From 827e8a199b8c490b4d774befb2a0bac6383a9d38 Mon Sep 17 00:00:00 2001 From: TZVanaalten Date: Thu, 27 Jul 2017 17:17:08 +0100 Subject: [PATCH] JAL-2629 implement hmmbuild --- resources/lang/Messages.properties | 2 +- src/jalview/datamodel/HiddenMarkovModel.java | 72 ++-- src/jalview/gui/AlignFrame.java | 34 +- src/jalview/hmmer/HMMERCommands.java | 91 +++++ src/jalview/hmmer/alignment_buffer.sto | 19 ++ src/jalview/hmmer/hmm_buffer.hmm | 464 ++++++++++++++++++++++++++ src/jalview/io/HMMFile.java | 20 +- src/jalview/io/StockholmFile.java | 7 +- src/jalview/jbgui/GAlignFrame.java | 24 ++ 9 files changed, 679 insertions(+), 54 deletions(-) create mode 100644 src/jalview/hmmer/HMMERCommands.java create mode 100644 src/jalview/hmmer/alignment_buffer.sto create mode 100644 src/jalview/hmmer/hmm_buffer.hmm diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index f05f7bc..97f8c8d 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1315,6 +1315,6 @@ label.warning_hidden = Warning: {0} {1} is currently hidden label.change_hmmer_directory = Change HMMER suite location label.auto_align_seqs = Automatically Align New Sequences label.hmmalign = Align Sequences to HMM -label.hmmbuild = Build HMM From Alignment +label.hmmbuild = Build HMM from Alignment label.hmmsearch = Search for Related Sequences diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java index 96a5a6f..727ffc7 100644 --- a/src/jalview/datamodel/HiddenMarkovModel.java +++ b/src/jalview/datamodel/HiddenMarkovModel.java @@ -469,14 +469,33 @@ public class HiddenMarkovModel */ public char getConsensusAtAlignColumn(int columnIndex) { - char value; + char mostLikely = '-'; + if (consensusResidueIsActive()) + { + Integer index = findNodeIndex(columnIndex); if (index == null) { return '-'; } - value = getNodes().get(index).getConsensusResidue(); - return value; + mostLikely = getNodes().get(index).getConsensusResidue(); + return mostLikely; + } + else + { + double highestProb = 0; + for (char character : symbols) + { + Double prob = getMatchEmissionProbability(columnIndex, character); + if (prob > highestProb) + { + highestProb = prob; + mostLikely = character; + } + } + return mostLikely; + } + } /** @@ -933,7 +952,9 @@ public class HiddenMarkovModel } Character cons; + cons = getConsensusAtAlignColumn(alignPos); + cons = Character.toUpperCase(cons); String description = String.format("%.3f", content); @@ -948,6 +969,7 @@ public class HiddenMarkovModel "The information content of each column, measured in bits", annotations, 0f, max, AlignmentAnnotation.BAR_GRAPH); + annotation.setHMM(this); return annotation; } @@ -1008,14 +1030,9 @@ public class HiddenMarkovModel for (int index = 0; index < length; index++) { Character character; - if (consensusResidueIsActive()) - { + character = getConsensusAtAlignColumn(index); - } - else - { - character = findConsensusCharacter(index); - } + if (character == null || character == '-') { sequence[index] = '-'; @@ -1031,29 +1048,6 @@ public class HiddenMarkovModel return seq; } - /** - * Finds the most probable character at a column in an alignment based on the - * HMM. - * - * @param nodeIndex - * The index of the node. - * @return - */ - Character findConsensusCharacter(int column) - { - Character mostLikely = null; - double highestProb = 0; - for (char character : symbols) - { - Double prob = getMatchEmissionProbability(column, character); - if (prob > highestProb) - { - highestProb = prob; - mostLikely = character; - } - } - return mostLikely; - } /** * Maps the nodes of the hidden Markov model to the reference annotation. @@ -1089,5 +1083,17 @@ public class HiddenMarkovModel } } + + public AlignmentI initPlaceholder(AlignmentI alignment) + { + int length = alignment.getWidth(); + Sequence consensus = getConsensusSequence(length); + consensus.setHMM(this); + SequenceI[] consensusArr = new Sequence[] { consensus }; + AlignmentI newAlignment = new Alignment(consensusArr); + newAlignment.append(alignment); + return newAlignment; + } + } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 0c951fa..8ac7c8a 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -63,6 +63,7 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.hmmer.HMMERCommands; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; @@ -125,6 +126,7 @@ import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; +import java.io.IOException; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; @@ -1033,6 +1035,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void hmmBuild_actionPerformed(ActionEvent e) + throws IOException, InterruptedException + { + + HMMERCommands.hmmBuild(this); + alignPanel.repaint(); + } + + @Override + public void hmmAlign_actionPerformed(ActionEvent e) + { + + alignPanel.repaint(); + } + + @Override + public void hmmSearch_actionPerformed(ActionEvent e) + { + + alignPanel.repaint(); + } + + @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) @@ -4703,13 +4728,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentAnnotation annotation = hmm.createAnnotation( getViewport().getAlignment().getWidth()); getViewport().getAlignment().addAnnotation(annotation); - int length = getViewport().getAlignment().getWidth(); - Sequence consensus = hmm.getConsensusSequence(length); - consensus.setHMM(hmm); - annotation.setHMM(hmm); - SequenceI[] consensusArr = new Sequence[] { consensus }; - AlignmentI newAlignment = new Alignment(consensusArr); - newAlignment.append(getViewport().getAlignment()); + AlignmentI newAlignment = hmm + .initPlaceholder(getViewport().getAlignment()); getViewport().setAlignment(newAlignment); isAnnotation = true; alignPanel.repaint(); diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java new file mode 100644 index 0000000..ac96c2a --- /dev/null +++ b/src/jalview/hmmer/HMMERCommands.java @@ -0,0 +1,91 @@ +package jalview.hmmer; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenMarkovModel; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.StockholmFile; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.PrintWriter; +import java.util.List; + +public class HMMERCommands +{ + // Path of hmmer binaries directory + private static final String HMMERFOLDER = "H:/Documents/"; + + private static final String HMMALIGN = HMMERFOLDER + "hmmalign"; + + private static final String HMMBUILD = HMMERFOLDER + "hmmbuild"; + + private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch"; + + private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/"; + + private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm"; + + private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto"; + + private static final String OUTPUTALIGNMENT = "-o " + ALIGNMENTBUFFER; + + private static final String SPACE = " "; + + public static void hmmBuild(AlignFrame af) + throws IOException, InterruptedException + { + HiddenMarkovModel hmm = null; + AlignmentI alignment = af.getViewport().getAlignment(); + List list = alignment.getSequences(); + SequenceI[] array = new SequenceI[list.size()]; + list.toArray(array); + StockholmFile file = new StockholmFile(alignment); + file.setSeqs(array); + String output = file.print(); + PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER); + writer.println(output); + writer.close(); + final String command = HMMBUILD + SPACE + JALVIEWDIRECTORY + HMMBUFFER + + SPACE + + JALVIEWDIRECTORY + ALIGNMENTBUFFER; + + runCommand(command); + + af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE, + FileFormat.HMMER3, null); + } + + private static void runCommand(String command) + throws IOException, InterruptedException + { + final Process p = Runtime.getRuntime().exec(command); + + new Thread(new Runnable() + { + @Override + public void run() + { + BufferedReader input = new BufferedReader( + new InputStreamReader(p.getInputStream())); + String line = null; + + try + { + while ((line = input.readLine()) != null) + { + System.out.println(line); + } + } catch (IOException e) + { + e.printStackTrace(); + } + } + }).start(); + + p.waitFor(); + } +} diff --git a/src/jalview/hmmer/alignment_buffer.sto b/src/jalview/hmmer/alignment_buffer.sto new file mode 100644 index 0000000..d0ad541 --- /dev/null +++ b/src/jalview/hmmer/alignment_buffer.sto @@ -0,0 +1,19 @@ +# STOCKHOLM 1.0 +FER_CAPAA -----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER_CAPAN MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG- +FER1_SOLLC MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA- +Q93XJ9_SOLTU MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA- +FER1_PEA MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA- +Q7XA98_TRIPR MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA- +FER1_MESCR MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA- +FER1_SPIOL MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA- +FER3_RAPSA -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV-- +FER2_ARATH MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV-- +FER_BRANA -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV-- +FER1_ARATH MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM-- +Q93Z60_ARATH MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------------------- +FER1_MAIZE MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA +O80429_MAIZE MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL-- +// + + diff --git a/src/jalview/hmmer/hmm_buffer.hmm b/src/jalview/hmmer/hmm_buffer.hmm new file mode 100644 index 0000000..9e3cb11 --- /dev/null +++ b/src/jalview/hmmer/hmm_buffer.hmm @@ -0,0 +1,464 @@ +HMMER3/b [3.0 | March 2010] +NAME alignment_buffer +LENG 148 +ALPH amino +RF no +CS no +MAP yes +DATE Thu Jul 27 17:11:32 2017 +NSEQ 15 +EFFN 0.648193 +CKSUM 2563184735 +STATS LOCAL MSV -10.0682 0.70956 +STATS LOCAL VITERBI -10.7870 0.70956 +STATS LOCAL FORWARD -4.6837 0.70956 +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 2.40816 3.71583 2.80837 2.63551 3.47092 2.77036 3.85028 2.88279 2.80267 2.53589 3.68425 3.22102 3.34428 3.14560 3.11474 2.53177 2.75990 2.58070 5.00144 3.51101 + 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 + 0.10433 3.97705 2.52157 0.61958 0.77255 0.00000 * + 1 2.99317 4.53706 4.08224 3.67789 3.22093 3.85692 4.40592 2.39958 3.44433 1.81088 1.32037 3.95163 4.31759 3.82413 3.64608 3.34553 3.29902 2.40928 5.06591 3.83044 1 - - + 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 + 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282 + 2 0.97044 4.20710 3.49350 3.28598 4.08269 3.03087 4.30444 3.21278 3.30302 3.09300 4.12129 3.42792 3.77296 3.64134 3.55157 2.55705 2.83652 2.86187 5.50678 4.31039 2 - - + 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 + 0.11955 3.90315 2.38048 0.61958 0.77255 0.55549 0.85282 + 3 1.74035 4.09199 3.34495 3.00819 4.05288 2.91638 4.05509 3.33461 3.01251 3.11462 3.97728 3.20348 3.62940 3.32849 3.32799 1.99191 1.99086 2.89563 5.42641 4.20726 3 - - + 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 + 0.03323 3.81683 4.53917 0.61958 0.77255 0.62561 0.76558 + 4 2.37663 4.18625 3.55838 3.17855 3.75132 3.18264 4.13666 2.64341 3.07328 2.62344 3.69712 3.39774 3.83139 3.44405 3.35689 2.61052 1.64486 2.15973 5.30034 4.05468 4 - - + 2.68617 4.42230 2.77525 2.73129 3.46359 2.40511 3.72500 3.29359 2.67746 2.69350 4.24695 2.90352 2.73719 3.18152 2.89806 2.37885 2.77501 2.98524 4.58482 3.61508 + 0.33937 1.47682 2.82312 0.71438 0.67236 0.50642 0.92294 + 5 1.78828 4.31568 3.18846 2.75366 3.97645 3.11838 3.84000 3.34055 2.67250 3.02453 3.87541 3.10729 3.71676 3.06391 2.67828 2.15246 2.50645 2.96422 5.30410 4.05011 9 - - + 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 + 0.03188 3.85742 4.57976 0.61958 0.77255 0.59400 0.80322 + 6 2.60146 4.34120 4.20318 3.64233 3.23200 4.03946 4.38229 1.91078 3.53317 1.46276 2.80385 3.95250 4.35454 3.78680 3.77614 3.34686 3.12310 1.90138 5.05979 3.90282 10 - - + 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 + 0.03188 3.85742 4.57976 0.61958 0.77255 0.59400 0.80322 + 7 2.51618 4.38929 3.20785 2.68482 3.53842 3.39630 3.71025 2.97988 2.63127 2.66315 3.23915 3.11866 3.35060 2.98059 3.01133 2.11689 2.77574 2.72369 4.95633 3.10650 11 - - + 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 + 0.03188 3.85742 4.57976 0.61958 0.77255 0.59400 0.80322 + 8 1.83112 4.12334 3.20156 2.95461 4.23963 1.79514 4.09699 3.64646 3.07597 3.33878 4.16582 3.16397 3.61350 3.35846 3.40724 1.96001 2.64648 3.10558 5.57497 4.34818 12 - - + 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 + 0.07518 3.85742 2.97012 0.61958 0.77255 0.59400 0.80322 + 9 2.02467 4.19921 3.47207 3.00878 3.03795 3.27081 3.95597 2.70270 2.96218 2.55248 3.54468 3.31239 3.83177 3.27950 3.28895 2.63385 2.09090 2.46488 5.06606 3.80489 13 - - + 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 + 0.03327 3.81551 4.53786 0.61958 0.77255 0.56041 0.84624 + 10 2.25155 4.19461 3.85704 3.29295 2.92371 3.72128 4.04839 2.07964 3.20853 2.08962 2.71310 3.60847 4.09120 3.47607 3.47945 3.00735 2.74040 2.14097 4.86082 3.65928 14 - - + 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 + 0.03170 3.86316 4.58551 0.61958 0.77255 0.53107 0.88667 + 11 2.97746 4.34766 4.53309 3.96552 2.78843 4.21079 4.53997 1.80103 3.85948 1.59494 2.57669 4.20401 4.48099 4.02954 4.02513 3.53069 3.20806 1.63119 5.03312 3.89134 15 - - + 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 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0.61958 0.77255 0.50828 0.92013 + 144 2.49167 5.21869 2.13891 1.38935 4.54510 3.23855 3.71342 3.98470 2.64038 3.55288 4.39217 2.73628 3.81159 2.87379 3.17028 2.74234 3.08340 3.59770 5.74876 4.31122 152 - - + 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 + 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013 + 145 2.67924 5.36825 1.81597 1.42545 4.67130 3.22067 3.71949 4.14895 2.68617 3.67868 4.51726 2.69278 3.81366 2.87890 3.25116 2.76699 3.13943 3.73938 5.85528 4.37934 153 - - + 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 + 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013 + 146 3.24708 4.60677 4.69416 4.13988 3.08947 4.47063 4.76500 1.92492 3.96672 0.95356 2.71915 4.43331 4.67883 4.15873 4.13317 3.81764 3.47493 2.15974 5.15578 4.04247 154 - - + 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 + 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013 + 147 2.69781 4.29649 3.84369 3.29786 3.44437 3.73086 4.15124 2.24231 3.19336 2.10104 3.11890 3.63278 4.14347 3.51043 3.49251 3.03876 2.03846 1.78833 5.07714 3.86271 155 - - + 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 + 0.18495 3.95434 1.89921 0.61958 0.77255 0.50828 0.92013 + 148 1.44115 4.10304 3.22225 2.99375 4.15355 2.08176 4.10711 3.47540 3.09081 3.24183 4.11431 3.18864 3.61518 3.39097 3.39593 2.35434 2.65737 2.99565 5.50492 4.29375 156 - - + 2.68608 4.42226 2.77520 2.73124 3.46354 2.40513 3.72495 3.29355 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37887 2.77520 2.98519 4.58477 3.61504 + 0.08120 2.55114 * 0.46726 0.98542 0.00000 * +// diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java index 95e2017..18d9e78 100644 --- a/src/jalview/io/HMMFile.java +++ b/src/jalview/io/HMMFile.java @@ -188,23 +188,23 @@ public class HMMFile extends AlignFile */ void parseModel(BufferedReader input) throws IOException { - for (int i = 0; i < hmm.getLength() + 1; i++) + String line = input.readLine(); + int node = 0; + while (!"//".equals(line)) { hmm.getNodes().add(new HMMNode()); String next; - String line; - line = input.readLine(); Scanner matchReader = new Scanner(line); next = matchReader.next(); - if (next.equals(COMPO) || i > 0) + if (next.equals(COMPO) || node > 0) { // stores match emission line in list List matches = new ArrayList<>(); matches = fillList(matchReader, numberOfSymbols); - hmm.getNodes().get(i).setMatchEmissions(matches); - if (i > 0) + hmm.getNodes().get(node).setMatchEmissions(matches); + if (node > 0) { - parseAnnotations(matchReader, i); + parseAnnotations(matchReader, node); } } matchReader.close(); @@ -213,7 +213,7 @@ public class HMMFile extends AlignFile Scanner insertReader = new Scanner(line); List inserts = new ArrayList<>(); inserts = fillList(insertReader, numberOfSymbols); - hmm.getNodes().get(i).setInsertEmissions(inserts); + hmm.getNodes().get(node).setInsertEmissions(inserts); insertReader.close(); // stores state transition line in list @@ -221,8 +221,10 @@ public class HMMFile extends AlignFile Scanner transitionReader = new Scanner(line); List transitions = new ArrayList<>(); transitions = fillList(transitionReader, NUMBER_OF_TRANSITIONS); - hmm.getNodes().get(i).setStateTransitions(transitions); + hmm.getNodes().get(node).setStateTransitions(transitions); transitionReader.close(); + line = input.readLine(); + node++; } } diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index c2f3683..dbb33f3 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -195,7 +195,7 @@ public class StockholmFile extends AlignFile String version; // String id; Hashtable seqAnn = new Hashtable(); // Sequence related annotations - LinkedHashMap seqs = new LinkedHashMap(); + LinkedHashMap seqs = new LinkedHashMap<>(); Regex p, r, rend, s, x; // Temporary line for processing RNA annotation // String RNAannot = ""; @@ -657,7 +657,7 @@ public class StockholmFile extends AlignFile strucAnn = new Hashtable(); } - Vector newStruc = new Vector(); + Vector newStruc = new Vector<>(); parseAnnotationRow(newStruc, type, ns); for (AlignmentAnnotation alan : newStruc) { @@ -709,7 +709,7 @@ public class StockholmFile extends AlignFile private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource) { DBRefEntry dbrf = null; - List dbrs = new ArrayList(); + List dbrs = new ArrayList<>(); String seqdb = "Unknown", sdbac = "" + dbr; int st = -1, en = -1, p; if ((st = sdbac.indexOf("/")) > -1) @@ -1151,7 +1151,6 @@ public class StockholmFile extends AlignFile out.append(newline); print(getSeqsAsArray(), false); - out.append("//"); out.append(newline); return out.toString(); } diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index ea56bbb..3f55752 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -40,6 +40,7 @@ import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.io.IOException; import java.util.HashMap; import java.util.Map; @@ -1690,6 +1691,28 @@ public class GAlignFrame extends JInternalFrame selectHighlightedColumns_actionPerformed(actionEvent); } }; + hmmBuild.setText(MessageManager.getString("label.hmmbuild")); + hmmBuild.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + try + { + hmmBuild_actionPerformed(e); + } catch (IOException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + } + + }); selectHighlighted.addActionListener(al); JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); @@ -2381,6 +2404,7 @@ public class GAlignFrame extends JInternalFrame } protected void hmmBuild_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { } -- 1.7.10.2