X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=090de6f9891aa680d0e27019a92714d33526e11f;hb=8dcca4766ed3d696a6160565ef43e21662557008;hp=ab0728943d3d6ba26ea12d7558a6042fb93da532;hpb=84ed42e8d0aa07b03441b045d240ebb51f94c53c;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index ab07289..090de6f 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -476,18 +476,20 @@ public class FeaturesFileTest */ FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); String exported = featuresFile - .printJalviewFormat(al.getSequencesArray(), fr, false); + .printJalviewFormat(al.getSequencesArray(), fr, false, false); String expected = "No Features Visible"; assertEquals(expected, exported); /* - * include non-positional features + * include non-positional features, but still no positional features */ fr.setGroupVisibility("uniprot", true); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - true); - expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" - + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" + true, false); + expected = "\nSTARTGROUP\tuniprot\n" + + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + + "ENDGROUP\tuniprot\n\n" + + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n" + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output assertEquals(expected, exported); @@ -497,12 +499,12 @@ public class FeaturesFileTest fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); 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); @@ -511,21 +513,48 @@ public class FeaturesFileTest */ fr.setVisible("Pfam"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); /* - * features are output within group, ordered by sequence and by type + * features are output within group, ordered by sequence and type */ expected = "METAL\tcc9900\n" + "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" + + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; + assertEquals(expected, exported); + + /* + * hide uniprot group + */ + fr.setGroupVisibility("uniprot", false); + expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" + + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" + + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false, false); + assertEquals(expected, exported); + + /* + * include non-positional (overrides group not shown) + */ + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + true, false); + expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" + + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + + "\nSTARTGROUP\tuniprot\n" + + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + "ENDGROUP\tuniprot\n" - // null / empty group features output after features in named - // groups: + + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" + + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; assertEquals(expected, exported); } @@ -544,11 +573,11 @@ public class FeaturesFileTest FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel .getFeatureRenderer(); String exported = featuresFile.printGffFormat(al.getSequencesArray(), - fr, false); + fr, false, false); String gffHeader = "##gff-version 2\n"; assertEquals(gffHeader, exported); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); + true, false); assertEquals(gffHeader, exported); /* @@ -585,7 +614,7 @@ public class FeaturesFileTest * with no features displayed, exclude non-positional features */ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); assertEquals(gffHeader, exported); /* @@ -594,7 +623,7 @@ public class FeaturesFileTest fr.setGroupVisibility("Uniprot", true); fr.setGroupVisibility("s3dm", false); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); + true, false); String expected = gffHeader + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n"; assertEquals(expected, exported); @@ -606,7 +635,7 @@ public class FeaturesFileTest fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); // METAL feature has null group: description used for column 2 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"; assertEquals(expected, exported); @@ -616,7 +645,7 @@ public class FeaturesFileTest */ fr.setGroupVisibility("s3dm", true); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); // METAL feature has null group: description used for column 2 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"; @@ -627,12 +656,12 @@ public class FeaturesFileTest */ fr.setVisible("Pfam"); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); // 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); } @@ -741,7 +770,7 @@ public class FeaturesFileTest fr.setVisible("METAL"); fr.setColour("METAL", new FeatureColour(Color.PINK)); String exported = featuresFile.printGffFormat(al.getSequencesArray(), - fr, false); + fr, false, false); String expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; @@ -750,13 +779,13 @@ 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); fr.setColour("METAL", fc); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"; assertEquals(expected, exported); @@ -765,7 +794,7 @@ public class FeaturesFileTest */ fc.setAboveThreshold(false); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; assertEquals(expected, exported); @@ -778,7 +807,7 @@ public class FeaturesFileTest "clin_sig")); fr.setFeatureFilter("METAL", filter); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; assertEquals(expected, exported); } @@ -814,7 +843,7 @@ public class FeaturesFileTest fr.setColour("METAL", new FeatureColour(Color.PINK)); String exported = featuresFile.printJalviewFormat( al.getSequencesArray(), - fr, false); + fr, false, false); String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n" + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n" @@ -826,13 +855,13 @@ 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); fr.setColour("METAL", fc); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n" + "STARTGROUP\tgrp1\n" + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" @@ -844,7 +873,7 @@ public class FeaturesFileTest */ fc.setAboveThreshold(false); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n" + "STARTGROUP\tgrp1\n" + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" @@ -861,7 +890,7 @@ public class FeaturesFileTest "clin_sig")); fr.setFeatureFilter("METAL", filter); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n" + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"