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JAL-2360 refactoring for JalviewColourScheme enum,
[jalview.git]
/
src
/
jalview
/
io
/
JSONFile.java
diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
7a12076
..
bdd2dcb
100644
(file)
--- a/
src/jalview/io/JSONFile.java
+++ b/
src/jalview/io/JSONFile.java
@@
-46,8
+46,9
@@
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.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.ColorUtils;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
@@
-215,10
+216,13
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
{
// These color schemes require annotation, disable them if annotations
// are not exported
{
// These color schemes require annotation, disable them if annotations
// are not exported
- if (globalColourScheme.equalsIgnoreCase("RNA Helices")
- || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+ if (globalColourScheme
+ .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
+ || globalColourScheme
+ .equalsIgnoreCase(JalviewColourScheme.TCoffee
+ .toString()))
{
{
- jsonAlignmentPojo.setGlobalColorScheme("None");
+ jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
}
}
}
}
@@
-235,8
+239,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
{
SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
seqGrpPojo.setGroupName(seqGrp.getName());
{
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());
seqGrpPojo.setColourText(seqGrp.getColourText());
seqGrpPojo.setDescription(seqGrp.getDescription());
seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@
-563,7
+566,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
annotations[count] = new Annotation(displayChar, desc, ss, val);
if (annot.get("colour") != null)
{
annotations[count] = new Annotation(displayChar, desc, ss, val);
if (annot.get("colour") != null)
{
- Color color = UserColourScheme.getColourFromString(annot.get(
+ Color color = ColorUtils.parseColourString(annot.get(
"colour").toString());
annotations[count].colour = color;
}
"colour").toString());
annotations[count].colour = color;
}
@@
-760,8
+763,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
}
}
}
}
}
}
- globalColourScheme = ColourSchemeProperty.getColourName(viewport
- .getGlobalColourScheme());
+ globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();