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Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...
[jalview.git]
/
src
/
jalview
/
io
/
JSONFile.java
diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
60e48a9
..
27ebe5a
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;
@@
-115,7
+116,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
}
@Override
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
String jsonOutput = null;
try
{
String jsonOutput = null;
try
@@
-168,7
+169,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
}
int count = 0;
}
int count = 0;
- for (SequenceI seq : seqs)
+ for (SequenceI seq : sqs)
{
StringBuilder name = new StringBuilder();
name.append(seq.getName()).append("/").append(seq.getStart())
{
StringBuilder name = new StringBuilder();
name.append(seq.getName()).append("/").append(seq.getStart())
@@
-215,17
+216,20
@@
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);
}
}
if (exportSettings.isExportFeatures())
{
jsonAlignmentPojo
}
}
if (exportSettings.isExportFeatures())
{
jsonAlignmentPojo
- .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+ .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
}
if (exportSettings.isExportGroups() && seqGroups != null
}
if (exportSettings.isExportGroups() && seqGroups != null
@@
-235,8
+239,8
@@
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.getColourScheme()
+ .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());
@@
-315,11
+319,16
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
}
public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
}
public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
- List<SequenceI> seqs, FeatureRenderer fr)
+ SequenceI[] sqs, FeatureRenderer fr)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
- for (SequenceI seq : seqs)
+ if (sqs == null)
+ {
+ return sequenceFeaturesPojo;
+ }
+
+ for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
{
SequenceI dataSetSequence = seq.getDatasetSequence();
SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
@@
-519,8
+528,8
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
displayBoxes, displayText, colourText, startRes, endRes);
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
displayBoxes, displayText, colourText, startRes, endRes);
- seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
- seqGrp);
+ seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
+ colourScheme, seqGrp));
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
@@
-558,7
+567,7
@@
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;
}
@@
-732,6
+741,10
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
@Override
public void configureForView(AlignmentViewPanel avpanel)
{
@Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ if (avpanel == null)
+ {
+ return;
+ }
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
@@
-751,8
+764,7
@@
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();