X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=9b15eb51b55f9040ff2bb99af4eb771ab2eee7a8;hb=refs%2Fheads%2Frelease%2FJAL-1645_r29;hp=39d713d5cd75032dab7dc346a079bcb9430d19ff;hpb=70f9c4700f20a8fa57ed7eb974277d8bad0723c2;p=jalview.git diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 39d713d..9b15eb5 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -1,6 +1,6 @@ /* - * 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) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -21,22 +21,13 @@ 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.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; @@ -46,24 +37,37 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.gui.AlignViewport; -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.json.binding.biojson.v1.AlignmentAnnotationPojo; +import jalview.json.binding.biojson.v1.AlignmentPojo; +import jalview.json.binding.biojson.v1.AnnotationPojo; +import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper; +import jalview.json.binding.biojson.v1.SequenceFeaturesPojo; +import jalview.json.binding.biojson.v1.SequenceGrpPojo; +import jalview.json.binding.biojson.v1.SequencePojo; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +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.Vector; + +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; public class JSONFile extends AlignFile implements ComplexAlignFile { private ColourSchemeI colourScheme; - private String version = "2.9"; + private static String version = new BuildDetails().getVersion(); - private String webstartUrl = "www.jalview.org/services/launchApp"; + private String webstartUrl = "http://www.jalview.org/services/launchApp"; private String application = "Jalview"; @@ -81,8 +85,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile private FeatureRenderer fr; - private JSONExportSettings jsonExportSettings; - private List hiddenColumns; private ColumnSelection columnSelection; @@ -109,13 +111,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile @Override public void parse() throws IOException { - StringBuilder jsonStringBuilder = new StringBuilder(); - String currentLine; - while ((currentLine = nextLine()) != null) - { - jsonStringBuilder.append(currentLine); - } - parse(jsonStringBuilder.toString()); + parse(getReader()); } @@ -125,24 +121,51 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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; @@ -160,45 +183,43 @@ public class JSONFile extends AlignFile implements ComplexAlignFile jsonSeqPojo.setSeq(seq.getSequenceAsString()); jsonAlignmentPojo.getSeqs().add(jsonSeqPojo); } - - if (jsonExportSettings.isExportJalviewSettings()) + 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 = 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)); } - if (jsonExportSettings.isExportSequenceFeatures()) + if (exportSettings.isExportFeatures()) { jsonAlignmentPojo .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr)); } - if (jsonExportSettings.isExportGroups() && seqGroups != null + if (exportSettings.isExportGroups() && seqGroups != null && seqGroups.size() > 0) { for (SequenceGroup seqGrp : seqGroups) @@ -216,7 +237,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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); } @@ -233,7 +255,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return jsonOutput; } - public String[] exportHiddenSections() + public String[] getHiddenSections() { String[] hiddenSections = new String[2]; if (getViewport() == null) @@ -283,11 +305,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return hiddenSections; } - public static List sequenceFeatureToJsonPojo( + public List sequenceFeatureToJsonPojo( List seqs, FeatureRenderer fr) { - FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr - .getFeaturesDisplayed(); + displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); List sequenceFeaturesPojo = new ArrayList(); for (SequenceI seq : seqs) { @@ -309,9 +330,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { 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())); @@ -365,7 +386,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } @SuppressWarnings("unchecked") - public JSONFile parse(String jsonAlignmentString) + public JSONFile parse(Reader jsonAlignmentString) { try { @@ -435,12 +456,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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 grpSeqs = new ArrayList(); - if (seqsHashArray.size() > 0) + if (sequenceRefs.size() > 0) { - Iterator seqHashIter = seqsHashArray.iterator(); + Iterator seqHashIter = sequenceRefs.iterator(); while (seqHashIter.hasNext()) { String seqHash = seqHashIter.next(); @@ -451,9 +472,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile } } } - ColourSchemeI scheme = getJalviewColorScheme(colourScheme); - SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, scheme, - displayBoxes, displayText, colourText, startRes, endRes); + ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme); + SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, + grpColourScheme, displayBoxes, displayText, colourText, + startRes, endRes); seqGrp.setShowNonconserved(showNonconserved); seqGrp.setDescription(description); this.seqGroups.add(seqGrp); @@ -482,9 +504,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile 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().charAt(0); + String displayChar = annot.get("displayCharacter") == null ? "" + : annot.get("displayCharacter").toString(); annotations[count] = new Annotation(displayChar, desc, ss, val); } @@ -508,9 +531,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { 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); } } @@ -518,15 +543,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile public void parseHiddenCols(JSONObject jvSettingsJson) { - // hiddenColumns = new ArrayList(); 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("-"); - // hiddenColumns.add(new int[] - // { Integer.valueOf(range[0]), Integer.valueOf(range[1]) }); columnSelection.hideColumns(Integer.valueOf(range[0]), Integer.valueOf(range[1])); } @@ -538,6 +562,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { if (jsonSeqFeatures != null) { + displayedFeatures = new FeaturesDisplayed(); for (Iterator seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr .hasNext();) { @@ -549,9 +574,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile String descripiton = (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(); @@ -572,6 +594,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile sequenceFeature.setBegin(seq.findPosition(begin.intValue())); sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1); seq.addSequenceFeature(sequenceFeature); + displayedFeatures.setVisible(type); } } } @@ -592,14 +615,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile return jalviewColor; } - public AlignViewportI getViewport(AlignmentI al) - { - AlignViewportI viewport = new AlignViewport(al, getColumnSelection()); - viewport.setGlobalColourScheme(getColourScheme()); - viewport.setShowSequenceFeatures(isShowSeqFeatures()); - return viewport; - } - public String getGlobalColorScheme() { return globalColorScheme; @@ -620,6 +635,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile this.colourScheme = colourScheme; } + @Override public FeaturesDisplayedI getDisplayedFeatures() { return displayedFeatures; @@ -630,44 +646,33 @@ public class JSONFile extends AlignFile implements ComplexAlignFile this.displayedFeatures = displayedFeatures; } - public JSONExportSettings getJsonExportSettings() + public void configureForView(AlignmentViewPanel avpanel) { - return jsonExportSettings; - } + super.configureForView(avpanel); + AlignViewportI viewport = avpanel.getAlignViewport(); + AlignmentI alignment = viewport.getAlignment(); + AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); - public void setJsonExportSettings(JSONExportSettings jsonExportSettings) - { - this.jsonExportSettings = jsonExportSettings; - } + seqGroups = alignment.getGroups(); + fr = avpanel.cloneFeatureRenderer(); - - public static String getJSONData(AlignViewportI av) - { - JSONFile jsonFile = new JSONFile(); - jsonFile.setViewport(av); - jsonFile.seqGroups = av.getAlignment().getGroups(); - jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed()); - - for (SequenceI seq : av.getAlignment().getSequences()) - { - jsonFile.seqs.add(seq); - } - // Add non auto calculated annotation to AlignFile - for (AlignmentAnnotation annot : av.getAlignment() - .getAlignmentAnnotation()) + for (AlignmentAnnotation annot : annots) { if (annot != null && !annot.autoCalculated) { - if (annot.label.equals("PDB.CATempFactor")) + if (!annot.visible) { continue; } - jsonFile.annotations.add(annot); + annotations.add(annot); } } - String jsonString = jsonFile.print(); - return jsonString; + globalColorScheme = ColourSchemeProperty.getColourName(viewport + .getGlobalColourScheme()); + setDisplayedFeatures(viewport.getFeaturesDisplayed()); + showSeqFeatures = viewport.isShowSequenceFeatures(); + } public boolean isShowSeqFeatures() @@ -704,8 +709,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile { if (hiddenSequences == null || hiddenSequences.isEmpty()) { - return new SequenceI[] - {}; + return new SequenceI[] {}; } synchronized (hiddenSequences) {