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JAL-1896 revised implementation to construct a ColourSchemeI instance after creating...
[jalview.git]
/
src
/
jalview
/
io
/
JSONFile.java
diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
717ab8b
..
8725556
100644
(file)
--- a/
src/jalview/io/JSONFile.java
+++ b/
src/jalview/io/JSONFile.java
@@
-28,7
+28,6
@@
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.bin.BuildDetails;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.bin.BuildDetails;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
@@
-45,7
+44,6
@@
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.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 jalview.schemes.ColourSchemeProperty;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
@@
-64,8
+62,6
@@
import org.json.simple.parser.JSONParser;
public class JSONFile extends AlignFile implements ComplexAlignFile
{
public class JSONFile extends AlignFile implements ComplexAlignFile
{
- private ColourSchemeI colourScheme;
-
private static String version = new BuildDetails().getVersion();
private String webstartUrl = "http://www.jalview.org/services/launchApp";
private static String version = new BuildDetails().getVersion();
private String webstartUrl = "http://www.jalview.org/services/launchApp";
@@
-76,7
+72,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
public static final String FILE_DESC = "JSON";
public static final String FILE_DESC = "JSON";
- private String globalColorScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
private boolean showSeqFeatures;
@@
-184,7
+180,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
jsonAlignmentPojo.getAppSettings().put("application", application);
jsonAlignmentPojo.getAppSettings().put("version", version);
jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
jsonAlignmentPojo.getAppSettings().put("application", application);
jsonAlignmentPojo.getAppSettings().put("version", version);
jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
@@
-389,7
+385,6
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
@SuppressWarnings("unchecked")
public JSONFile parse(Reader jsonAlignmentString)
{
@SuppressWarnings("unchecked")
public JSONFile parse(Reader jsonAlignmentString)
{
- String jsColourScheme = null;
try
{
JSONParser jsonParser = new JSONParser();
try
{
JSONParser jsonParser = new JSONParser();
@@
-407,7
+402,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
if (jvSettingsJsonObj != null)
{
if (jvSettingsJsonObj != null)
{
- jsColourScheme = (String) jvSettingsJsonObj
+ globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
.get("globalColorScheme");
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
@@
-437,12
+432,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
seqMap.put(seqUniqueId, seq);
}
seqMap.put(seqUniqueId, seq);
}
- if (jsColourScheme != null)
- {
- setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
- jsColourScheme,
- new Alignment(seqs.toArray(new SequenceI[0]))));
- }
+
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@
-529,7
+519,6
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
.toString(), annotations);
this.annotations.add(alignAnnot);
}
.toString(), annotations);
this.annotations.add(alignAnnot);
}
-
} catch (Exception e)
{
e.printStackTrace();
} catch (Exception e)
{
e.printStackTrace();
@@
-609,24
+598,14
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
}
}
}
}
- public String getGlobalColorScheme()
- {
- return globalColorScheme;
- }
-
- public void setGlobalColorScheme(String globalColorScheme)
- {
- this.globalColorScheme = globalColorScheme;
- }
-
- public ColourSchemeI getColourScheme()
+ public String getGlobalColourScheme()
{
{
- return colourScheme;
+ return globalColourScheme;
}
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setGlobalColorScheme(String globalColourScheme)
{
{
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
@Override
}
@Override
@@
-662,7
+641,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
annotations.add(annot);
}
}
annotations.add(annot);
}
}
- globalColorScheme = ColourSchemeProperty.getColourName(viewport
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();