+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
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.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.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.AlignmentViewport;
+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 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 ColourSchemeI colourScheme;
- private static boolean seqFeaturesEnabled;
+ private static String version = new BuildDetails().getVersion();
- private String jalviewVersion;
+ private String webstartUrl = "http://www.jalview.org/services/launchApp";
- private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+ private String application = "Jalview";
public static final String FILE_EXT = "json";
private FeaturesDisplayedI displayedFeatures;
- private AlignmentViewport av;
+ private FeatureRenderer fr;
+
+ private List<int[]> hiddenColumns;
+
+ private ColumnSelection columnSelection;
+
+ private List<String> hiddenSeqRefs;
- private JSONExportSettings jsonExportSettings;
+ private ArrayList<SequenceI> hiddenSequences;
public JSONFile()
{
@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()
{
+ 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 (Desktop.getCurrentAlignFrame() != 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(Desktop
- .getCurrentAlignFrame().getViewport()
- .getGlobalColourScheme());
- this.av = Desktop.getCurrentAlignFrame().getCurrentView();
- setDisplayedFeatures(av.getFeaturesDisplayed());
- showSeqFeatures = Desktop.getCurrentAlignFrame().showSeqFeatures
- .isSelected();
+ 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;
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());
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)
{
- 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 (jsonExportSettings.isExportAnnotations())
+ if (exportSettings.isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (jsonExportSettings.isExportSequenceFeatures())
+ if (exportSettings.isExportFeatures())
{
- jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(seqs,
- getDisplayedFeatures()));
+ jsonAlignmentPojo
+ .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (jsonExportSettings.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(
- seq.getName() + "_" + seq.hashCode());
+ seqGrpPojo.getSequenceRefs()
+ .add(String.valueOf(seq.hashCode()));
}
jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
}
}
- com.json.JSONObject generatedJSon = new com.json.JSONObject(
+ org.json.JSONObject generatedJSon = new org.json.JSONObject(
jsonAlignmentPojo);
- String jsonOutput = generatedJSon.toString();
+ jsonOutput = generatedJSon.toString();
return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
"xEnd");
} catch (Exception e)
{
e.printStackTrace();
- throw e;
}
+ return jsonOutput;
+ }
+
+ public String[] getHiddenSections()
+ {
+ String[] hiddenSections = new String[2];
+ if (getViewport() == null)
+ {
+ return null;
+ }
+
+ // hidden column business
+ if (getViewport().hasHiddenColumns())
+ {
+ List<int[]> hiddenCols = getViewport().getColumnSelection()
+ .getHiddenColumns();
+ StringBuilder hiddenColsBuilder = new StringBuilder();
+ for (int[] range : hiddenCols)
+ {
+ hiddenColsBuilder.append(";").append(range[0]).append("-")
+ .append(range[1]);
+ }
+
+ hiddenColsBuilder.deleteCharAt(0);
+ hiddenSections[0] = hiddenColsBuilder.toString();
+ }
+
+ // 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;
}
- public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- List<SequenceI> seqs, FeaturesDisplayedI displayedFeatures)
+ public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+ List<SequenceI> seqs, FeatureRenderer fr)
{
+ displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
for (SequenceI seq : seqs)
{
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
: seq.getDatasetSequence().getSequenceFeatures();
+ seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+ : seqFeatures;
if (seqFeatures == null)
{
continue;
&& displayedFeatures.isVisible(sf.getType()))
{
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
- seq.getName() + "_" + seq.hashCode());
+ 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.setLinks(sf.links);
jsonFeature.setOtherDetails(sf.otherDetails);
jsonFeature.setScore(sf.getScore());
+ jsonFeature.setFillColor(featureColour);
jsonFeature.setFeatureGroup(sf.getFeatureGroup());
sequenceFeaturesPojo.add(jsonFeature);
}
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
.get("seqGroups");
JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
- .get("jalviewSettings");
+ .get("appSettings");
if (jvSettingsJsonObj != null)
{
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
setColourScheme(getJalviewColorScheme(jsColourScheme));
- JSONFile.setSeqFeaturesEnabled(showFeatures);
+ setShowSeqFeatures(showFeatures);
+ parseHiddenSeqRefsAsList(jvSettingsJsonObj);
+ parseHiddenCols(jvSettingsJsonObj);
}
+ hiddenSequences = new ArrayList<SequenceI>();
seqMap = new Hashtable<String, Sequence>();
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
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);
}
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,
- 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);
.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();
+ 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);
}
return this;
}
+ public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
+ {
+ hiddenSeqRefs = new ArrayList<String>();
+ String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
+ if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
+ {
+ String[] seqRefs = hiddenSeqs.split(";");
+ for (String seqRef : seqRefs)
+ {
+ hiddenSeqRefs.add(seqRef);
+ }
+ }
+ }
+
+ public void parseHiddenCols(JSONObject jvSettingsJson)
+ {
+ String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
+ if (hiddenCols != null && !hiddenCols.isEmpty())
+ {
+ columnSelection = new ColumnSelection();
+ String[] rangeStrings = hiddenCols.split(";");
+ for (String rangeString : rangeStrings)
+ {
+ String[] range = rangeString.split("-");
+ columnSelection.hideColumns(Integer.valueOf(range[0]),
+ Integer.valueOf(range[1]));
+ }
+ }
+ }
@SuppressWarnings("unchecked")
private void parseFeatures(JSONArray jsonSeqFeatures)
{
if (jsonSeqFeatures != null)
{
+ displayedFeatures = new FeaturesDisplayed();
for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
.hasNext();)
{
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();
sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
seq.addSequenceFeature(sequenceFeature);
+ displayedFeatures.setVisible(type);
}
}
}
- public ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
+ public static ColourSchemeI getJalviewColorScheme(
+ String bioJsColourSchemeName)
{
ColourSchemeI jalviewColor = null;
for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
.values())
{
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
+ if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)
+ || cs.getJalviewName()
+ .equalsIgnoreCase(bioJsColourSchemeName))
{
jalviewColor = cs.getJvColourScheme();
break;
return jalviewColor;
}
- public void LoadAlignmentFeatures(AlignFrame af)
- {
- af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
- af.changeColour(getColourScheme());
- af.setMenusForViewport();
- }
-
public String getGlobalColorScheme()
{
return globalColorScheme;
this.globalColorScheme = globalColorScheme;
}
- public static ColourSchemeI getColourScheme()
+ public ColourSchemeI getColourScheme()
{
return colourScheme;
}
- public static void setColourScheme(ColourSchemeI colourScheme)
+ public void setColourScheme(ColourSchemeI colourScheme)
{
- JSONFile.colourScheme = colourScheme;
+ this.colourScheme = colourScheme;
}
- public static boolean isSeqFeaturesEnabled()
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
{
- return seqFeaturesEnabled;
+ return displayedFeatures;
}
- public static void setSeqFeaturesEnabled(boolean seqFeaturesEnabled)
+ public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
{
- JSONFile.seqFeaturesEnabled = seqFeaturesEnabled;
+ this.displayedFeatures = displayedFeatures;
}
- public FeaturesDisplayedI getDisplayedFeatures()
+ public void configureForView(AlignmentViewPanel avpanel)
{
- return displayedFeatures;
+ 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 : annots)
+ {
+ if (annot != null && !annot.autoCalculated)
+ {
+ if (!annot.visible)
+ {
+ continue;
+ }
+ annotations.add(annot);
+ }
+ }
+ globalColorScheme = ColourSchemeProperty.getColourName(viewport
+ .getGlobalColourScheme());
+ setDisplayedFeatures(viewport.getFeaturesDisplayed());
+ showSeqFeatures = viewport.isShowSequenceFeatures();
+
}
- public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
+ public boolean isShowSeqFeatures()
{
- this.displayedFeatures = displayedFeatures;
+ return showSeqFeatures;
+ }
+
+ public void setShowSeqFeatures(boolean showSeqFeatures)
+ {
+ this.showSeqFeatures = showSeqFeatures;
+ }
+
+ public Vector<AlignmentAnnotation> getAnnotations()
+ {
+ return annotations;
+ }
+
+ public List<int[]> getHiddenColumns()
+ {
+ return hiddenColumns;
+ }
+
+ public ColumnSelection getColumnSelection()
+ {
+ return columnSelection;
}
- public JSONExportSettings getJsonExportSettings()
+ public void setColumnSelection(ColumnSelection columnSelection)
{
- return jsonExportSettings;
+ this.columnSelection = columnSelection;
+ }
+
+ public SequenceI[] getHiddenSequences()
+ {
+ if (hiddenSequences == null || hiddenSequences.isEmpty())
+ {
+ return new SequenceI[] {};
+ }
+ synchronized (hiddenSequences)
+ {
+ return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
+ }
}
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+ public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
{
- this.jsonExportSettings = jsonExportSettings;
+ this.hiddenSequences = hiddenSequences;
}
public class JSONExportSettings
git://source.jalview.org / jalview.git / blobdiff