JAL-1769 added test for commandline input operations

diff --git a/examples/uniref50_test_annot b/examples/uniref50_test_annot
new file mode 100644 (file)
index 0000000..fd60c65
--- /dev/null
+++ b/examples/uniref50_test_annot
@@ -0,0 +1,11 @@
+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   
+

diff --git a/examples/uniref50_test_features b/examples/uniref50_test_features
new file mode 100644 (file)
index 0000000..60f995f
--- /dev/null
+++ b/examples/uniref50_test_features
@@ -0,0 +1,5 @@
+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     .       .

diff --git a/examples/uniref50_test_tree b/examples/uniref50_test_tree
new file mode 100644 (file)
index 0000000..585b68b
--- /dev/null
+++ b/examples/uniref50_test_tree
@@ -0,0 +1 @@
+(((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);

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f6d0099..8ad4cbd 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -109,7 +109,14 @@ public class Jalview
       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");
@@ -118,6 +125,8 @@ public class Jalview
       try
       {
         Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+        System.out.println("CMD [-jabaws " + jabawsUrl
+                + "] executed successfully!");
       } catch (MalformedURLException e)
       {
         System.err.println("Invalid jabaws parameter: " + jabawsUrl
@@ -195,6 +204,11 @@ public class Jalview
       {
         startUsageStats(desktop);
       }
+      else
+      {
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+
       if (!aparser.contains("noquestionnaire"))
       {
         String url = aparser.getValue("questionnaire");
@@ -204,6 +218,8 @@ public class Jalview
           // questionnaire
           Cache.log.debug("Starting questionnaire url at " + url);
           desktop.checkForQuestionnaire(url);
+          System.out.println("CMD questionnaire[-" + url
+                  + "] executed successfully!");
         }
         else
         {
@@ -222,6 +238,11 @@ public class Jalview
           }
         }
       }
+      else
+      {
+        System.err
+.println("CMD [-noquestionnaire] executed successfully!");
+      }
       desktop.checkForNews();
     }
 
@@ -340,7 +361,7 @@ public class Jalview
         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://"))
       {
@@ -382,8 +403,11 @@ public class Jalview
             ucs.parseAppletParameter(data);
             cs = ucs;
           }
-
-          System.out.println("colour is " + data);
+          else
+          {
+            System.out.println("CMD [-color " + data
+                    + "] executed successfully!");
+          }
           af.changeColour(cs);
         }
 
@@ -393,34 +417,55 @@ public class Jalview
         {
           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)
@@ -428,13 +473,14 @@ public class Jalview
           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)
           {
@@ -475,6 +521,9 @@ public class Jalview
             System.out.println("Executing script " + groovyscript);
             executeGroovyScript(groovyscript, new Object[]
             { desktop, af });
+
+            System.out.println("CMD groovy[" + groovyscript
+                    + "] executed successfully!");
           }
           else
           {
@@ -930,6 +979,8 @@ public class Jalview
         }
         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)
     {

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 3582dc5..70f6079 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -24,11 +24,10 @@ import java.io.BufferedReader;
 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;
@@ -36,15 +35,7 @@ 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
@@ -57,7 +48,8 @@ public class CommandLineOperations
   private static class Worker extends Thread
   {
     private final Process process;
-
+    private BufferedReader outputReader;
+    private BufferedReader errorReader;
     private Integer exit;
 
     private Worker(Process process)
@@ -75,36 +67,63 @@ public class CommandLineOperations
         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;
   }
 
@@ -114,25 +133,65 @@ public class CommandLineOperations
     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 uniref50_test_features -annotations uniref50_test_annot -tree 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 + "]");
@@ -142,7 +201,7 @@ public class CommandLineOperations
       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 + "]");
@@ -150,69 +209,80 @@ public class CommandLineOperations
     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 uniref50_test_features]  executed successfully!",
+            "Failed command : -features uniref50_test_features" },
+        { "CMD [-annotations uniref50_test_annot] executed successfully!",
+            "Failed command : -annotations uniref50_test_annot" },
+        { "CMD [-tree uniref50_test_tree] executed successfully!",
+            "Failed command : -tree 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, 3000 },
         { "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, 3000 },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test_uniref50_out.eps", true, 4096 },
+            "test_uniref50_out.eps", true, 4096, 3000 },
         { "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, 3000 },
+        { "headless -open examples/uniref50.fa", " -eps",
+            "test_uniref50_out.eps", true, 4096, 3000 },
         { "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 },
     };
   }
-
-
 }