--- /dev/null
+# Summary of TestNG for this branch
+"Functional" Tests: 242 ran, 121 failed.
--- /dev/null
+JALVIEW_ANNOTATION
+# Created: Wed Jul 08 18:48:01 BST 2015
+
+NO_GRAPH Test Annotation Test Annotation ||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|E,β|||||||||||||||||||||||||||||||||||||||||||||||||E,β|E,β|E,β|E,β|E,β|||||||||||||||H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|H,α|||||||||||||||||E,β|E,β||||
+BAR_GRAPH Conservation Conservation of total alignment less than 25% gaps 1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|1.0,1,hydrophobic ,[5d1500]|2.0,2,small tiny ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,-,[4d0000]|2.0,2,small tiny ,[6d2a00]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|0.0,0,[4d0000]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|6.0,6,polar !tiny !aromatic !negative !aliphatic !proline,[ae7d00]|8.0,8,hydrophobic !tiny !polar !negative !charged !small !positive !proline,[cea700]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,small polar !tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !tiny !aromatic !aliphatic,[7d3f00]|6.0,6, !tiny !aromatic !negative !charged !positive !proline,[ae7d00]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|7.0,7,hydrophobic !tiny !polar !negative !charged !positive !proline,[be9200]|7.0,7,polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[be9200]|9.0,9,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|5.0,5, !tiny !aromatic !hydrophobic !positive !aliphatic,[9e6800]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,aliphatic small hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[ffe600]|11.0,*,hydrophobic aromatic polar !tiny !negative !charged !small !positive !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|3.0,3, !negative !aliphatic !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|11.0,*,charged negative polar !tiny !aromatic !hydrophobic !small !positive !aliphatic !proline,[ffe600]|3.0,3, !aromatic !positive !proline,[7d3f00]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|5.0,5,hydrophobic !tiny !negative !small !proline,[9e6800]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|11.0,*,proline small !tiny !polar !aromatic !hydrophobic !negative !charged !positive !aliphatic,[ffe600]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged polar !tiny !aromatic !hydrophobic !negative !small !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small polar tiny !aromatic !hydrophobic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic !tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|11.0,*,positive charged hydrophobic polar !tiny !aromatic !negative !small !aliphatic !proline,[ffe600]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|3.0,3, !aromatic !negative !proline,[7d3f00]|7.0,7,small !aromatic !negative !charged !positive !aliphatic !proline,[be9200]|11.0,*,small hydrophobic tiny !polar !aromatic !negative !charged !positive !aliphatic !proline,[ffe600]|3.0,3, !positive !aliphatic !proline,[7d3f00]|9.0,9,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !positive !proline,[dfbc00]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|11.0,*,polar !tiny !aromatic !hydrophobic !negative !charged !small !positive !aliphatic !proline,[ffe600]|6.0,6,polar !aromatic !hydrophobic !positive !aliphatic !proline,[ae7d00]|11.0,*,small charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[ffe600]|4.0,4, !aromatic !positive !aliphatic !proline,[8d5300]|5.0,5,polar !aromatic !negative !aliphatic !proline,[9e6800]|9.0,9,hydrophobic aromatic !tiny !negative !charged !small !positive !aliphatic !proline,[dfbc00]|11.0,*,aliphatic hydrophobic !tiny !polar !aromatic !negative !charged !small !positive !proline,[ffe600]|8.0,8,small polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[cea700]|9.0,9,charged negative polar !tiny !aromatic !hydrophobic !positive !aliphatic !proline,[dfbc00]|0.0,0,[4d0000]|1.0,1,polar ,[5d1500]|0.0,0,[4d0000]|0.0,0,[4d0000]|0.0,0,[4d0000]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|2.0,2,aliphatic hydrophobic ,[6d2a00]|2.0,2,small polar ,[6d2a00]|2.0,2,small hydrophobic ,[6d2a00]|1.0,1,hydrophobic ,[5d1500]|3.0,3,small hydrophobic tiny ,[7d3f00]|2.0,2,hydrophobic aromatic ,[6d2a00]|2.0,2,proline small ,[6d2a00]|0.0,0,[4d0000]|1.0,1,small ,[5d1500]|4.0,4,small charged negative polar ,[8d5300]|3.0,3,aliphatic small hydrophobic ,[7d3f00]|1.0,1,small ,[5d1500]|2.0,2,aliphatic hydrophobic ,[6d2a00]|3.0,3,charged negative polar ,[7d3f00]|2.0,2,small polar ,[6d2a00]|5.0,5,positive charged hydrophobic aromatic polar ,[9e6800]|3.0,3,positive charged polar ,[7d3f00]|3.0,3,charged negative polar ,[7d3f00]|0.0,0,[4d0000]|0.0,0,[4d0000]|1.0,1,hydrophobic ,[5d1500]|0.0,0,[4d0000]|0.0,-,[4d0000]|0.0,-,[4d0000]|
+BAR_GRAPH Quality Alignment Quality based on Blosum62 scores 29.151815,29.151815,[cba200]|30.574812,30.574812,[d1aa00]|14.400199,14.400199,[8b5000]|16.93248,16.93248,[965e00]|2.1220763,2.1220763,[560c00]|2.2049963,2.2049963,[560c00]|3.647952,3.647952,[5c1400]|4.814642,4.814642,[611b00]|18.351393,18.351393,[9c6600]|17.532412,17.532412,[996200]|7.5054855,7.5054855,[6d2a00]|15.490477,15.490477,[905600]|14.241707,14.241707,[8a4f00]|9.905579,9.905579,[773700]|20.354017,20.354017,[a57100]|26.870352,26.870352,[c19600]|24.969187,24.969187,[b98b00]|27.419409,27.419409,[c39900]|15.350427,15.350427,[8f5600]|21.116522,21.116522,[a87600]|9.34032,9.34032,[753400]|14.1895275,14.1895275,[8a4f00]|10.104505,10.104505,[783800]|8.587312,8.587312,[723000]|18.694708,18.694708,[9e6800]|11.420612,11.420612,[7e4000]|6.8467255,6.8467255,[6a2600]|17.449827,17.449827,[986100]|16.825909,16.825909,[955e00]|2.4334474,2.4334474,[570e00]|15.685622,15.685622,[915700]|9.836516,9.836516,[773700]|3.4712791,3.4712791,[5c1300]|4.531816,4.531816,[601900]|7.8744216,7.8744216,[6f2c00]|0.0,0.0,[4d0000]|9.01113,9.01113,[743200]|3.174218,3.174218,[5a1200]|2.0395048,2.0395048,[550b00]|2.1654668,2.1654668,[560c00]|21.517344,21.517344,[aa7800]|15.738462,15.738462,[915800]|14.844854,14.844854,[8d5300]|22.159096,22.159096,[ad7c00]|13.956608,13.956608,[894e00]|20.147892,20.147892,[a47000]|25.067545,25.067545,[b98c00]|2.0943506,2.0943506,[560c00]|20.30842,20.30842,[a57100]|10.254437,10.254437,[793900]|6.5836596,6.5836596,[692500]|19.446732,19.446732,[a16c00]|6.2202287,6.2202287,[672300]|9.796006,9.796006,[773700]|6.0385494,6.0385494,[672200]|13.963727,13.963727,[894e00]|13.838549,13.838549,[884d00]|18.48424,18.48424,[9d6700]|18.302633,18.302633,[9c6600]|41.172745,41.172745,[ffe600]|32.59908,32.59908,[dab600]|41.172745,41.172745,[ffe600]|34.495945,34.495945,[e2c000]|41.172745,41.172745,[ffe600]|33.501804,33.501804,[debb00]|27.034466,27.034466,[c29700]|40.020737,40.020737,[fadf00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|29.252739,29.252739,[cba300]|41.172745,41.172745,[ffe600]|14.935498,14.935498,[8d5300]|0.88449144,0.88449144,[500500]|41.172745,41.172745,[ffe600]|20.81991,20.81991,[a77400]|31.73346,31.73346,[d6b100]|29.757969,29.757969,[cea600]|16.279755,16.279755,[935b00]|32.647984,32.647984,[dab600]|38.352337,38.352337,[f3d600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.6125,39.6125,[f8dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|9.671661,9.671661,[763600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|11.17141,11.17141,[7d3e00]|41.172745,41.172745,[ffe600]|3.2054348,3.2054348,[5a1200]|38.569283,38.569283,[f4d700]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.707684,39.707684,[f9dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.447525,39.447525,[f8dc00]|21.229778,21.229778,[a97600]|27.779364,27.779364,[c59b00]|41.172745,41.172745,[ffe600]|24.149143,24.149143,[b58700]|39.447525,39.447525,[f8dc00]|33.857655,33.857655,[dfbd00]|41.172745,41.172745,[ffe600]|28.69976,28.69976,[c9a000]|41.172745,41.172745,[ffe600]|14.611241,14.611241,[8c5100]|32.346375,32.346375,[d9b400]|39.24055,39.24055,[f7db00]|41.172745,41.172745,[ffe600]|38.352337,38.352337,[f3d600]|38.569283,38.569283,[f4d700]|22.374107,22.374107,[ae7d00]|36.98438,36.98438,[edce00]|12.34415,12.34415,[824500]|11.811655,11.811655,[804200]|14.798897,14.798897,[8d5200]|36.60138,36.60138,[ebcc00]|14.0762415,14.0762415,[8a4e00]|36.817875,36.817875,[eccd00]|36.53897,36.53897,[ebcc00]|37.583706,37.583706,[efd100]|35.536423,35.536423,[e7c600]|18.004925,18.004925,[9b6400]|37.633095,37.633095,[f0d200]|34.738743,34.738743,[e3c200]|36.451622,36.451622,[ebcb00]|19.948801,19.948801,[a36f00]|28.285,28.285,[c79e00]|35.93151,35.93151,[e8c800]|36.817875,36.817875,[eccd00]|26.762383,26.762383,[c19500]|36.37101,36.37101,[eacb00]|36.413998,36.413998,[eacb00]|37.583706,37.583706,[efd100]|36.282784,36.282784,[eaca00]|34.729824,34.729824,[e3c200]|36.413998,36.413998,[eacb00]|24.348654,24.348654,[b68800]|24.349539,24.349539,[b68800]|34.091675,34.091675,[e0be00]|21.114677,21.114677,[a87600]|13.676696,13.676696,[884c00]|2.1107035,2.1107035,[560c00]|
+BAR_GRAPH Consensus PID 80.0,M,M 80%|80.0,A,A 80%|20.0,+,[AST] 20%|53.333332,T,T 53%|6.6666665,L,L 6%|6.6666665,G,G 6%|13.333333,T,T 13%|20.0,P,P 20%|40.0,A,A 40%|40.0,L,L 40%|46.666668,S,S 46%|40.0,G,G 40%|33.333332,T,T 33%|20.0,+,[AIM] 20%|33.333332,V,V 33%|66.666664,S,S 66%|66.666664,T,T 66%|66.666664,S,S 66%|66.666664,F,F 66%|46.666668,L,L 46%|46.666668,R,R 46%|46.666668,R,R 46%|26.666666,Q,Q 26%|46.666668,P,P 46%|40.0,A,A 40%|60.0,P,P 60%|26.666666,T,T 26%|53.333332,S,S 53%|40.0,L,L 40%|20.0,R,R 20%|26.666666,S,S 26%|33.333332,L,L 33%|40.0,P,P 40%|26.666666,S,S 26%|33.333332,+,[AN] 33%|26.666666,V,V 26%|33.333332,G,G 33%|20.0,+,[EQ] 20%|6.6666665,F,F 6%|6.6666665,P,P 6%|33.333332,+,[AS] 33%|53.333332,L,L 53%|60.0,F,F 60%|73.333336,G,G 73%|66.666664,L,L 66%|66.666664,K,K 66%|53.333332,S,S 53%|6.6666665,V,V 6%|40.0,S,S 40%|26.666666,T,T 26%|20.0,A,A 20%|66.666664,R,R 66%|40.0,G,G 40%|53.333332,G,G 53%|46.666668,R,R 46%|33.333332,V,V 33%|46.666668,T,T 46%|53.333332,A,A 53%|66.666664,M,M 66%|100.0,A,A 100%|53.333332,T,T 53%|100.0,Y,Y 100%|86.666664,K,K 86%|100.0,V,V 100%|86.666664,K,K 86%|66.666664,L,L 66%|80.0,I,I 80%|100.0,T,T 100%|100.0,P,P 100%|66.666664,E,E 66%|100.0,G,G 100%|46.666668,E,E 46%|46.666668,Q,Q 46%|100.0,E,E 100%|46.666668,F,F 46%|60.0,E,E 60%|86.666664,C,C 86%|66.666664,P,P 66%|80.0,D,D 80%|93.333336,D,D 93%|100.0,V,V 100%|100.0,Y,Y 100%|66.666664,I,I 66%|100.0,L,L 100%|100.0,D,D 100%|46.666668,A,A 46%|100.0,A,A 100%|100.0,E,E 100%|100.0,E,E 100%|53.333332,A,A 53%|100.0,G,G 100%|60.0,I,I 60%|93.333336,D,D 93%|100.0,L,L 100%|100.0,P,P 100%|93.333336,Y,Y 93%|100.0,S,S 100%|100.0,C,C 100%|100.0,R,R 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,S,S 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,K,K 100%|80.0,V,V 80%|60.0,V,V 60%|53.333332,S,S 53%|100.0,G,G 100%|60.0,S,S 60%|80.0,V,V 80%|80.0,D,D 80%|100.0,Q,Q 100%|66.666664,S,S 66%|100.0,D,D 100%|46.666668,+,[GQ] 46%|73.333336,S,S 73%|93.333336,F,F 93%|100.0,L,L 100%|93.333336,D,D 93%|93.333336,D,D 93%|53.333332,D,D 53%|93.333336,Q,Q 93%|53.333332,I,I 53%|40.0,A,A 40%|53.333332,E,E 53%|93.333336,G,G 93%|46.666668,W,W 46%|93.333336,V,V 93%|93.333336,L,L 93%|93.333336,T,T 93%|93.333336,C,C 93%|53.333332,V,V 53%|93.333336,A,A 93%|86.666664,Y,Y 86%|93.333336,P,P 93%|60.0,T,T 60%|73.333336,S,S 73%|93.333336,D,D 93%|93.333336,V,V 93%|66.666664,T,T 66%|93.333336,I,I 93%|93.333336,E,E 93%|93.333336,T,T 93%|93.333336,H,H 93%|86.666664,K,K 86%|93.333336,E,E 93%|73.333336,E,E 73%|60.0,E,E 60%|73.333336,L,L 73%|46.666668,T,T 46%|40.0,A,A 40%|6.6666665,A,A 6%|
+
+SEQUENCE_GROUP JGroup:666531415 14 37 -1 FER_CAPAN FER1_SOLLC Q93XJ9_SOLTU FER1_PEA Q7XA98_TRIPR
+PROPERTIES JGroup:666531415 colour=Zappo outlineColour=000000 displayBoxes=true displayText=true colourText=false showUnconserved=false
+
--- /dev/null
+FER1_SOLLC Jalview test_feature 34 47 0.0 . .
+Q93XJ9_SOLTU Jalview test_feature 34 47 0.0 . .
+FER1_PEA Jalview test_feature 37 52 0.0 . .
+Q7XA98_TRIPR Jalview test_feature 39 55 0.0 . .
+FER1_MESCR Jalview test_feature 37 51 0.0 . .
--- /dev/null
+(((FER_BRANA:112.15387,FER3_RAPSA:110.84613):46.4375,FER_CAPAA:144.0625):177.2998,(O80429_MAIZE:184.40039,(FER1_MAIZE:195.79102,(((FER1_SPIOL:111.687515,FER1_MESCR:84.312485):51.929688,((Q93Z60_ARATH:398.14285,(FER2_ARATH:53.65625,FER1_ARATH:48.34375):0.0):86.725006,(Q7XA98_TRIPR:78.65277,FER1_PEA:68.34723):63.774994):7.7578125):0.58332825,((Q93XJ9_SOLTU:23.647736,FER1_SOLLC:20.352264):31.71875,FER_CAPAN:52.28125):101.7448):41.498047):37.208984):177.2998);
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>Filter Columns by Annotation</title>
+<title>Select/Hide Columns by Annotation</title>
</head>
<body>
<p>
- <strong> Filter Columns by Annotation </strong>
+ <strong> Select/Hide Columns by Annotation </strong>
</p>
- <p>Jalview allows the columns of an alignment to be filtered using
- any annotation rows added to that alignment.</p>
- From "Select" menu
- <strong>→</strong> "Select by Annotation..." to bring
- up the Select by Annotation window. The filter options vary depending
+ <p>From Jalview 2.9 columns of an alignment can be filtered using
+ any annotation row added to that alignment.</p>
+ To carry out this operation, navigate to "<b>Select</b><strong><b>→</b></strong><b>Select/Hide Columns by Annotation...</b>" to bring
+ up the 'Select/Hide by Annotation' window. The filter options vary depending
on the type of annotation selected. If an annotation that has a numeric
values is selected, the threshold filter option is activated as seen in the
- figure on the right below.
+ figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
<br>
- <br>
+ <br>
+ <table>
+ <tr>
+ <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ <td><img src="annotationColumnSelectionWithSM.gif"></td>
+ </tr>
+ </table>
- <div style="width: 48%; float: left; margin-left: 4%">
- <img src="annotationColumnSelectionWithoutSM.gif">
- </div>
- <div style="width: 48%; float: right">
- <img src="annotationColumnSelectionWithSM.gif">
- </div>
- <div> </div>
<ul>
- <li>Select which annotation to base the filtering on using the
- top-most selection box.</li>
+ <li>The target annotation row can be selected using the drop-down option menu in the top-most part of the window.</li>
<li><strong>Search Filter</strong>
<ul>
- <li>When a text is entered in the textfield on the search
- filter section, the "Display Label" and "Description"
- checkboxes becomes selectable.</li>
- <li>On selecting any of the checkboxes, a regular expresion
+ <li>When a text is entered in the text box within the Search
+ Filter section, the 'Display Label' and 'Description'
+ options becomes enabled for selection. </li>
+ <li>On selecting any of the options, a regular expression
search (RegEx) is executed on the specified field of the current
annotation row selected, and the matching columns will be highlighted
in the alignment.</li>
<li><strong>Structure Filter</strong>
<ul>
<li>Alignment columns can also be filtered by the type of
- secondary structure present in a choosen annotation row.</li>
+ secondary structure present in a target annotation row.</li>
<li>This can be achieved by ticking the type of structure you
wish to filter by under the structures filter section.</li>
</ul>
<ul>
<li>This filter is only activated for annotation which contain
numeric values</li>
- <li>Select whether to Filter the alignment above or below an
+ <li>Select whether to filter the alignment above or below an
adjustable threshold with the selection box within the threshold
filter section.</li>
<li>Change the threshold value with the slider, or enter the
</ul>
<li><strong>Actions</strong>
<ul>
- <li>The "Select" and "Hide" radio buttons
+ <li>The 'Select' and 'Hide' radio buttons
determines the action that will be carried out on the matching
columns in the alignment during the filtering process.</li>
- <li>The default option is "Select" and this simply
+ <li>The default option is 'Select' and this simply
enables column selection on the matching alignment column.</li>
- <li>While the "Hide" option enables the matching columns to
+ <li>While the 'Hide' option enables the matching columns to
be hidden automatically during the filtering process.</li>
- <li>The "Ok" button applies the filter when clicked.</li>
- <li>And finally, The "Cancel" button restores the alignment to its previous state before the filtering when clicked.
+ <li>The 'Ok' button applies the filter when clicked.</li>
+ <li>And finally, the 'Cancel' button restores the alignment to its previous state before any filtering was applied.
</ul></li>
</ul>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>BioJSON-1.0</title>
+</head>
+<body>
+ <h1>BioJSON</h1>
+ BioJSON is a standardise JavaScript Object Notation (JSON) format for exchange of Bio-informatics Sequence Alignment data.
+ BioJSON-1.0 schema/documentation is available at <a href="#">http://www.jalview.org/builds/develop/examples/biojson-doc/</a>.
+ You can keep up to date with BioJSON development and latest news at <a href="#">https://github.com/jalview/biojson/wiki</a>.
+
+ <h2>Features supported</h2>
+ Export/Import of the following alignment elements are supported in BioJSON-1.0:
+ <ul>
+ <li>Alignment Annotations</li>
+ <li>Alignment Features</li>
+ <li>Alignment Sequences</li>
+ <li>Color Scheme</li>
+ <li>Hidden Columns</li>
+ <li>Hidden Sequences</li>
+ <li>Sequence Groups</li>
+ </ul>
+
+ <h2>Features not yet supported</h2>
+ Export/Import of the following alignment elements are not supported in BioJSON-1.0:
+ <ul>
+ <li>Reference sequence</li>
+ <li>Representative sequence</li>
+ <li>Trees</li>
+ <li>3D Structures</li>
+ </ul>
+</body>
+</html>
<td><div align="center">-blc FILE</div></td>
<td><div align="left">Create alignment file FILE in BLC format.</div></td>
</tr>
+ <tr>
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in JSON format.</div></td>
+ </tr>
<tr>
<td><div align="center">-jalview FILE</div></td>
<body>
<strong>PDB Sequence Fetcher</strong>
- <p>From Jalview 2.x.x a speciliased interface was introduced for
+ <p>From Jalview 2.9, a specialised interface was introduced for
fast and efficient discovery/retrieval of sequence data from the PDB
database. The introduced interface enables live querying of PDB data
on-the-fly thereby eliminating the need to memorise database accession
- or to cross-reference other bioinformatics websites before retrieving
- a sequence data in jalview. The underlying technology is provided by
+ or to manually cross-reference other bioinformatics websites before retrieving
+ sequence data in Jalview. The underlying infrastructure is provided by
EBI and is based on Apache Solr which is a text based search engine.</p>
<p>
- The PDB Sequence Fetcher interface can be opened by selecting <strong>PDB</strong>
- as the choice database from the <strong>'Select Database
- Retrieval Source'</strong> interface of <a href="seqfetch.html">Sequence
- Fetcher</a>.
+ The PDB Sequence Fetcher interface can be accessed from <b>"File →Fetch Sequence(s) →Select Database →PDB"</b> click the ok button after selecting PDB from the 'Select Database
+ Retrieval Source' interface.
</p>
<p>
<img src="pdbseqfetcher.png" align="left"
- alt="PDB sequence fetcher (introduced in Jalview 2.x.x)">
+ alt="PDB sequence fetcher (introduced in Jalview 2.9)">
</p>
- <strong>Searching the PDB Database</strong>
- <br> Once the interface is opened, typing in the search text box
- will execute a live query to the PDB database and display the results
- on-the-fly as seen in the screen-shot above. Use the drop-down menu to
- select a specific field to search by in the PDB database, the default
- option is
- <strong>'ALL'</strong>. Furthermore, the PDB search interface also
- provides the following functionalities:
+ <p><strong>Searching the PDB Database</strong></p>
+ <p>When the interface is opened, a live query to the PDB database is
+ executed every time a character is typed into the search text box, and
+ a result is displayed on-the-fly as seen in the screenshot above.</p>
+
+ <p>Use the drop-down menu to select a specific field to search by in the PDB database, the default
+ option is 'ALL'.</p>
+
+ <p> Furthermore, the PDB search interface also provides the following functionalities:</p>
<ul>
<li>Retrieving a unique chain for a PDB entry: <br>To
retrieve a specific chain for a PDB entry, append the PDB ID with a
</ul>
<p>
<strong>Customising displayed meta-data</strong> <br>To change
- the displayed meta-data in the search result, click the <strong>'Configure
- Displayed Columns'</strong> tab, then tick off the options wanted.
+ the displayed meta-data in the search result, click the 'Configure
+ Displayed Columns' tab, then tick off the options wanted.
</p>
<p>
<strong>Importing Sequence</strong><br> After querying the PDB
database, to import the found data into Jalview, select the entries
- you wish to import then click the ok button at the bottom of the
+ you wish to import then click the 'Ok' button at the bottom of the
interface.
</p>
<p>
<em>The PDB Sequence Fetcher interface was introduced in Jalview
- 2.x.x.</em>
+ 2.9</em>
</p>
</body>
</html>
\ No newline at end of file
one or more accession ids (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the currently selected database into the retrieval box.
Finally, press "OK" to initiate the retrieval.</p>
- <p>Since Jalview 2.x.x if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequenec data. </p>
+ <p>Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequenec data. </p>
<p><strong>Specifying chains for PDB IDs</strong>
If you are retrieving sequences from the PDB, you can retrieve
specific chains by appending a colon and the chain id to the PDB
<strong>Associating PDB files with Sequences</strong><br>
- Discovery/Association of PDB entries to a sequence happens
+ Discovery/Association of PDB entries to a sequence now happens
automatically during the initialisation of the Structure Chooser
- Interface. Jalview uses the sequence's ID to query the PDB Rest API,
+ Interface. Jalview uses the sequence's ID to query the PDB Rest API
provided by the EBI to discover PDB Ids associated with the sequence.
<br><br>
<strong>Configuring displayed meta-data for Structures</strong><br>
- To configure the visible meta-data displayed for the discovered structures, click the <strong>'Configure Displayed Columns'</strong> tab, then tick the options which you intend to make visible.
+ To configure the visible meta-data displayed for the discovered structures, click the 'Configure Displayed Columns' tab, then tick the options which you intend to make visible.
<br><br>
<strong>Auto-selection of best Structures</strong>
<br> Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data
of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure
Chooser interface: Best Uniprot coverage, Higest Resolution,
-
- Best Quality, Highest Protein Chain etc. When the <strong>'Invert'</strong> option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.<p>
+ Best Quality, Highest Protein Chain etc. When the 'Invert' option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.<p>
+
<img src="schooser_main.png" style="width: 464px; height: 369px;">
<!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
</ul>
<p>
- <em>The Structure Chooser interface was introduced in Jalview 2.x.x.
+ <em>The Structure Chooser interface was introduced in Jalview 2.9.
</em>
</p>
</body>
<em>...</em><br>//</td>
<td width="23%">.phy</td>
</tr>
+<tr>
+<td width="17%">JSON</td>
+<td width="60%">Data starts with '{' <br>Data ends with '}' <br><br>See <a href="../features/bioJsonFormat.html">BioJson</a> for more info about Jalview JSON format <br></td>
+<td width="23%">.json</td>
+</tr>
</table>
<p>The file extensions are used to associate jalview alignment icons
with alignment files: <img src="file.png" width=12 height=12 >
<li><strong>AMSA</strong></li>
<li><strong>STH</strong></li>
<li><strong>Phylip</strong></li>
+ <li><strong>JSON</strong></li>
</ul></li>
<li><strong>Print (Control P)<br> </strong><em>Jalview
will print the alignment using the current fonts and colours of
label.structure = Structure
label.view_structure = View Structure
label.view_protein_structure = View Protein Structure
-label.view_rna_structure = View Nucleotide Structure
+label.show_pdbstruct_dialog = 3D Structure Data ...
+label.view_rna_structure = VARNA 2D Structure
label.clustalx_colours = Clustalx colours
label.above_identity_percentage = Above % Identity
label.create_sequence_details_report_annotation_for = Annotation for {0}
label.graduated_color_for_params = Graduated Feature Colour for {0}
label.select_backgroud_colour = Select Background Colour
label.invalid_font = Invalid Font
-label.separate_multiple_accession_ids = Enter one or more PDB Ids
+label.separate_multiple_accession_ids = Enter one or more accession IDs
label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire PDB database)
label.replace_commas_semicolons = Replace commas with semi-colons
info.search_in_annotation_label = Search in {0} Label
info.search_in_annotation_description = Search in {0} Description
info.change_threshold_mode_to_enable = Change Threshold Mode to Enable
+label.null_or_unidentifiable_data = Null or unidentifiable data content pasted!
+label.unidentifiable_data = Unidentifiable Data
+label.null_or_invalid_alignment = Null or invalid alignment data!
+label.unable_to_create_alignment = Unable to create alignment
System.setProperty("java.awt.headless", "true");
headless = true;
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
+ {
+ System.out.println("CMD [-props " + usrPropsFile
+ + "] executed successfully!");
+ }
+
// anything else!
final String jabawsUrl = aparser.getValue("jabaws");
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println("CMD [-jabaws " + jabawsUrl
+ + "] executed successfully!");
} catch (MalformedURLException e)
{
System.err.println("Invalid jabaws parameter: " + jabawsUrl
{
startUsageStats(desktop);
}
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
}
else
{
}
}
}
+ else
+ {
+ System.err
+.println("CMD [-noquestionnaire] executed successfully!");
+ }
desktop.checkForNews();
}
desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("Opening file: " + file);
+ System.out.println("CMD [-open " + file + "] executed successfully!");
if (!file.startsWith("http://"))
{
ucs.parseAppletParameter(data);
cs = ucs;
}
-
- System.out.println("colour is " + data);
+ else
+ {
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
+ }
af.changeColour(cs);
}
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-annotations " + data
+ + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
{
af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out
+.println("CMD [-sortbytree] executed successfully!");
+ }
}
if (aparser.contains("no-annotation"))
{
af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out
+.println("CMD no-annotation executed successfully!");
+ }
}
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
}
data = aparser.getValue("tree", true);
if (data != null)
jalview.io.NewickFile fin = null;
try
{
+ System.out.println("CMD [-tree " + data
+ + "] executed successfully!");
fin = new jalview.io.NewickFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
if (fin != null)
{
af.getViewport().setCurrentTree(
af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
}
} catch (IOException ex)
{
System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, new Object[]
{ desktop, af });
+
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
}
else
{
+ "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-svg FILE\tCreate SVG image FILE from alignment.\n"
}
source.addElement(nickname);
}
+ System.out.println("CMD [-dasserver " + data
+ + "] executed successfully!");
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
*/
package jalview.datamodel;
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
+
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Set;
import java.util.Vector;
-import jalview.analysis.AlignmentUtils;
-import jalview.io.FastaFile;
-import jalview.util.MessageManager;
-
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
}
return names;
}
+
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if (seq.getSequenceAsString().matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"))
+ {
+ hasValidSeq = true;
+ break;
+ }
+ }
+ return hasValidSeq;
+ }
}
* @return
*/
Set<String> getSequenceNames();
+
+ /**
+ * Checks if the alignment has at least one sequence with one non-gaped
+ * residue
+ *
+ * @return
+ */
+ public boolean hasValidSequence();
}
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
}
String format = new IdentifyFile().Identify(text, "Paste");
+ if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+ {
+ System.err.println(MessageManager
+ .getString("label.null_or_unidentifiable_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ JOptionPane.showMessageDialog(null,
+ MessageManager
+ .getString("label.null_or_unidentifiable_data"),
+ MessageManager.getString("label.unidentifiable_data"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ return;
+ }
+
// TODO: identify feature, annotation or tree file and parse appropriately.
AlignmentI al = null;
}
}
- if (al != null)
+ if (al != null && al.hasValidSequence())
{
String title = MessageManager.formatMessage(
"label.input_cut_paste_params", new String[]
}
}
}
+ else
+ {
+ System.err.println(MessageManager
+ .getString("label.null_or_invalid_alignment"));
+ if (!Jalview.isHeadlessMode())
+ {
+ JOptionPane
+ .showMessageDialog(
+ null,
+ MessageManager
+ .getString("label.null_or_invalid_alignment"),
+ MessageManager
+ .getString("label.unable_to_create_alignment"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
}
*/
package jalview.gui;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
/**
* DOCUMENT ME!
*
JMenu jMenu1 = new JMenu();
- JMenuItem proteinStructureMenu = new JMenuItem();
+ JMenuItem pdbStructureDialog = new JMenuItem();
JMenu rnaStructureMenu = new JMenu();
}
else
{
+ int origCount = rnaStructureMenu.getItemCount();
/*
* add menu items to 2D-render any alignment or sequence secondary
* structure annotation
}
}
}
+ if (rnaStructureMenu.getItemCount() == origCount)
+ {
+ remove(rnaStructureMenu);
+ }
}
menuItem = new JMenuItem(
if (seq == null)
{
sequenceMenu.setVisible(false);
- proteinStructureMenu.setVisible(false);
+ pdbStructureDialog.setVisible(false);
rnaStructureMenu.setVisible(false);
}
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- proteinStructureMenu.setText(MessageManager
- .getString("label.view_protein_structure"));
- proteinStructureMenu.addActionListener(new ActionListener()
+ pdbStructureDialog.setText(MessageManager
+ .getString("label.show_pdbstruct_dialog"));
+ pdbStructureDialog.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
add(groupMenu);
add(sequenceMenu);
add(rnaStructureMenu);
- add(proteinStructureMenu);
+ add(pdbStructureDialog);
if (sequence!=null)
{
add(hideInsertions);
public static final boolean isValidFormat(String format,
boolean forwriting)
{
+ if (format == null)
+ {
+ return false;
+ }
boolean valid = false;
String[] format_list = (forwriting) ? WRITEABLE_FORMATS
: READABLE_FORMATS;
{
Desktop.instance.stopLoading();
System.err.println("The input file \"" + file
- + "\" has no data content!");
+ + "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- JOptionPane.showMessageDialog(null, "The input file \""
- + file + "\" has no data content!", "Empty data file",
+ JOptionPane.showMessageDialog(null, "The input file \"" + file
+ + "\" has null or unidentifiable data content!",
+ "Empty data file",
JOptionPane.ERROR_MESSAGE);
}
return;
*/
public String Identify(FileParse source, boolean closeSource)
{
- String reply = "PFAM";
+ String reply = null;
String data;
int length = 0;
boolean lineswereskipped = false;
reply = "STH";
break;
}
- // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
- if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
- {
- reply = HtmlFile.FILE_DESC;
- break;
- }
- if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
+ // RNAML, XML
{
- reply = "RNAML";
- break;
+ boolean identified = false;
+ do
+ {
+ if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ {
+ reply = HtmlFile.FILE_DESC;
+ identified = true;
+ break;
+ }
+
+ if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ {
+ reply = "RNAML";
+ identified = true;
+ break;
+ }
+ } while ((data = source.nextLine()) != null);
+
+ if (identified)
+ {
+ break;
+ }
}
+
if (data.indexOf("{\"") > -1)
{
reply = JSONFile.FILE_DESC;
public class AnnotationRenderer
{
+ private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
+
+ private static final int CHAR_A = 'A'; // 65
+
+ private static final int CHAR_Z = 'Z'; // 90
+
/**
* flag indicating if timing and redraw parameter info should be output
*/
}
}
- if (ss >= 65)
+ if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
{
// distinguish between forward/backward base-pairing
- if (displayChar.indexOf(ss + 32) > -1)
+ int ssLowerCase = ss + UPPER_TO_LOWER;
+ // TODO would .equals() be safer here? or charAt(0)?
+ if (displayChar.indexOf(ssLowerCase) > -1)
{
-
- ss = (char) (ss + 32);
-
+ ss = (char) ssLowerCase;
}
}
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
+import java.util.ArrayList;
import org.testng.Assert;
import org.testng.FileAssert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class CommandLineOperations
{
- @BeforeClass
- public static void setUpBeforeClass() throws Exception
- {
- }
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception
- {
- }
+ private ArrayList<String> successfulCMDs = new ArrayList<String>();
/***
* from
private static class Worker extends Thread
{
private final Process process;
-
+ private BufferedReader outputReader;
+ private BufferedReader errorReader;
private Integer exit;
private Worker(Process process)
return;
}
}
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
}
private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
- int timeout) throws InterruptedException, IOException
+ int timeout)
{
String _cmd = "java "
+ (withAwt ? "-Djava.awt.headless=true" : "")
+ " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
- System.out.println("############ Testing Jalview CMD: " + _cmd + cmd);
- Process ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
- BufferedReader outputReader = new BufferedReader(new InputStreamReader(
- ls2_proc.getInputStream()));
-
- BufferedReader errorReader = new BufferedReader(new InputStreamReader(
- ls2_proc.getErrorStream()));
- Worker worker = new Worker(ls2_proc);
- worker.start();
- worker.join(timeout);
- // System.out.println("Output: ");
- // String ln = null;
- // while ((ln = outputReader.readLine()) != null)
- // {
- // System.out.println(ln);
- // }
- //
- // System.out.println("Error: ");
- // while ((ln = errorReader.readLine()) != null)
- // {
- // System.out.println(ln);
- // }
+ System.out.println("CMD [" + cmd + "]");
+ Process ls2_proc = null;
+ Worker worker = null;
+ try
+ {
+ ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ if (ls2_proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(ls2_proc.getInputStream()));
+
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(ls2_proc.getErrorStream()));
+ worker = new Worker(ls2_proc);
+ worker.start();
+ try
+ {
+ worker.join(timeout);
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
return worker;
}
new CommandLineOperations();
}
- @Test(groups =
- { "Functional" }, dataProvider = "headlessModeOutputParams")
- public void testHeadlessModeOutputs(String harg, String type,
- String fileName, boolean withAWT, int expectedMinFileSize)
+
+ @BeforeTest
+ public void setUpForHeadlessCommandLineInputOperations()
+ throws IOException
{
- String cmd = harg + type + " " + fileName;
- // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
- File file = new File(fileName);
- Worker worker = null;
- try
+ String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
+ + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
+ + "-features examples/uniref50_test_features -annotations examples/uniref50_test_annot -tree examples/uniref50_test_tree";
+ Worker worker = jalviewDesktopRunner(true, cmds, 9000);
+ String ln = null;
+ while ((ln = worker.getOutputReader().readLine()) != null)
{
- worker = jalviewDesktopRunner(withAWT, cmd, 9000);
- } catch (InterruptedException e)
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ }
+ }
+
+ @BeforeTest
+ public void setUpForCommandLineInputOperations() throws IOException
+ {
+ String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
+ Worker worker = jalviewDesktopRunner(false, cmds, 9000);
+ String ln = null;
+ int count = 0;
+ while ((ln = worker.getErrorReader().readLine()) != null)
{
- e.printStackTrace();
- } catch (IOException e)
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > 5)
+ {
+ break;
+ }
+ }
+ if (worker != null && worker.exit == null)
{
- e.printStackTrace();
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
}
+ }
+
+ @Test(groups =
+ { "Functional" }, dataProvider = "allInputOpearationsData")
+ public void testAllInputOperations(String expectedString,
+ String failureMsg)
+ {
+ Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
+ }
+
+ @Test(groups =
+ { "Functional" }, dataProvider = "headlessModeOutputOperationsData")
+ public void testHeadlessModeOutputOperations(String harg, String type,
+ String fileName, boolean withAWT, int expectedMinFileSize,
+ int timeout)
+ {
+ String cmd = harg + type + " " + fileName;
+ // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+ File file = new File(fileName);
+ Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
FileAssert.assertFile(file, "Didn't create an output" + type
+ " file.[" + harg + "]");
worker.interrupt();
Thread.currentThread().interrupt();
worker.process.destroy();
- Assert.fail("Jalview did not exit after "
+ Assert.fail("Jalview did not exit after "
+ type
+ " generation (try running test again to verify - timeout at 9000ms). ["
+ harg + "]");
new File(fileName).delete();
}
- @DataProvider(name = "headlessModeOutputParams")
- public static Object[][] headlessModeOutput()
+
+ @DataProvider(name = "allInputOpearationsData")
+ public Object[][] getHeadlessModeInputParams()
+ {
+ return new Object[][]
+ {
+ // headless mode input operations
+ { "CMD [-color zappo] executed successfully!",
+ "Failed command : -color zappo" },
+ { "CMD [-props FILE] executed successfully!",
+ "Failed command : -props File" },
+ { "CMD [-sortbytree] executed successfully!",
+ "Failed command : -sortbytree" },
+ {
+ "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
+ "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
+ { "CMD [-open examples/uniref50.fa] executed successfully!",
+ "Failed command : -open examples/uniref50.fa" },
+ { "CMD [-nosortbytree] executed successfully!",
+ "Failed command : -nosortbytree" },
+ { "CMD [-dasserver nickname=www.test.com] executed successfully!",
+ "Failed command : -dasserver nickname=www.test.com" },
+ {
+ "CMD [-features examples/uniref50_test_features] executed successfully!",
+ "Failed command : -features examples/uniref50_test_features" },
+ {
+ "CMD [-annotations examples/uniref50_test_annot] executed successfully!",
+ "Failed command : -annotations examples/uniref50_test_annot" },
+ { "CMD [-tree examples/uniref50_test_tree] executed successfully!",
+ "Failed command : -tree examples/uniref50_test_tree" },
+ // non headless mode input operations
+ { "CMD [-nousagestats] executed successfully!",
+ "Failed command : -nousagestats" },
+ { "CMD [-noquestionnaire] executed successfully!",
+ "Failed command : -noquestionnaire nickname=www.test.com" }
+ };
+
+ }
+
+ @DataProvider(name = "headlessModeOutputOperationsData")
+ public static Object[][] getHeadlessModeOutputParams()
{
return new Object[][]
{
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
+ "test_uniref50_out.eps", true, 4096, 4000 },
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
- { "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
- { "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
+ "test_uniref50_out.eps", false, 4096, 4000 },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
+ "test_uniref50_out.eps", true, 4096, 4000 },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
- { "headless -open examples/uniref50.fa", " -svg",
- "test_uniref50_out.svg", true, 4096 },
+ "test_uniref50_out.eps", false, 4096, 4000 },
+ { "headless -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", true, 4096, 4000 },
{ "headless -open examples/uniref50.fa", " -svg",
- "test_uniref50_out.svg", false, 4096 },
+ "test_uniref50_out.svg", false, 4096, 3000 },
{ "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", true, 4096 },
- { "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", false, 4096 },
- { "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", true, 4096 },
+ "test_uniref50_out.png", true, 4096, 3000 },
{ "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", false, 4096 },
+ "test_uniref50_out.html", true, 4096, 3000 },
{ "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", true, 2096 },
- { "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", false, 2096 },
- { "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", true, 2096 },
+ "test_uniref50_out.mfa", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", false, 2096 },
- { "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", true, 2096 },
+ "test_uniref50_out.aln", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", false, 2096 },
+ "test_uniref50_out.msf", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", true, 2096 },
- { "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", false, 2096 },
- { "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", true, 2096 },
+ "test_uniref50_out.aln", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", false, 2096 },
+ "test_uniref50_out.pir", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", true, 2096 },
- { "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", false, 2096 },
- { "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", true, 2096 },
+ "test_uniref50_out.pfam", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", false, 2096 },
- { "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", true, 2096 },
+ "test_uniref50_out.blc", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", false, 2096 },
+ "test_uniref50_out.jvp", true, 2096, 3000 },
};
}
-
-
}
private Alignment al;
- @BeforeMethod
+ @BeforeMethod(groups =
+ { "Functional" })
public void setUp()
{
testee = new EditCommand();
git://source.jalview.org / jalview.git / commitdiff