From 36f0df29daedd58814b8a6ccd67a16dc3b1614b8 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 26 May 2016 10:38:07 +0100 Subject: [PATCH] JAL-2079 update examples to new pfam.xfam.org domain --- examples/exampleFeatures.txt | 28 ++++++++++++++-------------- examples/plantfdx.features | 30 +++++++++++++++--------------- test/jalview/io/FeaturesFileTest.java | 6 +++--- 3 files changed, 32 insertions(+), 32 deletions(-) diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt index 2dc4b6d..63c8326 100755 --- a/examples/exampleFeatures.txt +++ b/examples/exampleFeatures.txt @@ -30,69 +30,69 @@ Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL -Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam +Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL -Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam +Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL -Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam +Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath -Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam +Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL -Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam +Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath -Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam +Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL -Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam +Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL -Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam +Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL -Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam +Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL -Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam +Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL -Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam +Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath -Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam +Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL -Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam +Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath -Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam +Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath ENDGROUP uniprot diff --git a/examples/plantfdx.features b/examples/plantfdx.features index a23d152..872dadc 100644 --- a/examples/plantfdx.features +++ b/examples/plantfdx.features @@ -14,22 +14,22 @@ Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL -Description: Fer2 Status: True Positive Pfam 8_83 FER_CAPAA -1 8 83 Pfam +Description: Fer2 Status: True Positive Pfam 8_83 FER_CAPAA -1 8 83 Pfam Chloroplast FER_CAPAN -1 1 47 TRANSIT Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL Phosphothreonine FER_CAPAN -1 136 136 MOD_RES -Description: Fer2 Status: True Positive Pfam 55_130 FER_CAPAN -1 55 130 Pfam +Description: Fer2 Status: True Positive Pfam 55_130 FER_CAPAN -1 55 130 Pfam Chloroplast FER1_SOLLC -1 1 47 TRANSIT Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL -Description: Fer2 Status: True Positive Pfam 55_130 FER1_SOLLC -1 55 130 Pfam +Description: Fer2 Status: True Positive Pfam 55_130 FER1_SOLLC -1 55 130 Pfam Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL -Description: Fer2 Status: True Positive Pfam 55_130 Q93XJ9_SOLTU -1 55 130 Pfam +Description: Fer2 Status: True Positive Pfam 55_130 Q93XJ9_SOLTU -1 55 130 Pfam Chloroplast FER1_PEA -1 1 52 TRANSIT L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT @@ -38,14 +38,14 @@ Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT -Description: Fer2 Status: True Positive Pfam 60_135 FER1_PEA -1 60 135 Pfam -Description: Fer2 Status: True Positive Pfam 63_138 Q7XA98_TRIPR -1 63 138 Pfam +Description: Fer2 Status: True Positive Pfam 60_135 FER1_PEA -1 60 135 Pfam +Description: Fer2 Status: True Positive Pfam 63_138 Q7XA98_TRIPR -1 63 138 Pfam Chloroplast FER1_MESCR -1 1 51 TRANSIT Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL -Description: Fer2 Status: True Positive Pfam 59_134 FER1_MESCR -1 59 134 Pfam +Description: Fer2 Status: True Positive Pfam 59_134 FER1_MESCR -1 59 134 Pfam Chloroplast FER1_SPIOL -1 1 50 TRANSIT STRAND FER1_SPIOL -1 52 59 STRAND TURN FER1_SPIOL -1 60 61 TURN @@ -68,7 +68,7 @@ Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL STRAND FER1_SPIOL -1 130 133 STRAND STRAND FER1_SPIOL -1 135 138 STRAND HELIX FER1_SPIOL -1 142 144 HELIX -Description: Fer2 Status: True Positive Pfam 58_133 FER1_SPIOL -1 58 133 Pfam +Description: Fer2 Status: True Positive Pfam 58_133 FER1_SPIOL -1 58 133 Pfam I -> V FER3_RAPSA -1 8 8 VARIANT Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL @@ -77,25 +77,25 @@ S -> T FER3_RAPSA -1 55 55 VARIANT Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL R -> K FER3_RAPSA -1 91 91 VARIANT M -> V FER3_RAPSA -1 95 95 VARIANT -Description: Fer2 Status: True Positive Pfam 8_83 FER3_RAPSA -1 8 83 Pfam +Description: Fer2 Status: True Positive Pfam 8_83 FER3_RAPSA -1 8 83 Pfam Chloroplast FER1_ARATH -1 1 52 TRANSIT Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL -Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam +Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL -Description: Fer2 Status: True Positive Pfam 8_83 FER_BRANA -1 8 83 Pfam +Description: Fer2 Status: True Positive Pfam 8_83 FER_BRANA -1 8 83 Pfam Chloroplast FER2_ARATH -1 1 52 TRANSIT Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL -Description: Fer2 Status: True Positive Pfam 60_135 FER2_ARATH -1 60 135 Pfam -Description: Fer2 Status: True Positive Pfam 60_118 Q93Z60_ARATH -1 60 118 Pfam +Description: Fer2 Status: True Positive Pfam 60_135 FER2_ARATH -1 60 135 Pfam +Description: Fer2 Status: True Positive Pfam 60_118 Q93Z60_ARATH -1 60 118 Pfam Chloroplast FER1_MAIZE -1 1 52 TRANSIT STRAND FER1_MAIZE -1 57 59 STRAND STRAND FER1_MAIZE -1 72 74 STRAND @@ -113,6 +113,6 @@ Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL STRAND FER1_MAIZE -1 132 135 STRAND STRAND FER1_MAIZE -1 137 141 STRAND TURN FER1_MAIZE -1 142 142 TURN -Description: Fer2 Status: True Positive Pfam 60_135 FER1_MAIZE -1 60 135 Pfam -Description: Fer2 Status: True Positive Pfam 52_127 O80429_MAIZE -1 52 127 Pfam +Description: Fer2 Status: True Positive Pfam 60_135 FER1_MAIZE -1 60 135 Pfam +Description: Fer2 Status: True Positive Pfam 52_127 O80429_MAIZE -1 52 127 Pfam ENDGROUP uniprot diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 81d5b05..73d8826 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -104,7 +104,7 @@ public class FeaturesFileTest sf = sfs[4]; assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%", sf.description); - assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111", + assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111", sf.links.get(0).toString()); assertEquals(8, sf.begin); assertEquals(83, sf.end); @@ -428,7 +428,7 @@ public class FeaturesFileTest + "STARTGROUP\tuniprot\n" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n" + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n" - + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" + "ENDGROUP\tuniprot\n"; FeaturesFile featuresFile = new FeaturesFile(features, FormatAdapter.PASTE); @@ -478,7 +478,7 @@ public class FeaturesFileTest + "\nSTARTGROUP\tuniprot\n" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" - + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" + "ENDGROUP\tuniprot\n"; assertEquals(expected, exported); } -- 1.7.10.2