/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.io;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
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.HiddenSequences;
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.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
import java.io.IOException;
public class JSONFile extends AlignFile implements ComplexAlignFile
{
- private ColourSchemeI colourScheme;
+ private static String version = new BuildDetails().getVersion();
- private String version = "2.9";
-
- private String webstartUrl = "www.jalview.org/services/launchApp";
+ private String webstartUrl = "http://www.jalview.org/services/launchApp";
private String application = "Jalview";
public static final String FILE_DESC = "JSON";
- private String globalColorScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
private ArrayList<SequenceI> hiddenSequences;
+ private final static String TCOFFEE_SCORE = "TCoffeeScore";
+
public JSONFile()
{
super();
parse(getReader());
}
+
@Override
public String print()
{
try
{
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
+ AlignExportSettingI exportSettings = getExportSettings();
+
+ // if no export settings were supplied use the following with all values
+ // defaulting to true
+ if (exportSettings == null)
+ {
+ 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)
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
-
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
jsonAlignmentPojo.getAppSettings().put("application", application);
jsonAlignmentPojo.getAppSettings().put("version", version);
jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
if (hiddenSections != null)
{
if (hiddenSections[0] != null
- && getExportSettings()
- .isExportHiddenColumns())
+ && exportSettings.isExportHiddenColumns())
{
jsonAlignmentPojo.getAppSettings().put("hiddenCols",
String.valueOf(hiddenSections[0]));
}
if (hiddenSections[1] != null
- && getExportSettings()
- .isExportHiddenSequences())
+ && exportSettings.isExportHiddenSequences())
{
jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
String.valueOf(hiddenSections[1]));
}
}
- if (getExportSettings().isExportAnnotations())
+ if (exportSettings.isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
+ else
+ {
+ // These color schemes require annotation, disable them if annotations
+ // are not exported
+ if (globalColourScheme.equalsIgnoreCase("RNA Helices")
+ || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+ {
+ jsonAlignmentPojo.setGlobalColorScheme("None");
+ }
+ }
- if (getExportSettings().isExportFeatures())
+ if (exportSettings.isExportFeatures())
{
jsonAlignmentPojo
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (getExportSettings().isExportGroups()
- && seqGroups != null
+ if (exportSettings.isExportGroups() && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
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 hiddenSections;
}
- public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
List<SequenceI> seqs, FeatureRenderer fr)
{
- FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
- .getFeaturesDisplayed();
+ displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
for (SequenceI seq : seqs)
{
{
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
String.valueOf(seq.hashCode()));
+
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr
- .findFeatureColour(Color.white, seq,
+ .getHexString(fr.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
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);
if (jvSettingsJsonObj != null)
{
- String jsColourScheme = (String) jvSettingsJsonObj
+ globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
- setColourScheme(getJalviewColorScheme(jsColourScheme));
setShowSeqFeatures(showFeatures);
parseHiddenSeqRefsAsList(jvSettingsJsonObj);
parseHiddenCols(jvSettingsJsonObj);
seqs.add(seq);
seqMap.put(seqUniqueId, seq);
}
+
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
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)
+ 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.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
+ seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
.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();
+ 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 = UserColourScheme.getColourFromString(annot.get(
+ "colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
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();
{
hiddenSeqRefs = new ArrayList<String>();
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)
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
- if(hiddenCols != null && !hiddenCols.isEmpty()){
+ if (hiddenCols != null && !hiddenCols.isEmpty())
+ {
columnSelection = new ColumnSelection();
String[] rangeStrings = hiddenCols.split(";");
- for(String rangeString : rangeStrings){
+ for (String rangeString : rangeStrings)
+ {
String[] range = rangeString.split("-");
columnSelection.hideColumns(Integer.valueOf(range[0]),
Integer.valueOf(range[1]));
{
if (jsonSeqFeatures != null)
{
+ displayedFeatures = new FeaturesDisplayed();
for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
.hasNext();)
{
sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
seq.addSequenceFeature(sequenceFeature);
+ displayedFeatures.setVisible(type);
}
}
}
- public static ColourSchemeI getJalviewColorScheme(
- String bioJsColourSchemeName)
- {
- ColourSchemeI jalviewColor = null;
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
- {
- jalviewColor = cs.getJvColourScheme();
- break;
- }
- }
- return jalviewColor;
- }
-
- public String getGlobalColorScheme()
- {
- return globalColorScheme;
- }
-
- public void setGlobalColorScheme(String globalColorScheme)
- {
- this.globalColorScheme = globalColorScheme;
- }
-
- public ColourSchemeI getColourScheme()
+ 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;
}
- @Override
public void configureForView(AlignmentViewPanel avpanel)
{
super.configureForView(avpanel);
- if (isExporting())
- {
- setViewport(avpanel.getAlignViewport());
- seqGroups = avpanel.getAlignment().getGroups();
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- fr = avpanel.cloneFeatureRenderer();
+ AlignViewportI viewport = avpanel.getAlignViewport();
+ AlignmentI alignment = viewport.getAlignment();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
- for (SequenceI seq : getViewport().getAlignment().getSequences())
- {
- seqs.add(seq);
- }
+ seqGroups = alignment.getGroups();
+ fr = avpanel.cloneFeatureRenderer();
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : getViewport().getAlignment()
- .getAlignmentAnnotation())
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : annots)
+ {
+ if (annot != null && !annot.autoCalculated)
{
- if (annot != null && !annot.autoCalculated)
- {
- if (annot.label.equals("PDB.CATempFactor"))
- {
- continue;
- }
- annotations.add(annot);
- }
+ annotations.add(annot);
}
-
- globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
}
- }
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
+ .getGlobalColourScheme());
+ setDisplayedFeatures(viewport.getFeaturesDisplayed());
+ showSeqFeatures = viewport.isShowSequenceFeatures();
-
- public static String getJSONData(AlignmentViewPanel av)
- {
- JSONFile jsonFile = new JSONFile();
- jsonFile.configureForView(av);
- String jsonString = jsonFile.print();
- return jsonString;
}
public boolean isShowSeqFeatures()
{
if (hiddenSequences == null || hiddenSequences.isEmpty())
{
- return new SequenceI[]
- {};
+ return new SequenceI[] {};
}
synchronized (hiddenSequences)
{
git://source.jalview.org / jalview.git / blobdiff