if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
+ if (hiddenSections[0] != null
+ && exportSettings.isExportHiddenColumns())
{
- if (hiddenSections[0] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenCols",
- String.valueOf(hiddenSections[0]));
- }
- if (hiddenSections[1] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
- String.valueOf(hiddenSections[1]));
- }
+ jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+ String.valueOf(hiddenSections[0]));
+ }
+ if (hiddenSections[1] != null
+ && exportSettings.isExportHiddenSequences())
+ {
+ jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+ String.valueOf(hiddenSections[1]));
}
}
- if (jsonExportSettings.isExportAnnotations())
+ if (exportSettings.isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
+ else
+ {
+ // 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(ResidueColourScheme.NONE);
+ }
+ }
- if (jsonExportSettings.isExportSequenceFeatures())
+ if (exportSettings.isExportFeatures())
{
- jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+ jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
}
- if (jsonExportSettings.isExportGroups() && seqGroups != null
+ if (exportSettings.isExportGroups() && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
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());
seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
for (SequenceI seq : seqGrp.getSequences())
{
- seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
+ seqGrpPojo.getSequenceRefs()
+ .add(String.valueOf(seq.hashCode()));
}
jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
}
return jsonOutput;
}
- public String[] exportHiddenSections()
+ public String[] getHiddenSections()
{
String[] hiddenSections = new String[2];
if (getViewport() == null)
return null;
}
- System.out.println("--- Hidden Sections ---");
// hidden column business
if (getViewport().hasHiddenColumns())
{
- System.out.print("Hidden Cols : ");
- 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();
- System.out.println(hiddenSections[0]);
+ hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
+ .regionsToString(";", "-");
}
// hidden rows/seqs business
}
SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
- System.out.print("Hidden Seqs : ");
- // if(hiddenSeqs != null){
StringBuilder hiddenSeqsBuilder = new StringBuilder();
for (SequenceI hiddenSeq : hiddenSeqs)
{
}
}
if (hiddenSeqsBuilder.length() > 0)
- {
+ {
hiddenSeqsBuilder.deleteCharAt(0);
- }
+ }
hiddenSections[1] = hiddenSeqsBuilder.toString();
- System.out.println(hiddenSections[1]);
- // }
return hiddenSections;
}
- public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- List<SequenceI> seqs, FeatureRenderer fr)
+ protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ SequenceI[] sqs)
{
- FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
- .getFeaturesDisplayed();
- List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
- for (SequenceI seq : seqs)
+ displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
+ List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
+ if (sqs == null)
{
- SequenceI dataSetSequence = seq.getDatasetSequence();
- SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
- : seq.getDatasetSequence().getSequenceFeatures();
+ return sequenceFeaturesPojo;
+ }
- seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
- : seqFeatures;
- if (seqFeatures == null)
- {
- continue;
- }
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
+ String[] visibleFeatureTypes = displayedFeatures == null ? null
+ : displayedFeatures.getVisibleFeatures().toArray(
+ new String[displayedFeatures.getVisibleFeatureCount()]);
+ for (SequenceI seq : sqs)
+ {
+ /*
+ * 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(fr
- .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;
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);
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
if (jvSettingsJsonObj != null)
{
- String jsColourScheme = (String) jvSettingsJsonObj
+ globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
- Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
- "showSeqFeatures").toString());
- setColourScheme(getJalviewColorScheme(jsColourScheme));
+ Boolean showFeatures = Boolean.valueOf(
+ jvSettingsJsonObj.get("showSeqFeatures").toString());
setShowSeqFeatures(showFeatures);
parseHiddenSeqRefsAsList(jvSettingsJsonObj);
parseHiddenCols(jvSettingsJsonObj);
}
- 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();
end);
if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
{
- seq.setHidden(true);
+ hiddenSequences.add(seq);
}
seqs.add(seq);
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 seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
+ JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
- ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
- if (seqsHashArray.size() > 0)
+ ArrayList<SequenceI> grpSeqs = new ArrayList<>();
+ if (sequenceRefs.size() > 0)
{
- Iterator<String> seqHashIter = seqsHashArray.iterator();
+ Iterator<String> seqHashIter = sequenceRefs.iterator();
while (seqHashIter.hasNext())
{
String seqHash = seqHashIter.next();
}
}
}
- ColourSchemeI scheme = getJalviewColorScheme(colourScheme);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme,
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
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();
-
- char ss = annot.get("secondaryStructure") == null ? ' '
- : annot.get("secondaryStructure").toString().charAt(0);
- String displayChar = annot.get("displayCharacter").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);
+ 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)
{
e.printStackTrace();
public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
{
- hiddenSeqRefs = new ArrayList<String>();
+ hiddenSeqRefs = new ArrayList<>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
- if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
+ if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
+ {
String[] seqRefs = hiddenSeqs.split(";");
- for(String seqRef : seqRefs){
+ for (String seqRef : seqRefs)
+ {
hiddenSeqRefs.add(seqRef);
}
}
public void parseHiddenCols(JSONObject jvSettingsJson)
{
- hiddenColumns = new ArrayList<int[]>();
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
- if(hiddenCols != null && !hiddenCols.isEmpty()){
+ if (hiddenCols != null && !hiddenCols.isEmpty())
+ {
+ hiddenColumns = new HiddenColumns();
String[] rangeStrings = hiddenCols.split(";");
- for(String rangeString : rangeStrings){
+ for (String rangeString : rangeStrings)
+ {
String[] range = rangeString.split("-");
- hiddenColumns.add(new int[]
- { Integer.valueOf(range[0]), Integer.valueOf(range[1]) });
+ hiddenColumns.hideColumns(Integer.valueOf(range[0]),
+ Integer.valueOf(range[1]));
}
}
}
{
if (jsonSeqFeatures != null)
{
- for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
- .hasNext();)
+ displayedFeatures = new FeaturesDisplayed();
+ 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 featureGrp = (String) jsonFeature.get("featureGroup");
- String descripiton = (String) jsonFeature.get("description");
+ String description = (String) jsonFeature.get("description");
String seqRef = (String) jsonFeature.get("sequenceRef");
Float score = Float.valueOf(jsonFeature.get("score").toString());
- // Hashtable otherDetails = (Hashtable) jsonFeature
- // .get("otherDetails");
- // sequenceFeature.otherDetails = otherDetails;
Sequence seq = seqMap.get(seqRef);
- SequenceFeature sequenceFeature = new SequenceFeature();
+
+ /*
+ * 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);
+
JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
if (linksJsonArray != null && linksJsonArray.size() > 0)
{
sequenceFeature.addLink(link);
}
}
- sequenceFeature.setFeatureGroup(featureGrp);
- sequenceFeature.setScore(score);
- sequenceFeature.setDescription(descripiton);
- sequenceFeature.setType(type);
- sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
- sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
- seq.addSequenceFeature(sequenceFeature);
- }
- }
- }
- public static ColourSchemeI getJalviewColorScheme(
- String bioJsColourSchemeName)
- {
- ColourSchemeI jalviewColor = null;
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
- {
- jalviewColor = cs.getJvColourScheme();
- break;
+ seq.addSequenceFeature(sequenceFeature);
+ displayedFeatures.setVisible(type);
}
}
- return jalviewColor;
}
- public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
- {
- avc.setShowSeqFeatures(isShowSeqFeatures());
- avc.changeColour(getColourScheme());
- avc.setMenusForViewport();
- avc.hideColumns(hiddenColumns);
- avc.syncHiddenSequences();
- }
-
- public String getGlobalColorScheme()
- {
- return globalColorScheme;
- }
-
- public void setGlobalColorScheme(String globalColorScheme)
- {
- this.globalColorScheme = globalColorScheme;
- }
-
- public ColourSchemeI getColourScheme()
+ @Override
+ public String getGlobalColourScheme()
{
- return colourScheme;
+ return globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setGlobalColorScheme(String globalColourScheme)
{
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
+ @Override
public FeaturesDisplayedI getDisplayedFeatures()
{
return displayedFeatures;
this.displayedFeatures = displayedFeatures;
}
- public JSONExportSettings getJsonExportSettings()
- {
- return jsonExportSettings;
- }
-
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
- {
- this.jsonExportSettings = jsonExportSettings;
- }
-
- public static String getJSONData(AlignViewportI av)
+ @Override
+ public void configureForView(AlignmentViewPanel avpanel)
{
- JSONFile jsonFile = new JSONFile();
- jsonFile.setViewport(av);
- jsonFile.seqGroups = av.getAlignment().getGroups();
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
-
- for (SequenceI seq : av.getAlignment().getSequences())
+ if (avpanel == null)
{
- jsonFile.seqs.add(seq);
+ return;
}
-
+ super.configureForView(avpanel);
+ AlignViewportI viewport = avpanel.getAlignViewport();
+ AlignmentI alignment = viewport.getAlignment();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+
+ seqGroups = alignment.getGroups();
+ fr = avpanel.cloneFeatureRenderer();
+
// Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
+ if (annots != null)
{
- if (annot != null && !annot.autoCalculated)
+ for (AlignmentAnnotation annot : annots)
{
- if (annot.label.equals("PDB.CATempFactor"))
+ if (annot != null && !annot.autoCalculated)
{
- continue;
+ annotations.add(annot);
}
- jsonFile.annotations.add(annot);
}
}
- String jsonString = jsonFile.print();
- return jsonString;
+ 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 void setHiddenColumns(HiddenColumns hidden)
+ {
+ this.hiddenColumns = hidden;
+ }
+
+ @Override
+ public SequenceI[] getHiddenSequences()
+ {
+ if (hiddenSequences == null || hiddenSequences.isEmpty())
+ {
+ return new SequenceI[] {};
+ }
+ synchronized (hiddenSequences)
+ {
+ return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
+ }
+ }
+
+ public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
+ {
+ this.hiddenSequences = hiddenSequences;
+ }
+
public class JSONExportSettings
{
private boolean exportSequence;
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