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JAL-2416 order score models by order of addition rather than name
[jalview.git]
/
src
/
jalview
/
io
/
FeaturesFile.java
diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
07a3b25
..
48eeee3
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-35,11
+35,12
@@
import jalview.io.gff.GffHelperBase;
import jalview.io.gff.GffHelperFactory;
import jalview.io.gff.GffHelperI;
import jalview.schemes.FeatureColour;
import jalview.io.gff.GffHelperFactory;
import jalview.io.gff.GffHelperI;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MapList;
import jalview.util.ParseHtmlBodyAndLinks;
import jalview.util.StringUtils;
import jalview.util.MapList;
import jalview.util.ParseHtmlBodyAndLinks;
import jalview.util.StringUtils;
+import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
@@
-140,8
+141,7
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
* @return true if features were added
*/
public boolean parse(AlignmentI align,
* @return true if features were added
*/
public boolean parse(AlignmentI align,
- Map<String, FeatureColourI> colours,
- boolean removeHTML)
+ Map<String, FeatureColourI> colours, boolean removeHTML)
{
return parse(align, colours, removeHTML, false);
}
{
return parse(align, colours, removeHTML, false);
}
@@
-178,8
+178,8
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
* @return true if features were added
*/
public boolean parse(AlignmentI align,
* @return true if features were added
*/
public boolean parse(AlignmentI align,
- Map<String, FeatureColourI> colours,
- boolean removeHTML, boolean relaxedIdmatching)
+ Map<String, FeatureColourI> colours, boolean removeHTML,
+ boolean relaxedIdmatching)
{
Map<String, String> gffProps = new HashMap<String, String>();
/*
{
Map<String, String> gffProps = new HashMap<String, String>();
/*
@@
-356,8
+356,8
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
* Perhaps an old style groups file with no colours -
* synthesize a colour from the feature type
*/
* Perhaps an old style groups file with no colours -
* synthesize a colour from the feature type
*/
- UserColourScheme ucs = new UserColourScheme(ft);
- featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
+ Color colour = ColorUtils.createColourFromName(ft);
+ featureColours.put(ft, new FeatureColour(colour));
}
SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
endPos, featureGroup);
}
SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
endPos, featureGroup);
@@
-589,7
+589,8
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
{
for (SequenceFeature sequenceFeature : features)
{
{
for (SequenceFeature sequenceFeature : features)
{
- isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
+ isnonpos = sequenceFeature.begin == 0
+ && sequenceFeature.end == 0;
if ((!nonpos && isnonpos)
|| (!isnonpos && visOnly && !visible
.containsKey(sequenceFeature.type)))
if ((!nonpos && isnonpos)
|| (!isnonpos && visOnly && !visible
.containsKey(sequenceFeature.type)))