From: hansonr Date: Mon, 2 Jul 2018 09:14:19 +0000 (+0100) Subject: JAL-3032 JTable work; JSUtil.jQuery object; drag-drop; X-Git-Tag: Release_2_11_4_0~45^2~18^2~614 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d74e358a8496d97f08ac44ad4dc879125016d94;p=jalview.git JAL-3032 JTable work; JSUtil.jQuery object; drag-drop; reflect.Constructor; adds core:"NONE" to {project}/template.html fixes drag-drop for first call in Firefox/win fixes java.lang.reflect.Constructor for Integer Remove the core:"NONE" if you do not want to see all the core files separately. --- diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt deleted file mode 100755 index 99af214..0000000 --- a/examples/exampleFeatures.txt +++ /dev/null @@ -1,369 +0,0 @@ -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/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 75e8ec9..5709ab5 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -233,7 +233,7 @@ public class FeatureSettings extends JPanel table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this)); table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); - + TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, new ColorRenderer(), new ColorEditor(this)); table.addColumn(colourColumn); diff --git a/src/jalview/gui/JvSwingUtils.java b/src/jalview/gui/JvSwingUtils.java index 4658668..d44080a 100644 --- a/src/jalview/gui/JvSwingUtils.java +++ b/src/jalview/gui/JvSwingUtils.java @@ -96,8 +96,19 @@ public final class JvSwingUtils } return (enclose ? "" : "") - + "

" - + ttext + "

" + ((enclose ? "" : "")); + + // BH 2018 + + + "
" + +// + "

" + + + ttext + + + "

" +// + "

" + + ((enclose ? "" : "")); } diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 8b2e7bc..18c6acc 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -62,7 +62,9 @@ import java.awt.event.MouseWheelListener; import java.util.Collections; import java.util.List; +import javax.swing.JLabel; import javax.swing.JPanel; +import javax.swing.JToolTip; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -158,6 +160,8 @@ public class SeqPanel extends JPanel ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); + + this.av = viewport; setBackground(Color.white); @@ -694,6 +698,8 @@ public class SeqPanel extends JPanel String lastMessage; + private String formattedTooltipText; + @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { @@ -863,16 +869,20 @@ public class SeqPanel extends JPanel String textString = tooltipText.toString(); if (lastTooltip == null || !lastTooltip.equals(textString)) { - String formattedTooltipText = JvSwingUtils.wrapTooltip(true, + formattedTooltipText = JvSwingUtils.wrapTooltip(true, textString); setToolTipText(formattedTooltipText); + lastTooltip = textString; } } } + private Point lastp = null; + private JToolTip tempTip = new JLabel().createToolTip(); + /* * (non-Javadoc) * @@ -881,19 +891,31 @@ public class SeqPanel extends JPanel @Override public Point getToolTipLocation(MouseEvent event) { - int x = event.getX(), w = getWidth(); - int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too - // close to edge + // BH 2018 + + if (tooltipText == null || tooltipText.length() == 6) + return null; + + if (lastp != null && event.isShiftDown()) + return lastp; + Point p = lastp; - if (!event.isShiftDown() || p == null) - { - p = (tooltipText != null && tooltipText.length() > 6) - ? new Point(event.getX() + wdth, event.getY() - 20) - : null; - } + int x = event.getX(); + int y = event.getY(); + int w = getWidth(); + + tempTip.setTipText(formattedTooltipText); + int tipWidth = (int) tempTip.getPreferredSize().getWidth(); + + // was x += (w - x < 200) ? -(w / 2) : 5; + x = (x + tipWidth < w ? x + 10 : w - tipWidth); + p = new Point(x, y + 20); // BH 2018 was - 20? /* * TODO: try to modify position region is not obcured by tooltip + * + * Done? */ + return lastp = p; } diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip index edd8197..ddaa87b 100644 Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ diff --git a/template.html b/template.html index 5005060..2a22a77 100644 --- a/template.html +++ b/template.html @@ -8,6 +8,7 @@ if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs fo Info = { code: _CODE_, main: _MAIN_, + core: "NONE", width: 850, height: 550, readyFunction: null,