From: tva Date: Fri, 7 Jun 2019 14:23:34 +0000 (+0100) Subject: JAL-3291 issue fixed, passing tests added X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f452bcb5ddecb4378e952447031ddb076bdf8268;p=jalview.git JAL-3291 issue fixed, passing tests added --- diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java index e3eb160..e917474 100644 --- a/src/jalview/datamodel/HiddenMarkovModel.java +++ b/src/jalview/datamodel/HiddenMarkovModel.java @@ -520,12 +520,18 @@ public class HiddenMarkovModel int start = hasMap ? getNode(1).getResidueNumber() : 1; int endResNo = hasMap ? getNode(nodes.size() - 1).getResidueNumber() : (start + getLength() - 1); - char[] sequence = new char[endResNo - start + 1]; + char[] sequence = new char[endResNo + 1]; int lastResNo = start - 1; - int seqOffset = 0; + int seqOffset = -1; int gapCount = 0; + for (int seqN = 0; seqN < start; seqN++) + { + sequence[seqN] = GAP_DASH; + seqOffset++; + } + for (int nodeNo = 1; nodeNo < nodes.size(); nodeNo++) { HMMNode node = nodes.get(nodeNo); @@ -536,7 +542,7 @@ public class HiddenMarkovModel */ while (resNo > lastResNo + 1) { - sequence[seqOffset++] = '-'; + sequence[seqOffset++] = GAP_DASH; lastResNo++; gapCount++; } diff --git a/test/jalview/datamodel/HiddenMarkovModelTest.java b/test/jalview/datamodel/HiddenMarkovModelTest.java index 7978da2..65241b4 100644 --- a/test/jalview/datamodel/HiddenMarkovModelTest.java +++ b/test/jalview/datamodel/HiddenMarkovModelTest.java @@ -18,6 +18,8 @@ public class HiddenMarkovModelTest { HiddenMarkovModel hmm; + HiddenMarkovModel alignmentHmm; + @BeforeClass(alwaysRun = true) public void setUp() throws MalformedURLException, IOException { @@ -27,6 +29,12 @@ public class HiddenMarkovModelTest { HMMFile file = new HMMFile(new FileParse( "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE)); hmm = file.getHMM(); + + // used to check if consensus sequence is automatically aligned with alignment + HMMFile alignmentTest = new HMMFile( + new FileParse("test/jalview/io/HMMAlignmentTestHMM.hmm", + DataSourceType.FILE)); + alignmentHmm = alignmentTest.getHMM(); } @Test(groups = "Functional") @@ -115,6 +123,14 @@ public class HiddenMarkovModelTest { assertEquals(subStr, "yelleklGsG"); subStr = seq.getSequenceAsString().substring(150, 161); assertEquals(subStr, "-dllk------"); + + // test to see if consensus sequence maps to alignment correctly + // see HMMAlignmentTest.sto for corresponding alignment file + SequenceI seq2 = alignmentHmm.getConsensusSequence(); + assertEquals(seq2.getCharAt(0), '-'); + assertEquals(seq2.getCharAt(7), '-'); + assertEquals(seq2.getCharAt(8), 's'); + } /** diff --git a/test/jalview/io/HMMAlignmentTest.sto b/test/jalview/io/HMMAlignmentTest.sto new file mode 100644 index 0000000..f0f1f4a --- /dev/null +++ b/test/jalview/io/HMMAlignmentTest.sto @@ -0,0 +1,16 @@ +# STOCKHOLM 1.0 +#=GS Q7XA98_TRIPR/1-152 DR UNIPROT ; Q7XA98 +#=GS FER1_PEA/1-149 DR UNIPROT ; P09911 +#=GS Q93XJ9_SOLTU/1-144 DR UNIPROT ; Q93XJ9 +#=GS FER_CAPAN/1-144 DR UNIPROT ; Q9ZTS2 +#=GS FER1_SOLLC/1-144 DR UNIPROT ; Q43517 +#=GS FER_CAPAA/1-97 DR UNIPROT ; P83527 +FER_CAPAA/1-97 ------------------------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER1_SOLLC/1-144 -------------MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +Q93XJ9_SOLTU/1-144 --------MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +FER1_PEA/1-149 -------------MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +Q7XA98_TRIPR/1-152 -------------MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +#=GC SS_cons EEE EEEEEEEE HHHHH e e e EE EE HHHH E e EE EEEEE +#=GC Iron_Sulphur_Contacts -------------------------------------------------------------------------------------------------e----e--e-----------------------------e--------------------- +// diff --git a/test/jalview/io/HMMAlignmentTestHMM.hmm b/test/jalview/io/HMMAlignmentTestHMM.hmm new file mode 100644 index 0000000..649f5f9 --- /dev/null +++ b/test/jalview/io/HMMAlignmentTestHMM.hmm @@ -0,0 +1,478 @@ +HMMER3/f [3.2 | June 2018] +NAME Alignment_HMM +LENG 152 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Fri Jun 7 14:44:10 2019 +NSEQ 6 +EFFN 2.071289 +CKSUM 2312940853 +STATS LOCAL MSV -10.2278 0.70920 +STATS LOCAL VITERBI -10.8843 0.70920 +STATS LOCAL FORWARD -4.3996 0.70920 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d + COMPO 2.41432 3.67931 2.75921 2.60121 3.50018 2.76530 3.83614 2.93106 2.71371 2.66765 3.66760 3.24838 3.26026 3.17831 3.19279 2.51076 2.65615 2.59873 5.09464 3.62512 + 2.68544 4.42237 2.77531 2.73135 3.46365 2.40524 3.72506 3.29365 2.67752 2.69366 4.24294 2.90358 2.73751 3.18158 2.89812 2.37898 2.77531 2.98530 4.58488 3.61515 + 0.78057 1.55851 1.10441 0.67815 0.70837 0.00000 * + 1 2.59800 4.39329 3.63625 3.18787 3.71456 3.43841 4.11392 3.03068 3.09157 2.71409 1.85445 3.48425 4.00395 3.44434 3.39575 1.59145 2.94832 2.79270 5.21434 3.95539 9 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02133 4.25401 4.97636 0.61958 0.77255 0.98598 0.46693 + 2 1.50579 4.32755 4.18645 3.78216 3.88559 3.56425 4.59767 2.41074 3.70275 2.69336 3.78707 3.89382 4.19613 3.99133 3.94010 2.99086 3.05698 1.28977 5.52248 4.31320 10 v - - - + 2.68550 4.42242 2.77537 2.73141 3.46371 2.40530 3.72512 3.29371 2.67758 2.69372 4.24707 2.90364 2.73757 3.18164 2.89818 2.37841 2.77443 2.98536 4.58494 3.61520 + 0.90209 1.16285 1.26696 1.01535 0.44985 0.39057 1.12909 + 3 3.42707 4.91214 4.61207 4.26925 3.52422 4.22326 4.89422 2.75377 4.00666 2.06722 0.68834 4.47974 4.70831 4.36739 4.15005 3.81331 3.75358 2.81142 5.41119 4.20659 14 M - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01938 4.34894 5.07129 0.61958 0.77255 0.90177 0.52062 + 4 1.43643 4.42503 4.31312 3.86585 3.75424 3.86050 4.64018 1.40277 3.76673 2.49922 3.64972 4.05060 4.39156 4.05997 3.99981 3.25891 3.19718 2.11006 5.45161 4.24039 15 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.14665 4.34894 2.09167 0.61958 0.77255 0.90177 0.52062 + 5 2.37098 4.31475 3.56770 3.24979 4.37798 3.10030 4.31086 3.75066 3.26247 3.47251 4.31621 3.42494 3.83407 3.57718 3.57680 1.30947 1.53387 3.24501 5.72919 4.50336 16 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02198 4.22428 4.94663 0.61958 0.77255 0.54114 0.87248 + 6 2.50652 4.44141 3.83949 3.54853 4.61304 3.23185 4.57545 3.99871 3.56049 3.72110 4.55726 3.64948 3.99392 3.85973 3.84879 1.49216 1.01986 3.44946 5.96659 4.76085 17 t - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.24086 4.47354 1.59630 0.61958 0.77255 0.76398 0.62700 + 7 2.65517 4.36127 3.81549 3.38335 3.69064 3.54500 4.25486 1.58799 3.30272 2.65201 3.68407 3.64162 4.10535 3.63002 3.58335 1.61226 3.00284 2.44965 5.24306 3.98781 18 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02133 4.25401 4.97636 0.61958 0.77255 0.98598 0.46693 + 8 2.74723 4.45808 3.83003 3.43336 1.55716 3.57739 4.01030 3.12129 3.39844 2.75883 3.78862 3.64312 4.13759 3.66183 3.66464 1.60155 3.09781 2.89427 4.64509 3.10366 19 f - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02133 4.25401 4.97636 0.61958 0.77255 0.98598 0.46693 + 9 2.65532 4.43699 3.65638 3.26130 3.78761 1.68622 4.19753 3.09268 3.18548 2.76736 1.66329 3.54773 4.04431 3.53861 3.47551 2.87376 3.01742 2.85730 5.28180 4.04464 20 m - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02133 4.25401 4.97636 0.61958 0.77255 0.55834 0.84900 + 10 2.62413 4.55150 3.73217 3.46502 4.58891 3.32606 4.53947 3.93771 3.48022 3.66044 4.54532 3.64966 1.08714 3.81713 3.77509 2.80225 1.57704 3.45878 5.93284 4.72852 21 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01709 4.47354 5.19589 0.61958 0.77255 0.51701 0.90709 + 11 1.99709 4.68552 3.40260 2.84388 3.94615 3.60689 3.90388 3.32023 2.73340 2.98773 2.29384 3.29447 4.03205 3.12399 2.03393 2.35985 2.99523 3.04365 5.29921 4.03061 22 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 12 3.03612 4.58206 4.17469 3.58665 3.60032 4.09338 4.33760 1.51772 1.94651 1.71212 3.50362 3.91731 4.43832 3.70785 3.50867 3.39096 3.26453 2.43051 5.23091 4.03724 23 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 13 2.76197 4.70799 3.41034 2.96484 3.84310 3.56022 4.02290 3.51807 2.97071 3.16868 4.04204 3.37800 2.07618 3.30589 3.36146 1.59778 3.07503 3.20545 5.27554 2.20871 24 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 14 1.42932 4.46589 4.02364 3.69643 4.72988 1.43294 4.68906 4.13282 3.71549 3.83309 4.64260 3.74322 4.03851 3.97444 4.00639 2.72003 1.63454 3.53847 6.07503 4.89460 25 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 15 2.63382 4.43500 3.98903 3.52691 4.05377 3.47381 4.41118 3.21360 3.46955 3.09630 4.00516 3.71495 4.11115 3.75748 3.76367 1.74048 1.56254 1.69711 5.50933 4.30015 26 t - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 16 1.97870 4.28154 4.12278 3.55312 2.14335 3.81420 4.17500 2.68382 3.44988 2.41995 2.61784 3.79310 4.21338 3.68984 3.66833 3.11084 1.96434 2.49922 4.91664 3.71472 27 t - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 17 2.91846 4.34842 4.48199 3.90988 3.46317 4.07572 4.44144 1.98330 3.78456 1.67828 3.41359 4.10010 4.43748 4.00384 3.95399 2.01206 3.16092 1.64497 5.07625 3.88829 28 v - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 18 2.70635 4.56892 3.60528 3.14080 3.96671 3.53723 4.15403 3.33644 3.10057 1.82443 3.93202 3.49380 2.11690 3.43662 3.45226 1.62468 3.04334 3.04998 5.39218 4.13558 29 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.26457 4.57201 1.50451 0.61958 0.77255 0.62415 0.76726 + 19 2.81401 4.82005 3.48128 2.94818 4.34473 3.53963 3.92028 3.69738 2.45527 3.31575 4.19707 3.33652 4.04563 3.10077 1.62480 2.90920 1.49986 3.36258 5.52959 4.29493 30 t - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01981 4.32725 5.04960 0.61958 0.77255 0.42245 1.06549 + 20 2.99742 5.17558 3.29695 2.86766 4.77169 3.64255 3.98284 4.20460 1.15211 3.71930 4.54717 3.31939 4.14896 3.12831 2.80934 1.59962 3.28379 3.79417 5.81941 4.54197 31 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 21 3.28763 4.90910 4.31235 3.99239 1.36983 4.02580 4.37777 3.48169 3.95787 2.96396 4.13543 4.15449 1.08518 4.20039 4.16663 3.51751 3.64052 3.33099 4.84797 3.27396 32 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01548 4.57201 5.29435 0.61958 0.77255 0.62415 0.76726 + 22 3.45018 4.70771 5.41218 4.85806 3.55317 4.84496 5.27184 1.41698 4.72877 1.42021 2.43827 4.98314 5.05481 4.81112 4.77841 4.21177 3.68367 1.42720 5.55642 4.46185 33 i - 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