X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=2ee305f811678d8819d329f1ffa0f2f2d3e335c4;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=26ffb7c8d32d0da4797b1fe6c4643e2472c7d5cc;hpb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 26ffb7c..2ee305f 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -1,52 +1,80 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + package jalview.io; +import jalview.api.AlignExportSettingsI; +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.AlignExportSettingsAdapter; 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.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.json.binding.v1.AlignmentAnnotationPojo; -import jalview.json.binding.v1.AlignmentPojo; -import jalview.json.binding.v1.AnnotationPojo; -import jalview.json.binding.v1.JalviewSettingsPojo; -import jalview.json.binding.v1.JalviewSettingsPojo.JalviewBioJsColorSchemeMapper; -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.viewmodel.AlignmentViewport; - +import jalview.schemes.JalviewColourScheme; +import jalview.schemes.ResidueColourScheme; +import jalview.util.ColorUtils; +import jalview.util.Format; +import jalview.util.JSONUtils; +import jalview.viewmodel.seqfeatures.FeaturesDisplayed; + +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.Map; import java.util.Vector; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; - -public class JSONFile extends AlignFile +public class JSONFile extends AlignFile implements ComplexAlignFile { - private static ColourSchemeI colourScheme; - - private static boolean seqFeaturesEnabled; - - private String jalviewVersion; + private static String version = new BuildDetails().getVersion(); - private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp"; + private String webstartUrl = "https://www.jalview.org/services/launchApp"; - public static final String FILE_EXT = "json"; + private String application = "Jalview"; - public static final String FILE_DESC = "JSON"; - - private String globalColorScheme; + private String globalColourScheme; private boolean showSeqFeatures; @@ -54,9 +82,15 @@ public class JSONFile extends AlignFile private FeaturesDisplayedI displayedFeatures; - private AlignmentViewport av; + private FeatureRenderer fr; + + private HiddenColumns hiddenColumns; + + private List hiddenSeqRefs; + + private ArrayList hiddenSequences; - private jalview.api.FeatureRenderer fr; + private final static String TCOFFEE_SCORE = "TCoffeeScore"; public JSONFile() { @@ -68,57 +102,44 @@ public class JSONFile extends AlignFile 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 { - JSONExportSettings exportSettings = new JSONExportSettings(); - exportSettings.setExportAnnotations(true); - exportSettings.setExportGroups(true); - exportSettings.setExportJalviewSettings(true); - exportSettings.setExportSequenceFeatures(true); - AlignmentPojo jsonAlignmentPojo = new AlignmentPojo(); - if (Desktop.getCurrentAlignFrame() != null) + AlignExportSettingsI exportSettings = getExportSettings(); + + /* + * if no export settings were supplied, provide an 'export all' setting + */ + if (exportSettings == null) { - globalColorScheme = ColourSchemeProperty.getColourName(Desktop - .getCurrentAlignFrame().getViewport() - .getGlobalColourScheme()); - this.av = Desktop.getCurrentAlignFrame().getCurrentView(); - this.fr = Desktop.getCurrentAlignFrame().alignPanel - .cloneFeatureRenderer(); - displayedFeatures = av.getFeaturesDisplayed(); - showSeqFeatures = Desktop.getCurrentAlignFrame().showSeqFeatures - .isSelected(); + exportSettings = new AlignExportSettingsAdapter(true); } int count = 0; - for (SequenceI seq : seqs) + for (SequenceI seq : sqs) { StringBuilder name = new StringBuilder(); name.append(seq.getName()).append("/").append(seq.getStart()) .append("-").append(seq.getEnd()); SequencePojo jsonSeqPojo = new SequencePojo(); - jsonSeqPojo.setId(seq.getName() + "_" + seq.hashCode()); + jsonSeqPojo.setId(String.valueOf(seq.hashCode())); jsonSeqPojo.setOrder(++count); jsonSeqPojo.setEnd(seq.getEnd()); jsonSeqPojo.setStart(seq.getStart()); @@ -126,15 +147,28 @@ public class JSONFile extends AlignFile jsonSeqPojo.setSeq(seq.getSequenceAsString()); jsonAlignmentPojo.getSeqs().add(jsonSeqPojo); } - - if (exportSettings.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) { - JalviewSettingsPojo jvSettings = new JalviewSettingsPojo(); - jvSettings.setGlobalColorScheme(globalColorScheme); - jvSettings.setJalviewVersion(jalviewVersion); - jvSettings.setWebStartUrl(webStartLaunchServletUrl); - jvSettings.setShowSeqFeatures(showSeqFeatures); - jsonAlignmentPojo.setJalviewSettings(jvSettings); + if (hiddenSections[0] != null + && exportSettings.isExportHiddenColumns()) + { + jsonAlignmentPojo.getAppSettings().put("hiddenCols", + String.valueOf(hiddenSections[0])); + } + if (hiddenSections[1] != null + && exportSettings.isExportHiddenSequences()) + { + jsonAlignmentPojo.getAppSettings().put("hiddenSeqs", + String.valueOf(hiddenSections[1])); + } } if (exportSettings.isExportAnnotations()) @@ -142,22 +176,33 @@ public class JSONFile extends AlignFile 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 (exportSettings.isExportSequenceFeatures()) + if (exportSettings.isExportFeatures()) { - jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, - displayedFeatures)); + jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs)); } - if (exportSettings.isExportGroups() && seqGroups.size() > 0) + if (exportSettings.isExportGroups() && seqGroups != null + && seqGroups.size() > 0) { - ArrayList sequenceGroupsPojo = new ArrayList(); 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()); @@ -167,54 +212,108 @@ public class JSONFile extends AlignFile seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved()); for (SequenceI seq : seqGrp.getSequences()) { - seqGrpPojo.getSeqsHash().add( - seq.getName() + "_" + seq.hashCode()); + seqGrpPojo.getSequenceRefs() + .add(String.valueOf(seq.hashCode())); } jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo); } } - com.json.JSONObject generatedJSon = new com.json.JSONObject( - jsonAlignmentPojo); - String jsonOutput = generatedJSon.toString(); + + jsonOutput = JSONUtils.stringify(jsonAlignmentPojo); return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend", "xEnd"); } catch (Exception e) { e.printStackTrace(); - throw e; } + return jsonOutput; } - public static List sequenceFeatureToJsonPojo( - List seqs, FeaturesDisplayedI displayedFeatures) + public String[] getHiddenSections() { - List sequenceFeaturesPojo = new ArrayList(); - for (SequenceI seq : seqs) + String[] hiddenSections = new String[2]; + if (getViewport() == null) + { + return null; + } + + // hidden column business + if (getViewport().hasHiddenColumns()) { - SequenceI dataSetSequence = seq.getDatasetSequence(); - SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null - : seq.getDatasetSequence().getSequenceFeatures(); + hiddenSections[0] = getViewport().getAlignment().getHiddenColumns() + .regionsToString(";", "-"); + } + + // hidden rows/seqs business + HiddenSequences hiddenSeqsObj = getViewport().getAlignment() + .getHiddenSequences(); + if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null) + { + return hiddenSections; + } + + SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences; + StringBuilder hiddenSeqsBuilder = new StringBuilder(); + for (SequenceI hiddenSeq : hiddenSeqs) + { + if (hiddenSeq != null) + { + hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode()); + } + } + if (hiddenSeqsBuilder.length() > 0) + { + hiddenSeqsBuilder.deleteCharAt(0); + } + hiddenSections[1] = hiddenSeqsBuilder.toString(); + + return hiddenSections; + } + + protected List sequenceFeatureToJsonPojo( + SequenceI[] sqs) + { + displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); + List sequenceFeaturesPojo = new ArrayList<>(); + if (sqs == null) + { + return sequenceFeaturesPojo; + } + + 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 seqFeatures = seq.getFeatures() + .getAllFeatures(visibleFeatureTypes); 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.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(fillColor); - 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; @@ -223,12 +322,36 @@ public class JSONFile extends AlignFile public static List annotationToJsonPojo( Vector annotations) { - List jsonAnnotations = new ArrayList(); + List jsonAnnotations = new ArrayList<>(); + if (annotations == null) + { + return jsonAnnotations; + } for (AlignmentAnnotation annot : annotations) { 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(); @@ -238,12 +361,28 @@ public class JSONFile extends AlignFile 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); @@ -251,40 +390,42 @@ public class JSONFile extends AlignFile return jsonAnnotations; } - public void parse(String jsonAlignmentString) + @SuppressWarnings("unchecked") + public JSONFile parse(Reader jsonAlignmentString) { try { - JSONParser jsonParser = new JSONParser(); - JSONObject alignmentJsonObj = (JSONObject) jsonParser + Map alignmentJsonObj = (Map) JSONUtils .parse(jsonAlignmentString); - JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs"); - JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj + List seqJsonArray = (List) alignmentJsonObj + .get("seqs"); + List alAnnotJsonArray = (List) alignmentJsonObj .get("alignAnnotation"); - JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj + List jsonSeqArray = (List) alignmentJsonObj .get("seqFeatures"); - JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj + List seqGrpJsonArray = (List) alignmentJsonObj .get("seqGroups"); - JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj - .get("jalviewSettings"); + Map jvSettingsJsonObj = (Map) alignmentJsonObj + .get("appSettings"); if (jvSettingsJsonObj != null) { - String jsColourScheme = (String) jvSettingsJsonObj + globalColourScheme = (String) jvSettingsJsonObj .get("globalColorScheme"); - Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get( - "showSeqFeatures").toString()); - setColourScheme(getJalviewColorScheme(jsColourScheme)); - JSONFile.setSeqFeaturesEnabled(showFeatures); - // Desktop.setCurrentSeqFeaturesVisible(showFeatures); + Boolean showFeatures = Boolean.valueOf( + jvSettingsJsonObj.get("showSeqFeatures").toString()); + setShowSeqFeatures(showFeatures); + parseHiddenSeqRefsAsList(jvSettingsJsonObj); + parseHiddenCols(jvSettingsJsonObj); } - seqMap = new Hashtable(); - // Desktop.setCurrentGlobalColourScheme(cs); - for (Iterator sequenceIter = seqJsonArray.iterator(); sequenceIter - .hasNext();) + hiddenSequences = new ArrayList<>(); + seqMap = new Hashtable<>(); + for (Iterator sequenceIter = seqJsonArray + .iterator(); sequenceIter.hasNext();) { - JSONObject sequence = sequenceIter.next(); + Map sequence = (Map) sequenceIter + .next(); String sequcenceString = sequence.get("seq").toString(); String sequenceName = sequence.get("name").toString(); String seqUniqueId = sequence.get("id").toString(); @@ -292,193 +433,354 @@ public class JSONFile extends AlignFile int end = Integer.valueOf(sequence.get("end").toString()); Sequence seq = new Sequence(sequenceName, sequcenceString, start, end); + if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId)) + { + hiddenSequences.add(seq); + } seqs.add(seq); seqMap.put(seqUniqueId, seq); } + parseFeatures(jsonSeqArray); - for (Iterator seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter - .hasNext();) + for (Iterator seqGrpIter = seqGrpJsonArray + .iterator(); seqGrpIter.hasNext();) { - JSONObject seqGrpObj = seqGrpIter.next(); + Map seqGrpObj = (Map) 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"); + List sequenceRefs = (List) seqGrpObj + .get("sequenceRefs"); - ArrayList grpSeqs = new ArrayList(); - if (seqsHashArray.size() > 0) + ArrayList grpSeqs = new ArrayList<>(); + if (sequenceRefs.size() > 0) { - Iterator seqHashIter = seqsHashArray.iterator(); + Iterator seqHashIter = sequenceRefs.iterator(); while (seqHashIter.hasNext()) { - String seqHash = seqHashIter.next(); - Sequence sequence = seqMap.get(seqHash); + Sequence sequence = seqMap.get(seqHashIter.next()); if (sequence != null) { grpSeqs.add(sequence); } } } - 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 alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter - .hasNext();) + for (Iterator alAnnotIter = alAnnotJsonArray + .iterator(); alAnnotIter.hasNext();) { - JSONObject alAnnot = alAnnotIter.next(); - JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations"); + Map alAnnot = (Map) alAnnotIter + .next(); + List annotJsonArray = (List) alAnnot + .get("annotations"); Annotation[] annotations = new Annotation[annotJsonArray.size()]; int count = 0; - for (Iterator annotIter = annotJsonArray.iterator(); annotIter - .hasNext();) + for (Iterator annotIter = annotJsonArray + .iterator(); annotIter.hasNext();) { - JSONObject annot = annotIter.next(); + Map annot = (Map) annotIter + .next(); if (annot == null) { annotations[count] = 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 ? 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()); + + Map diplaySettings = (Map) 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(); } + return this; } + public void parseHiddenSeqRefsAsList(Map jvSettingsJson) + { + hiddenSeqRefs = new ArrayList<>(); + String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs"); + if (hiddenSeqs != null && !hiddenSeqs.isEmpty()) + { + String[] seqRefs = hiddenSeqs.split(";"); + for (int i = 0, n = seqRefs.length; i < n; i++) + { + hiddenSeqRefs.add(seqRefs[i]); + } + } + } - private void parseFeatures(JSONArray jsonSeqFeatures) + public void parseHiddenCols(Map jvSettingsJson) + { + String hiddenCols = (String) jvSettingsJson.get("hiddenCols"); + if (hiddenCols != null && !hiddenCols.isEmpty()) + { + hiddenColumns = new HiddenColumns(); + String[] rangeStrings = hiddenCols.split(";"); + for (int i = 0, n = rangeStrings.length; i < n; i++) + { + String[] range = rangeStrings[i].split("-"); + hiddenColumns.hideColumns(Integer.valueOf(range[0]), + Integer.valueOf(range[1])); + } + } + } + + @SuppressWarnings("unchecked") + private void parseFeatures(List jsonSeqFeatures) { if (jsonSeqFeatures != null) { - for (@SuppressWarnings("unchecked") - Iterator seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr - .hasNext();) + displayedFeatures = new FeaturesDisplayed(); + for (Object o : jsonSeqFeatures) { - JSONObject jsonFeature = seqFeatureItr.next(); + Map jsonFeature = (Map) o; 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 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(); - JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links"); + + /* + * 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); + + List linksJsonArray = (List) jsonFeature + .get("links"); if (linksJsonArray != null && linksJsonArray.size() > 0) { - Iterator linkList = linksJsonArray.iterator(); + Iterator linkList = linksJsonArray.iterator(); while (linkList.hasNext()) { - String link = linkList.next(); - sequenceFeature.addLink(link); + sequenceFeature.addLink((String) linkList.next()); } } - 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); + displayedFeatures.setVisible(type); } } } - private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName) + @Override + public String getGlobalColourScheme() { - ColourSchemeI jalviewColor = null; - for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper - .values()) + return globalColourScheme; + } + + public void setGlobalColorScheme(String globalColourScheme) + { + this.globalColourScheme = globalColourScheme; + } + + @Override + public FeaturesDisplayedI getDisplayedFeatures() + { + return displayedFeatures; + } + + public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures) + { + this.displayedFeatures = displayedFeatures; + } + + @Override + public void configureForView(AlignmentViewPanel avpanel) + { + if (avpanel == null) { - if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)) + 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 + if (annots != null) + { + for (AlignmentAnnotation annot : annots) { - jalviewColor = cs.getJvColourScheme(); - break; + if (annot != null && !annot.autoCalculated) + { + annotations.add(annot); + } } } - return jalviewColor; + globalColourScheme = ColourSchemeProperty + .getColourName(viewport.getGlobalColourScheme()); + setDisplayedFeatures(viewport.getFeaturesDisplayed()); + showSeqFeatures = viewport.isShowSequenceFeatures(); + } - public void LoadAlignmentFeatures(AlignFrame af) + @Override + public boolean isShowSeqFeatures() { - af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled()); - af.changeColour(getColourScheme()); - af.setMenusForViewport(); + return showSeqFeatures; } - public String getGlobalColorScheme() + public void setShowSeqFeatures(boolean showSeqFeatures) { - return globalColorScheme; + this.showSeqFeatures = showSeqFeatures; } - public void setGlobalColorScheme(String globalColorScheme) + public Vector getAnnotations() { - this.globalColorScheme = globalColorScheme; + return annotations; } - public static ColourSchemeI getColourScheme() + @Override + public HiddenColumns getHiddenColumns() { - return colourScheme; + return hiddenColumns; } - public static void setColourScheme(ColourSchemeI colourScheme) + public void setHiddenColumns(HiddenColumns hidden) { - JSONFile.colourScheme = colourScheme; + this.hiddenColumns = hidden; } - public static boolean isSeqFeaturesEnabled() + @Override + public SequenceI[] getHiddenSequences() { - return seqFeaturesEnabled; + if (hiddenSequences == null || hiddenSequences.isEmpty()) + { + return new SequenceI[] {}; + } + synchronized (hiddenSequences) + { + return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]); + } } - public static void setSeqFeaturesEnabled(boolean seqFeaturesEnabled) + public void setHiddenSequences(ArrayList hiddenSequences) { - JSONFile.seqFeaturesEnabled = seqFeaturesEnabled; + this.hiddenSequences = hiddenSequences; } public class JSONExportSettings @@ -543,4 +845,19 @@ public class JSONFile extends AlignFile this.exportJalviewSettings = exportJalviewSettings; } } + + /** + * Returns a descriptor for suitable feature display settings with + *
    + *
  • ResNums or insertions features visible
    • + *
  • insertions features coloured red
    • + *
  • ResNum features coloured by label
    • + *
  • Insertions displayed above (on top of) ResNums
    • + *
+ */ + @Override + public FeatureSettingsModelI getFeatureColourScheme() + { + return new PDBFeatureSettings(); + } }