From: hansonr Date: Sat, 1 Dec 2018 11:44:39 +0000 (-0600) Subject: adding jaxbtest.jvx and directing JalviewJS2.java to open it. X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~362 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=d18f36d6bb22fa26f13ea1857d3ec644e854432e adding jaxbtest.jvx and directing JalviewJS2.java to open it. --- diff --git a/examples/jaxbtest.jvx b/examples/jaxbtest.jvx new file mode 100644 index 0000000..5720bd0 Binary files /dev/null and b/examples/jaxbtest.jvx differ diff --git a/site-resources/examples/exampleFeatures.txt b/site-resources/examples/exampleFeatures.txt new file mode 100644 index 0000000..99af214 --- /dev/null +++ b/site-resources/examples/exampleFeatures.txt @@ -0,0 +1,369 @@ +ST-TURN-IIL blue +GAMMA-TURN-CLASSIC lightgray +BETA-TURN-IR 9a6a94 +BETA-TURN-IL d6a6ca +BETA-BULGE 1dc451 +Pfam dc206a +PHOSPHORYLATION (S) b974a5 +PHOSPHORYLATION (Y) 7d3881 +Cath 93b1d1 +ASX-TURN-IR 4ccc6e +BETA-BULGE-LOOP-5 4066da +CATMAT-4 4dc465 +CATMAT-3 3eb555 +GAMMA-TURN-INVERSE 7881c7 +SCHELLMANN-LOOP-6 a28bbb +METAL cc9900 +ALPHA-BETA-MOTIF 7bd649 +ASX-MOTIF 6addbb +NEST-LR 3e16d0 +ASX-TURN-IIR 6a4062 +NEST-RL 3e16b2 +ASX-TURN-IIL a67c98 +BETA-TURN-IIR c79792 +PHOSPHORYLATION (T) c88395 +BETA-TURN-IIL 8b5b50 +ST-MOTIF ac25a1 +kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0 + +STARTFILTERS +GAMMA-TURN-INVERSE Label Contains PDB +kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8) +ENDFILTERS + +STARTGROUP uniprot +Pfam family FER_CAPAA -1 0 0 Pfam +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 +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 +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 +Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath +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 +Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath +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 +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 +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 +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 +Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath +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 +Fer2 Status: True Positive Pfam 60_13 FER1_ARATH -1 60 135 Pfam +Ferredoxin_fold Status: True Positive FER1_ARATH -1 50 145 Cath +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 +Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath +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 + + +STARTGROUP netphos +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_CAPAA -1 89 89 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 22_2 FER1_SOLLC -1 22 22 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER1_SOLLC -1 38 38 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 102_10 FER1_SOLLC -1 102 102 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 136_13 FER1_SOLLC -1 136 136 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 136_13 Q93XJ9_SOLTU -1 136 136 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 22_2 Q93XJ9_SOLTU -1 22 22 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 Q93XJ9_SOLTU -1 38 38 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 33_3 FER1_PEA -1 33 33 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 42_4 FER1_PEA -1 42 42 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_PEA -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_PEA -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 4_ FER1_PEA -1 4 4 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 28_2 FER1_PEA -1 28 28 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_PEA -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 117_11 Q7XA98_TRIPR -1 117 117 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 137_13 Q7XA98_TRIPR -1 137 137 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 144_14 Q7XA98_TRIPR -1 144 144 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 30_3 Q7XA98_TRIPR -1 30 30 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 31_3 Q7XA98_TRIPR -1 31 31 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 4_ Q7XA98_TRIPR -1 4 4 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 45_4 Q7XA98_TRIPR -1 45 45 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 46_4 Q7XA98_TRIPR -1 46 46 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 93_9 Q7XA98_TRIPR -1 93 93 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 88_8 FER1_SPIOL -1 88 88 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 112_11 FER1_SPIOL -1 112 112 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 139_13 FER1_SPIOL -1 139 139 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 73_7 FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER2_ARATH -1 19 19 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER2_ARATH -1 24 24 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER2_ARATH -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER2_ARATH -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER2_ARATH -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER2_ARATH -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER2_ARATH -1 75 75 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER_BRANA -1 38 38 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 62_6 FER_BRANA -1 62 62 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_BRANA -1 89 89 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 23_2 FER_BRANA -1 23 23 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 Q93Z60_ARATH -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 Q93Z60_ARATH -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 21_2 Q93Z60_ARATH -1 21 21 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 Q93Z60_ARATH -1 24 24 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 Q93Z60_ARATH -1 75 75 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 7_ FER1_MAIZE -1 7 7 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER1_MAIZE -1 19 19 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 44_4 FER1_MAIZE -1 44 44 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 45_4 FER1_MAIZE -1 45 45 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_MAIZE -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER1_MAIZE -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_MAIZE -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 134_13 FER1_MAIZE -1 134 134 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_MAIZE -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 115_11 FER1_MAIZE -1 115 115 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 133_13 O80429_MAIZE -1 133 133 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 82_8 O80429_MAIZE -1 82 82 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 9_ O80429_MAIZE -1 9 9 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 99_9 O80429_MAIZE -1 99 99 PHOSPHORYLATION (S) +ENDGROUP netphos + +STARTGROUP s3dm +Found in PDBs: 1a70.,1a70. ALPHA-BETA-MOTIF 115_11 FER1_SPIOL -1 115 119 ALPHA-BETA-MOTIF +Found in PDBs: 1a70. ASX-TURN-IIL 107_10 FER1_SPIOL -1 107 109 ASX-TURN-IIL +Found in PDBs: 1a70. ASX-TURN-IR 115_11 FER1_SPIOL -1 115 117 ASX-TURN-IR +Found in PDBs: 1a70. BETA-BULGE 102_10 FER1_SPIOL -1 102 103 BETA-BULGE +Found in PDBs: 1a70. BETA-TURN-IR 59_6 FER1_SPIOL -1 59 62 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 69_7 FER1_SPIOL -1 69 72 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 95_9 FER1_SPIOL -1 95 98 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 108_11 FER1_SPIOL -1 108 111 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 125_12 FER1_SPIOL -1 125 128 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 141_14 FER1_SPIOL -1 141 144 BETA-TURN-IR +Found in PDBs: 1a70. NEST-LR 90_9 FER1_SPIOL -1 90 92 NEST-LR +Found in PDBs: 1a70. NEST-LR 92_9 FER1_SPIOL -1 92 94 NEST-LR +Found in PDBs: 1a70. NEST-LR 140_14 FER1_SPIOL -1 140 142 NEST-LR +Found in PDBs: 1a70. NEST-RL 81_8 FER1_SPIOL -1 81 83 NEST-RL +Found in PDBs: 1a70. NEST-RL 89_9 FER1_SPIOL -1 89 91 NEST-RL +Found in PDBs: 1a70. NEST-RL 91_9 FER1_SPIOL -1 91 93 NEST-RL +Found in PDBs: 1a70. NEST-RL 121_12 FER1_SPIOL -1 121 123 NEST-RL +Found in PDBs: 1a70. SCHELLMANN-LOOP-6 78_8 FER1_SPIOL -1 78 83 SCHELLMANN-LOOP-6 +Found in PDBs: 1a70. SCHELLMANN-LOOP-6 118_12 FER1_SPIOL -1 118 123 SCHELLMANN-LOOP-6 +Found in PDBs: 1a70. ST-MOTIF 59_6 FER1_SPIOL -1 59 63 ST-MOTIF +ALPHA-BETA-MOTIF FER1_SPIOL -1 65 69 ALPHA-BETA-MOTIF +ASX-MOTIF FER1_SPIOL -1 65 69 ASX-MOTIF +ASX-TURN-IIL FER1_SPIOL -1 57 59 ASX-TURN-IIL +ASX-TURN-IR FER1_SPIOL -1 65 67 ASX-TURN-IR +BETA-BULGE FER1_SPIOL -1 52 53 BETA-BULGE +BETA-TURN-IR FER1_SPIOL -1 9 12 BETA-TURN-IR +BETA-TURN-IR FER1_SPIOL -1 19 22 BETA-TURN-IR +BETA-TURN-IR FER1_SPIOL -1 45 48 BETA-TURN-IR +BETA-TURN-IR FER1_SPIOL -1 58 61 BETA-TURN-IR +BETA-TURN-IR FER1_SPIOL -1 75 78 BETA-TURN-IR +BETA-TURN-IR FER1_SPIOL -1 91 94 BETA-TURN-IR +NEST-LR FER1_SPIOL -1 40 42 NEST-LR +NEST-LR FER1_SPIOL -1 42 44 NEST-LR +NEST-LR FER1_SPIOL -1 90 92 NEST-LR +NEST-RL FER1_SPIOL -1 31 33 NEST-RL +NEST-RL FER1_SPIOL -1 39 41 NEST-RL +NEST-RL FER1_SPIOL -1 41 43 NEST-RL +NEST-RL FER1_SPIOL -1 71 73 NEST-RL +SCHELLMANN-LOOP-6 FER1_SPIOL -1 28 33 SCHELLMANN-LOOP-6 +SCHELLMANN-LOOP-6 FER1_SPIOL -1 68 73 SCHELLMANN-LOOP-6 +ST-MOTIF FER1_SPIOL -1 9 13 ST-MOTIF +Found in PDBs: 1gaq.B ALPHA-BETA-MOTIF 76_8 FER1_MAIZE -1 76 80 ALPHA-BETA-MOTIF +Found in PDBs: 1gaq.B ALPHA-BETA-MOTIF 77_8 FER1_MAIZE -1 77 81 ALPHA-BETA-MOTIF +Found in PDBs: 1gaq.B BETA-TURN-IR 127_13 FER1_MAIZE -1 127 130 BETA-TURN-IR +Found in PDBs: 1gaq.B GAMMA-TURN-CLASSIC 113_11 FER1_MAIZE -1 113 115 GAMMA-TURN-CLASSIC +Found in PDBs: 1gaq.B GAMMA-TURN-INVERSE 59_6 FER1_MAIZE -1 59 61 GAMMA-TURN-INVERSE +Found in PDBs: 1gaq.B GAMMA-TURN-INVERSE 104_10 FER1_MAIZE -1 104 106 GAMMA-TURN-INVERSE +Found in PDBs: 1gaq.B NEST-LR 92_9 FER1_MAIZE -1 92 94 NEST-LR +Found in PDBs: 1gaq.B NEST-LR 94_9 FER1_MAIZE -1 94 96 NEST-LR +Found in PDBs: 1gaq.B NEST-RL 83_8 FER1_MAIZE -1 83 85 NEST-RL +Found in PDBs: 1gaq.B NEST-RL 91_9 FER1_MAIZE -1 91 93 NEST-RL +Found in PDBs: 1gaq.B NEST-RL 93_9 FER1_MAIZE -1 93 95 NEST-RL +Found in PDBs: 1gaq.B NEST-RL 123_12 FER1_MAIZE -1 123 125 NEST-RL +ALPHA-BETA-MOTIF FER1_MAIZE -1 132 136 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 174 178 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 175 179 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 180 184 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 181 185 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 214 218 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 215 219 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 218 222 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 223 227 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 246 250 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 251 255 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 254 258 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 258 262 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 279 283 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 280 284 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 289 293 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 296 300 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 299 303 ALPHA-BETA-MOTIF +ASX-TURN-IIL FER1_MAIZE -1 160 162 ASX-TURN-IIL +ASX-TURN-IIR FER1_MAIZE -1 107 109 ASX-TURN-IIR +BETA-BULGE FER1_MAIZE -1 31 32 BETA-BULGE +BETA-BULGE FER1_MAIZE -1 43 44 BETA-BULGE +BETA-TURN-IIL FER1_MAIZE -1 170 173 BETA-TURN-IIL +BETA-TURN-IIR FER1_MAIZE -1 71 74 BETA-TURN-IIR +BETA-TURN-IIR FER1_MAIZE -1 140 143 BETA-TURN-IIR +BETA-TURN-IIR FER1_MAIZE -1 274 277 BETA-TURN-IIR +BETA-TURN-IL FER1_MAIZE -1 64 67 BETA-TURN-IL +BETA-TURN-IR FER1_MAIZE -1 33 36 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 50 53 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 100 103 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 103 106 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 136 139 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 171 174 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 172 175 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 206 209 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 207 210 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 223 226 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 233 236 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 252 255 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 264 267 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 289 292 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 295 298 BETA-TURN-IR +CATMAT-3 FER1_MAIZE -1 20 22 CATMAT-3 +CATMAT-3 FER1_MAIZE -1 47 49 CATMAT-3 +CATMAT-3 FER1_MAIZE -1 97 99 CATMAT-3 +CATMAT-4 FER1_MAIZE -1 189 192 CATMAT-4 +GAMMA-TURN-INVERSE FER1_MAIZE -1 68 70 GAMMA-TURN-INVERSE +GAMMA-TURN-INVERSE FER1_MAIZE -1 84 86 GAMMA-TURN-INVERSE +GAMMA-TURN-INVERSE FER1_MAIZE -1 232 234 GAMMA-TURN-INVERSE +GAMMA-TURN-INVERSE FER1_MAIZE -1 240 242 GAMMA-TURN-INVERSE +GAMMA-TURN-INVERSE FER1_MAIZE -1 244 246 GAMMA-TURN-INVERSE +NEST-LR FER1_MAIZE -1 30 32 NEST-LR +NEST-LR FER1_MAIZE -1 66 68 NEST-LR +NEST-LR FER1_MAIZE -1 106 108 NEST-LR +NEST-LR FER1_MAIZE -1 108 110 NEST-LR +NEST-LR FER1_MAIZE -1 212 214 NEST-LR +NEST-LR FER1_MAIZE -1 276 278 NEST-LR +NEST-LR FER1_MAIZE -1 307 309 NEST-LR +NEST-RL FER1_MAIZE -1 64 66 NEST-RL +NEST-RL FER1_MAIZE -1 105 107 NEST-RL +NEST-RL FER1_MAIZE -1 107 109 NEST-RL +NEST-RL FER1_MAIZE -1 306 308 NEST-RL +ST-TURN-IIL FER1_MAIZE -1 20 22 ST-TURN-IIL +ALPHA-BETA-MOTIF FER1_MAIZE -1 24 28 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 25 29 ALPHA-BETA-MOTIF +BETA-TURN-IR FER1_MAIZE -1 75 78 BETA-TURN-IR +GAMMA-TURN-CLASSIC FER1_MAIZE -1 61 63 GAMMA-TURN-CLASSIC +GAMMA-TURN-INVERSE FER1_MAIZE -1 7 9 GAMMA-TURN-INVERSE +GAMMA-TURN-INVERSE FER1_MAIZE -1 52 54 GAMMA-TURN-INVERSE +NEST-LR FER1_MAIZE -1 40 42 NEST-LR +NEST-LR FER1_MAIZE -1 42 44 NEST-LR +NEST-RL FER1_MAIZE -1 31 33 NEST-RL +NEST-RL FER1_MAIZE -1 39 41 NEST-RL +NEST-RL FER1_MAIZE -1 41 43 NEST-RL +NEST-RL FER1_MAIZE -1 71 73 NEST-RL +ALPHA-BETA-MOTIF FER1_MAIZE -1 176 180 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 233 237 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 247 251 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 278 282 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 286 290 ALPHA-BETA-MOTIF +ALPHA-BETA-MOTIF FER1_MAIZE -1 295 299 ALPHA-BETA-MOTIF +ASX-MOTIF FER1_MAIZE -1 122 126 ASX-MOTIF +ASX-MOTIF FER1_MAIZE -1 160 164 ASX-MOTIF +ASX-TURN-IR FER1_MAIZE -1 122 124 ASX-TURN-IR +BETA-BULGE-LOOP-5 FER1_MAIZE -1 122 126 BETA-BULGE-LOOP-5 +BETA-BULGE-LOOP-5 FER1_MAIZE -1 239 243 BETA-BULGE-LOOP-5 +BETA-TURN-IR FER1_MAIZE -1 122 125 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 160 163 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 239 242 BETA-TURN-IR +BETA-TURN-IR FER1_MAIZE -1 261 264 BETA-TURN-IR +CATMAT-3 FER1_MAIZE -1 80 82 CATMAT-3 +CATMAT-3 FER1_MAIZE -1 87 89 CATMAT-3 +CATMAT-3 FER1_MAIZE -1 262 264 CATMAT-3 +NEST-RL FER1_MAIZE -1 124 126 NEST-RL +NEST-RL FER1_MAIZE -1 241 243 NEST-RL +NEST-RL FER1_MAIZE -1 292 294 NEST-RL +ENDGROUP s3dm + +STARTGROUP kd +A Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8 +A Q93XJ9_SOLTU -1 49 49 kdHydrophobicity -0.8 +A Q93XJ9_SOLTU -1 50 50 kdHydrophobicity -1.3 +A Q93XJ9_SOLTU -1 51 51 kdHydrophobicity -3.9 +A Q93XJ9_SOLTU -1 52 52 kdHydrophobicity 4.2 +A Q93XJ9_SOLTU -1 53 53 kdHydrophobicity -3.9 +A Q93XJ9_SOLTU -1 54 54 kdHydrophobicity 3.8 +A Q93XJ9_SOLTU -1 55 55 kdHydrophobicity 4.5 +A Q93XJ9_SOLTU -1 56 56 kdHydrophobicity -0.7 +A Q93XJ9_SOLTU -1 57 57 kdHydrophobicity -1.6 +A Q93XJ9_SOLTU -1 58 58 kdHydrophobicity -3.5 +A Q93XJ9_SOLTU -1 59 59 kdHydrophobicity -0.4 +A Q93XJ9_SOLTU -1 60 60 kdHydrophobicity -1.6 +A Q93XJ9_SOLTU -1 61 61 kdHydrophobicity 4.5 +A Q93XJ9_SOLTU -1 62 62 kdHydrophobicity -3.5 +A Q93XJ9_SOLTU -1 63 63 kdHydrophobicity 2.8 +A FER1_SPIOL -1 51 51 kdHydrophobicity 1.8 +A FER1_SPIOL -1 52 52 kdHydrophobicity 1.8 +A FER1_SPIOL -1 53 53 kdHydrophobicity -1.3 +A FER1_SPIOL -1 54 54 kdHydrophobicity -3.9 +A FER1_SPIOL -1 55 55 kdHydrophobicity 4.2 +A FER1_SPIOL -1 56 56 kdHydrophobicity -0.7 +A FER1_SPIOL -1 57 57 kdHydrophobicity 3.8 +A FER1_SPIOL -1 58 58 kdHydrophobicity 4.2 +A FER1_SPIOL -1 59 59 kdHydrophobicity -0.7 +A FER1_SPIOL -1 60 60 kdHydrophobicity -1.6 +A FER1_SPIOL -1 61 61 kdHydrophobicity -0.7 +A FER1_SPIOL -1 62 62 kdHydrophobicity -0.4 +A FER1_SPIOL -1 63 63 kdHydrophobicity -3.5 +A FER1_SPIOL -1 64 64 kdHydrophobicity 4.2 +A FER1_SPIOL -1 65 65 kdHydrophobicity -3.5 +A FER1_SPIOL -1 66 66 kdHydrophobicity 2.8 +C FER1_MAIZE -1 53 53 kdHydrophobicity 1.8 +C FER1_MAIZE -1 54 54 kdHydrophobicity -0.7 +C FER1_MAIZE -1 55 55 kdHydrophobicity -1.3 +C FER1_MAIZE -1 56 56 kdHydrophobicity -3.5 +C FER1_MAIZE -1 57 57 kdHydrophobicity 4.2 +C FER1_MAIZE -1 58 58 kdHydrophobicity -3.9 +C FER1_MAIZE -1 59 59 kdHydrophobicity 3.8 +C FER1_MAIZE -1 60 60 kdHydrophobicity 4.5 +C FER1_MAIZE -1 61 61 kdHydrophobicity -0.7 +C FER1_MAIZE -1 62 62 kdHydrophobicity -1.6 +C FER1_MAIZE -1 63 63 kdHydrophobicity -3.5 +C FER1_MAIZE -1 64 64 kdHydrophobicity -0.4 +C FER1_MAIZE -1 65 65 kdHydrophobicity -3.5 +C FER1_MAIZE -1 66 66 kdHydrophobicity 4.2 +C FER1_MAIZE -1 67 67 kdHydrophobicity -3.5 +C FER1_MAIZE -1 68 68 kdHydrophobicity 3.8 +ENDGROUP kd diff --git a/site-resources/examples/jaxbtest.jvx b/site-resources/examples/jaxbtest.jvx new file mode 100644 index 0000000..5720bd0 Binary files /dev/null and b/site-resources/examples/jaxbtest.jvx differ diff --git a/site-resources/examples/uniref50.fa b/site-resources/examples/uniref50.fa new file mode 100644 index 0000000..6e6c670 --- /dev/null +++ b/site-resources/examples/uniref50.fa @@ -0,0 +1,60 @@ +>FER_CAPAA Ferredoxin +-----------------------------------------------------------ASYKVKLITPDGP +IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER_CAPAN Ferredoxin, chloroplast precursor +MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP +IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER1_SOLLC Ferredoxin-1, chloroplast precursor +MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV +TIETHKEEELTA- +>Q93XJ9_SOLTU Ferredoxin I precursor +MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV +TIETHKEEELTA- +>FER1_PEA Ferredoxin-1, chloroplast precursor +MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT +QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV +VIETHKEEDLTA- +>Q7XA98_TRIPR Ferredoxin I +MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP +QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV +TIETHKEEELTA- +>FER1_MESCR Ferredoxin-1, chloroplast precursor +MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK +QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV +TIETHKEEELTA- +>FER1_SPIOL Ferredoxin-1, chloroplast precursor +MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKEEELTA- +>FER3_RAPSA Ferredoxin, leaf L-A +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV +TIETHREEDMV-- +>FER2_ARATH Ferredoxin-2, chloroplast precursor +MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE +LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV +TIETHKEEDIV-- +>FER_BRANA Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV-- +>FER1_ARATH Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM-- +>Q93Z60_ARATH At1g10960/T19D16_12 +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- +------------- +>FER1_MAIZE Ferredoxin-1, chloroplast precursor +MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE +VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV +VIETHKEEELTGA +>O80429_MAIZE Ferredoxin +MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE +VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV +VIETHKEDDLL-- diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java index 037f41e..516cc20 100644 --- a/src/jalview/bin/JalviewJS2.java +++ b/src/jalview/bin/JalviewJS2.java @@ -13,13 +13,21 @@ public class JalviewJS2 static { /** - * @j2sNative + * --j2sNative * * thisApplet.__Info.args = - * ["open","http://www.jalview.org/builds/release/examples/uniref50.fa","features", - * "http://www.jalview.org/builds/release/examples/exampleFeatures.txt"]; + * ["open","examples/uniref50.fa","features", + * "examples/exampleFeatures.txt"]; */ - + + + /** + * @j2sNative + * + * thisApplet.__Info.args = + * ["open","examples/jaxbtest.jvx"]; + */ + } public static void main(String[] args) throws Exception