expected = "METAL\tcc9900\n"
+ "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
expected = "METAL\tcc9900\n"
+ "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ "ENDGROUP\tuniprot\n"
// null / empty group features are output after named groups
+ "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ "ENDGROUP\tuniprot\n"
// null / empty group features are output after named groups
+ "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
// Pfam feature columns include strand(+), phase(2), attributes
expected = gffHeader
+ "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
// Pfam feature columns include strand(+), phase(2), attributes
expected = gffHeader
+ "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
- + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
- + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
+ + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
+ + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
- FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK,
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
* now threshold to Score > 1.1 - should exclude sf2
* (and there should be no empty STARTGROUP/ENDGROUP output)
*/
* now threshold to Score > 1.1 - should exclude sf2
* (and there should be no empty STARTGROUP/ENDGROUP output)
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK,
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,