X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=6f7bebe9f7025b160e17405758fb3053b724cad1;hb=74393b51f368cb9f58589472d432a433d9c4386d;hp=3632cc74957d8b0eee2af92a03ec912694571a45;hpb=bb620cae1e4c44ae9efaf975c7bbbc63b0558db3;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 3632cc7..6f7bebe 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -503,8 +503,8 @@ public class FeaturesFileTest expected = "METAL\tcc9900\n" + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" - + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "ENDGROUP\tuniprot\n"; assertEquals(expected, exported); @@ -521,9 +521,9 @@ public class FeaturesFileTest + "Pfam\tff0000\n" + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" - + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "ENDGROUP\tuniprot\n" // null / empty group features are output after named groups + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" @@ -660,8 +660,8 @@ public class FeaturesFileTest // 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"; assertEquals(expected, exported); } @@ -779,7 +779,7 @@ public class FeaturesFileTest /* * now threshold to Score > 1.1 - should exclude sf2 */ - FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK, + FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK, Color.white, 0f, 2f); fc.setAboveThreshold(true); fc.setThreshold(1.1f); @@ -855,7 +855,7 @@ public class FeaturesFileTest * 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, Color.white, 0f, 2f); fc.setAboveThreshold(true); fc.setThreshold(1.1f);