X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=bdd2dcbccd1a4b2bcc4741897556221cb98bd3c2;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=fcedb2b6abbfd84b739681c167042f6584fd13a5;hpb=e2d6753e8cf3c5eaf8bccf34f4f5e9d651e9cb8e;p=jalview.git
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index fcedb2b..bdd2dcb 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -1,28 +1,59 @@
+/*
+ * 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.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.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.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.schemes.ColourSchemeProperty;
+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.JalviewColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.ColorUtils;
+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;
@@ -33,21 +64,15 @@ 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 ColourSchemeI colourScheme;
-
- // private static boolean seqFeaturesEnabled;
-
- private String jalviewVersion;
+ private static String version = new BuildDetails().getVersion();
- private String webStartLaunchServletUrl;
+ private String webstartUrl = "http://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;
@@ -55,11 +80,17 @@ public class JSONFile extends AlignFile
private FeaturesDisplayedI displayedFeatures;
- // private AlignViewportI viewport;
-
private FeatureRenderer fr;
- private JSONExportSettings jsonExportSettings;
+ private List hiddenColumns;
+
+ private ColumnSelection columnSelection;
+
+ private List hiddenSeqRefs;
+
+ private ArrayList hiddenSequences;
+
+ private final static String TCOFFEE_SCORE = "TCoffeeScore";
public JSONFile()
{
@@ -71,58 +102,80 @@ 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
{
- 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();
- // setSeqFeaturesEnabled(viewport.isShowSequenceFeatures());
+ 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())
.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());
@@ -130,43 +183,63 @@ public class JSONFile extends AlignFile
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)
{
- jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
- webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
- "www.jalview.org", "http://www.jalview.org")
- + "/services/launchApp";
-
- 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));
}
+ 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));
+ .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
}
- 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));
+ seqGrpPojo.setColourScheme(seqGrp.cs.getSchemeName());
seqGrpPojo.setColourText(seqGrp.getColourText());
seqGrpPojo.setDescription(seqGrp.getDescription());
seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@ -176,36 +249,92 @@ 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(
+ 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 static List sequenceFeatureToJsonPojo(
- List seqs, FeatureRenderer fr)
+ public String[] getHiddenSections()
{
- FeaturesDisplayedI displayedFeatures = (fr == null) ? null : fr
- .getFeaturesDisplayed();
+ String[] hiddenSections = new String[2];
+ if (getViewport() == null)
+ {
+ return null;
+ }
+
+ // hidden column business
+ if (getViewport().hasHiddenColumns())
+ {
+ List 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 List sequenceFeatureToJsonPojo(
+ SequenceI[] sqs, FeatureRenderer fr)
+ {
+ displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List sequenceFeaturesPojo = new ArrayList();
- for (SequenceI seq : seqs)
+ if (sqs == null)
+ {
+ return sequenceFeaturesPojo;
+ }
+
+ for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
: seq.getDatasetSequence().getSequenceFeatures();
+ seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+ : seqFeatures;
if (seqFeatures == null)
{
continue;
@@ -217,10 +346,10 @@ public class JSONFile extends AlignFile
&& 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,
+ .getHexString(fr.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
@@ -251,6 +380,26 @@ public class JSONFile extends AlignFile
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();
@@ -260,12 +409,28 @@ 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);
@@ -274,7 +439,7 @@ public class JSONFile extends AlignFile
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
@@ -289,19 +454,20 @@ public class JSONFile extends AlignFile
JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
.get("seqGroups");
JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
- .get("jalviewSettings");
+ .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);
setShowSeqFeatures(showFeatures);
+ parseHiddenSeqRefsAsList(jvSettingsJsonObj);
+ parseHiddenCols(jvSettingsJsonObj);
}
+ hiddenSequences = new ArrayList();
seqMap = new Hashtable();
for (Iterator sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
@@ -314,9 +480,14 @@ 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
@@ -338,12 +509,12 @@ public class JSONFile extends AlignFile
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();
@@ -354,9 +525,10 @@ public class JSONFile extends AlignFile
}
}
}
- 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);
@@ -384,12 +556,20 @@ public class JSONFile extends AlignFile
.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);
+ if (annot.get("colour") != null)
+ {
+ Color color = ColorUtils.parseColourString(annot.get(
+ "colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
@@ -397,9 +577,65 @@ public class JSONFile extends AlignFile
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();
@@ -407,12 +643,42 @@ public class JSONFile extends AlignFile
return this;
}
+ public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
+ {
+ hiddenSeqRefs = new ArrayList();
+ 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 seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
.hasNext();)
{
@@ -424,9 +690,6 @@ public class JSONFile extends AlignFile
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();
@@ -447,110 +710,113 @@ public class JSONFile extends AlignFile
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)
+ @Override
+ public String getGlobalColourScheme()
{
- ColourSchemeI jalviewColor = null;
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
- {
- jalviewColor = cs.getJvColourScheme();
- break;
- }
- }
- return jalviewColor;
+ return globalColourScheme;
}
- public void LoadAlignmentFeatures(AlignFrame af)
+ public void setGlobalColorScheme(String globalColourScheme)
{
- af.setShowSeqFeatures(isShowSeqFeatures());
- af.changeColour(getColourScheme());
- af.setMenusForViewport();
+ this.globalColourScheme = globalColourScheme;
}
- public String getGlobalColorScheme()
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
{
- return globalColorScheme;
+ return displayedFeatures;
}
- public void setGlobalColorScheme(String globalColorScheme)
+ public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
{
- this.globalColorScheme = globalColorScheme;
+ this.displayedFeatures = displayedFeatures;
}
- public ColourSchemeI getColourScheme()
+ @Override
+ public void configureForView(AlignmentViewPanel avpanel)
{
- return colourScheme;
+ if (avpanel == null)
+ {
+ 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)
+ {
+ if (annot != null && !annot.autoCalculated)
+ {
+ annotations.add(annot);
+ }
+ }
+ }
+ globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
+ setDisplayedFeatures(viewport.getFeaturesDisplayed());
+ showSeqFeatures = viewport.isShowSequenceFeatures();
+
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ @Override
+ public boolean isShowSeqFeatures()
{
- this.colourScheme = colourScheme;
+ return showSeqFeatures;
}
- public FeaturesDisplayedI getDisplayedFeatures()
+ public void setShowSeqFeatures(boolean showSeqFeatures)
{
- return displayedFeatures;
+ this.showSeqFeatures = showSeqFeatures;
}
- public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)
+ public Vector getAnnotations()
{
- this.displayedFeatures = displayedFeatures;
+ return annotations;
}
- public JSONExportSettings getJsonExportSettings()
+ public List getHiddenColumns()
{
- return jsonExportSettings;
+ return hiddenColumns;
}
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+ @Override
+ public ColumnSelection getColumnSelection()
{
- this.jsonExportSettings = jsonExportSettings;
+ return columnSelection;
}
- public static String getJSONData(AlignViewportI av)
+ public void setColumnSelection(ColumnSelection columnSelection)
{
- JSONFile jsonFile = new JSONFile();
- jsonFile.setViewport(av);
- jsonFile.seqGroups = av.getAlignment().getGroups();
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+ this.columnSelection = columnSelection;
+ }
- for (SequenceI seq : av.getAlignment().getSequences())
+ @Override
+ public SequenceI[] getHiddenSequences()
+ {
+ if (hiddenSequences == null || hiddenSequences.isEmpty())
{
- jsonFile.seqs.add(seq);
+ return new SequenceI[] {};
}
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
+ synchronized (hiddenSequences)
{
- if (annot != null && !annot.autoCalculated)
- {
- if (annot.label.equals("PDB.CATempFactor"))
- {
- continue;
- }
- jsonFile.annotations.add(annot);
- }
+ return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
}
- String jsonString = jsonFile.print();
- return jsonString;
- }
-
- public boolean isShowSeqFeatures()
- {
- return showSeqFeatures;
}
- public void setShowSeqFeatures(boolean showSeqFeatures)
+ public void setHiddenSequences(ArrayList hiddenSequences)
{
- this.showSeqFeatures = showSeqFeatures;
+ this.hiddenSequences = hiddenSequences;
}
public class JSONExportSettings
@@ -615,4 +881,19 @@ 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();
+ }
}