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JAL-2446 optimised new method to find feature colour for overview
[jalview.git]
/
src
/
jalview
/
io
/
JSONFile.java
diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
bdd2dcb
..
053a65e
100644
(file)
--- a/
src/jalview/io/JSONFile.java
+++ b/
src/jalview/io/JSONFile.java
@@
-46,6
+46,7
@@
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.renderer.seqfeatures.FeatureColourFinder;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
@@
-239,7
+240,8
@@
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(seqGrp.cs.getSchemeName());
+ 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());
@@
-327,6
+329,8
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
return sequenceFeaturesPojo;
}
return sequenceFeaturesPojo;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
@@
-349,7
+353,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr.findFeatureColour(Color.white, seq,
+ .getHexString(finder.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
@@
-527,8
+531,8
@@
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);