From 29cd3c8168e0b16d14d58b9dedfe738ebb6070ac Mon Sep 17 00:00:00 2001 From: TZVanaalten Date: Mon, 7 Aug 2017 16:22:23 +0100 Subject: [PATCH] JAL-2629 current hmmer commands are now executed in threads --- resources/lang/Messages.properties | 3 + src/jalview/bin/Jalview.java | 19 +- src/jalview/gui/AlignFrame.java | 25 +-- src/jalview/hmmer/HMMAlignThread.java | 128 +++++++++++ src/jalview/hmmer/HMMBuildThread.java | 112 ++++++++++ src/jalview/hmmer/HMMERCommands.java | 170 ++++---------- src/jalview/hmmer/alignment_input.sto | 139 +++++++++++- src/jalview/hmmer/hmm_buffer.hmm | 304 +++++++++++++------------- src/jalview/io/FileFormat.java | 2 +- src/jalview/io/HMMFile.java | 7 +- src/jalview/viewmodel/AlignmentViewport.java | 99 ++++----- 11 files changed, 636 insertions(+), 372 deletions(-) create mode 100644 src/jalview/hmmer/HMMAlignThread.java create mode 100644 src/jalview/hmmer/HMMBuildThread.java diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index ce9cb62..5291493 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1144,6 +1144,9 @@ status.loading_cached_pdb_entries = Loading Cached PDB Entries status.searching_for_pdb_structures = Searching for PDB Structures status.opening_file_for = opening file for status.colouring_chimera = Colouring Chimera +status.running_hmmbuild = "Building hidden Markov model" +status.running_hmmalign = "Creating alignment with hidden Markov model" +status.running_hmmsearch = "Searching for matching sequences" label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data label.font_too_small = Font size is too small label.error_loading_file_params = Error loading file {0} diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 954bb34..76f9958 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,9 +20,6 @@ */ package jalview.bin; -import groovy.lang.Binding; -import groovy.util.GroovyScriptEngine; - import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; @@ -66,6 +63,9 @@ import java.util.Vector; import javax.swing.UIManager; +import groovy.lang.Binding; +import groovy.util.GroovyScriptEngine; + /** * Main class for Jalview Application
*
@@ -175,8 +175,11 @@ public class Jalview * * @param args * open filename + * @throws InterruptedException + * @throws IOException */ public static void main(String[] args) + throws IOException, InterruptedException { instance = new Jalview(); instance.doMain(args); @@ -184,8 +187,10 @@ public class Jalview /** * @param args + * @throws InterruptedException + * @throws IOException */ - void doMain(String[] args) + void doMain(String[] args) throws IOException, InterruptedException { System.setSecurityManager(null); System.out.println("Java version: " @@ -968,7 +973,7 @@ public class Jalview } try { - Map vbinding = new HashMap(); + Map vbinding = new HashMap<>(); vbinding.put("Jalview", this); if (af != null) { @@ -1035,7 +1040,7 @@ public class Jalview + nickname + "|" + url); if (source == null) { - source = new Vector(); + source = new Vector<>(); } source.addElement(nickname); } @@ -1053,7 +1058,7 @@ public class Jalview System.out.println("adding source '" + data + "'"); if (source == null) { - source = new Vector(); + source = new Vector<>(); } source.addElement(data); } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 05b1e33..dba6717 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -63,7 +63,8 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.hmmer.HMMERCommands; +import jalview.hmmer.HMMAlignThread; +import jalview.hmmer.HMMBuildThread; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; @@ -92,7 +93,6 @@ import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; -import jalview.workers.InformationThread; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -1044,8 +1044,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hmmBuild_actionPerformed(ActionEvent e) throws IOException, InterruptedException { - - HMMERCommands.hmmBuild(this); + new Thread(new HMMBuildThread(this)).start(); alignPanel.repaint(); } @@ -1056,7 +1055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { SequenceI seq = getViewport().getAlignment() .getHMMConsensusSequences(false).get(0); - HMMERCommands.hmmAlign(this, true, seq.getHMM()); + new Thread(new HMMAlignThread(this, true)).start(); alignPanel.repaint(); } @@ -4727,20 +4726,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else if (FileFormat.HMMER3.equals(format)) { - HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO - // need - // to - // follow - // standard - // pipeline - hmmFile.parse(); + HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); HiddenMarkovModel hmm = hmmFile.getHMM(); SequenceI hmmSeq = hmm.initHMMSequence(this, 0); getViewport().initInformation(hmmSeq); - new Thread(new InformationThread(getViewport(), - getViewport().getAlignPanel()) - { - }).start(); + getViewport().updateInformation(alignPanel); isAnnotation = true; @@ -4803,7 +4793,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, recurring = true; HiddenMarkovModel hmm = getViewport().getAlignment() .getHMMConsensusSequences(false).get(0).getHMM(); - HMMERCommands.hmmAlign(this, false, hmm); + new Thread(new HMMAlignThread(this, false)).start(); } recurring = false; } @@ -5761,4 +5751,5 @@ class PrintThread extends Thread } } } + } diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java new file mode 100644 index 0000000..8cd4270 --- /dev/null +++ b/src/jalview/hmmer/HMMAlignThread.java @@ -0,0 +1,128 @@ +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.FileLoader; +import jalview.util.MessageManager; + +import java.io.FileNotFoundException; +import java.io.IOException; +import java.util.Map; + +public class HMMAlignThread implements Runnable +{ + + AlignFrame af; + + AlignmentI alignment; + + HiddenMarkovModel hmm; + + boolean newFrame; + + long barID; + + Map hmmSeqs; + + public HMMAlignThread(AlignFrame af, boolean createNewFrame) + { + this.af = af; + alignment = af.getViewport().getAlignment(); + hmm = alignment.getSequenceAt(0).getHMM(); + newFrame = createNewFrame; + } + + @Override + public void run() + { + barID = System.currentTimeMillis(); + af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), + barID); + + try + { + try + { + hmmSeqs = alignment.getHMMConsensusSequences(true); + HMMERCommands.exportData(alignment, true, true, hmm); + } catch (FileNotFoundException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + + } + try + { + runCommand(); + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + try + { + importData(); + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } catch (Exception e) + { + + } finally + { + af.setProgressBar(MessageManager.getString("status.running_hmmalign"), + barID); + } + } + + private void runCommand() throws IOException, InterruptedException + { + String command = HMMERCommands.HMMALIGN; + if (!hmm.getFileHeader().contains("HMMER3/f")) + { + command += HMMERCommands.ALLCOL; + } + command += HMMERCommands.TRIM + HMMERCommands.OUTPUTALIGNMENT + + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER + + HMMERCommands.JALVIEWDIRECTORY + + HMMERCommands.ALIGNMENTBUFFER; + HMMERCommands.runCommand(command); + } + + private void importData() throws IOException, InterruptedException + { + if (newFrame) + { + FileLoader loader = new FileLoader(); + AlignFrame newAFrame = loader.LoadFileWaitTillLoaded( + HMMERCommands.ALIGNMENTINPUT, DataSourceType.FILE); + addSeqs(newAFrame); + } + else + { + af.getViewport().getAlignment().getSequences().clear(); + af.loadJalviewDataFile(HMMERCommands.ALIGNMENTBUFFER, + DataSourceType.FILE, FileFormat.Stockholm, null); + addSeqs(af); + } + } + + private void addSeqs(AlignFrame alignFrame) + { + for (Map.Entry entry : hmmSeqs.entrySet()) + { + SequenceI seq = entry.getValue(); + Integer pos = entry.getKey(); + HMMERCommands.addHMMConsensusSequence(alignFrame, seq, pos); + } + } + + } + + diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java new file mode 100644 index 0000000..868404b --- /dev/null +++ b/src/jalview/hmmer/HMMBuildThread.java @@ -0,0 +1,112 @@ +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.util.MessageManager; + +import java.io.FileNotFoundException; +import java.io.IOException; +import java.util.Map; + +public class HMMBuildThread implements Runnable +{ + + AlignFrame af; + AlignmentI alignment; + + long barID; + + Map hmmSeqs; + + public HMMBuildThread(AlignFrame af) + { + this.af = af; + alignment = af.getViewport().getAlignment(); + } + + @Override + public void run() + { + barID = System.currentTimeMillis(); + af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), + barID); + + try + { + try + { + exportAlignment(); + } catch (FileNotFoundException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + + } + try + { + runCommand(); + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + try + { + importData(); + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } catch (Exception e) + { + + } finally + { + af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), + barID); + } + } + + + private void exportAlignment() throws IOException + { + hmmSeqs = alignment.getHMMConsensusSequences(true); + if (!alignment.isAligned()) + { + alignment.padGaps(); + } + HMMERCommands.exportData(alignment, true, false, + new HiddenMarkovModel()); + } + + private void runCommand() throws IOException, InterruptedException + { + final String command = HMMERCommands.HMMBUILD + HMMERCommands.NAME + + af.getName() + HMMERCommands.SPACE + + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER + + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER; + HMMERCommands.runCommand(command); + } + + private void importData() throws IOException, InterruptedException + { + af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE, + FileFormat.HMMER3, null); + for (Map.Entry entry : hmmSeqs.entrySet()) + { + SequenceI seq = entry.getValue(); + Integer pos = entry.getKey(); + HMMERCommands.addHMMConsensusSequence(af, seq, pos); + } + af.alignPanel.alignmentChanged(); + } + + + + +} diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java index c8d26e4..5a84989 100644 --- a/src/jalview/hmmer/HMMERCommands.java +++ b/src/jalview/hmmer/HMMERCommands.java @@ -5,149 +5,44 @@ 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.FileLoader; import jalview.io.HMMFile; import jalview.io.StockholmFile; -import jalview.util.MessageManager; import java.io.BufferedReader; -import java.io.FileNotFoundException; import java.io.IOException; import java.io.InputStreamReader; import java.io.PrintWriter; import java.util.List; -import java.util.Map; - -import javax.swing.JOptionPane; public class HMMERCommands { // Path of hmmer binaries directory - private static final String HMMERFOLDER = "H:/Documents/"; + static final String HMMERFOLDER = "H:/Documents/"; - private static final String HMMALIGN = HMMERFOLDER + "hmmalign "; + static final String HMMALIGN = HMMERFOLDER + "hmmalign "; - private static final String HMMBUILD = HMMERFOLDER + "hmmbuild "; + static final String HMMBUILD = HMMERFOLDER + "hmmbuild "; - private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch "; + static final String HMMSEARCH = HMMERFOLDER + "hmmsearch "; - private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/"; + static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/"; - private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm "; + static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm "; - private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto "; + static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto "; - private static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto "; + static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto "; - private static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY + static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY + ALIGNMENTINPUT; - private static final String NAME = "-n "; - - private static final String SPACE = " "; - - private static final String ALLCOL = "--allcol "; + static final String NAME = "-n "; - private static final String TRIM = "--trim "; - - public static void hmmBuild(AlignFrame af) - throws IOException, InterruptedException - { + static final String SPACE = " "; - PrintWriter clearer = new PrintWriter(HMMBUFFER); - clearer.print(""); - clearer.close(); - AlignmentI alignment = af.getViewport().getAlignment(); - if (!alignment.isAligned()) - { - alignment.padGaps(); - } - Map seqs = alignment.getHMMConsensusSequences(true); - exportAlignment(alignment); - final String command = HMMBUILD + NAME + af.getName() + SPACE - + JALVIEWDIRECTORY + HMMBUFFER - + JALVIEWDIRECTORY + ALIGNMENTBUFFER; + static final String ALLCOL = "--allcol "; - runCommand(command); - - af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE, - FileFormat.HMMER3, null); - for (Map.Entry entry : seqs.entrySet()) - { - SequenceI seq = entry.getValue(); - Integer pos = entry.getKey(); - addHMMConsensusSequence(af, seq, pos); - } - af.alignPanel.alignmentChanged(); - } - - public static void hmmAlign(AlignFrame af, boolean createNewFrame, - HiddenMarkovModel hmm) - throws IOException, InterruptedException - { - - PrintWriter clearer = new PrintWriter(ALIGNMENTINPUT); - clearer.print(""); - clearer.close(); - AlignmentI al = af.getViewport().getAlignment(); - if (!al.isAligned()) - { - al.padGaps(); - } - Map seqs = al.getHMMConsensusSequences(true); - int index = 0; - if (hmm == null) - { - JOptionPane.showMessageDialog(af, - MessageManager.getString("warn.null_hmm")); - return; - } - exportAlignment(al); - - HMMFile file = new HMMFile(hmm); - file.exportFile(HMMBUFFER); - - String command = HMMALIGN; - if (!hmm.getFileHeader().contains("HMMER3/f")) - { - command += ALLCOL; - } - command += TRIM + OUTPUTALIGNMENT + JALVIEWDIRECTORY + HMMBUFFER - + JALVIEWDIRECTORY + ALIGNMENTBUFFER; - - runCommand(command); - - if (createNewFrame) - { - FileLoader loader = new FileLoader(); - AlignFrame newFrame = loader.LoadFileWaitTillLoaded(ALIGNMENTINPUT, - DataSourceType.FILE); - for (Map.Entry entry : seqs.entrySet()) - { - SequenceI seq = entry.getValue(); - Integer pos = entry.getKey(); - addHMMConsensusSequence(newFrame, seq, pos); - } - newFrame.alignPanel.alignmentChanged(); - } - else - { - af.getViewport().getAlignment().getSequences().clear(); - af.loadJalviewDataFile(ALIGNMENTBUFFER, DataSourceType.FILE, - FileFormat.Stockholm, null); - for (Map.Entry entry : seqs.entrySet()) - { - SequenceI seq = entry.getValue(); - Integer pos = entry.getKey(); - addHMMConsensusSequence(af, seq, pos); - } - - } - - - } + static final String TRIM = "--trim "; /** @@ -157,7 +52,7 @@ public class HMMERCommands * @throws IOException * @throws InterruptedException */ - private static void runCommand(String command) + public static void runCommand(String command) throws IOException, InterruptedException { final Process p = Runtime.getRuntime().exec(command); @@ -191,24 +86,33 @@ public class HMMERCommands * Exports an alignment to the buffer location in Jalview. * * @param alignment - * @throws FileNotFoundException + * @throws IOException */ - private static void exportAlignment(AlignmentI alignment) - throws FileNotFoundException + public static void exportData(AlignmentI alignment, + boolean exportAlignment, boolean exportHMM, HiddenMarkovModel hmm) + throws IOException { - List list = alignment.getSequences(); - SequenceI[] array = new SequenceI[list.size()]; - list.toArray(array); - - StockholmFile file = new StockholmFile(new Alignment(array)); - file.setSeqs(array); - String output = file.print(); - PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER); - writer.println(output); - writer.close(); + if (exportAlignment) + { + List list = alignment.getSequences(); + SequenceI[] array = new SequenceI[list.size()]; + list.toArray(array); + StockholmFile file = new StockholmFile(new Alignment(array)); + file.setSeqs(array); + String output = file.print(); + PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER); + writer.println(output); + writer.close(); + } + + if (exportHMM) + { + HMMFile file = new HMMFile(hmm); + file.exportFile(HMMBUFFER); + } } - private static void addHMMConsensusSequence(AlignFrame af, SequenceI seq, + public static void addHMMConsensusSequence(AlignFrame af, SequenceI seq, Integer position) { seq.getHMM().initHMMSequence(af, position); diff --git a/src/jalview/hmmer/alignment_input.sto b/src/jalview/hmmer/alignment_input.sto index ccfac69..0c2d626 100644 --- a/src/jalview/hmmer/alignment_input.sto +++ b/src/jalview/hmmer/alignment_input.sto @@ -1,11 +1,134 @@ # STOCKHOLM 1.0 -seq1 TwWWGILK -#=GR seq1 PP 88*****9 -seq2 T.WW-IIK -#=GR seq2 PP 9.**.**9 -seq3 -.WWGLLK -#=GR seq3 PP ..*****9 -#=GC PP_cons 9.*****9 -#=GC RF x.xxxxxx +FER_CAPAA ----..---------------------.--------..-------.---- +#=GR FER_CAPAA PP .................................................. +FER_CAPAN -A--..SVSATMISTSFMPRKPAVTSL.KPIPNVGE..ALFGLKS.A--N +#=GR FER_CAPAN PP .4....689******************.********..*******.9..8 +FER1_SOLLC -A--..SISGTMISTSFLPRKPAVTSL.KAISNVGE..ALFGLKS.G--R +#=GR FER1_SOLLC PP .4....789******************.********..*******.*..9 +Q93XJ9_SOLTU -A--..SISGTMISTSFLPRKPVVTSL.KAISNVGE..ALFGLKS.G--R +#=GR Q93XJ9_SOLTU PP .4....789******************.********..*******.*..9 +FER1_PEA MATT.pALYGTAVSTSFLRTQPMPMSV.TTTKAFSN..GFLGLKT.SLKR +#=GR FER1_PEA PP 8999.9*********************.********..*******.**** +Q7XA98_TRIPR MATT.pALYGTAVSTSFMRRQPVPMSV.ATTTTTKAfpSGFGLKSvSTKR +#=GR Q7XA98_TRIPR PP 8999.9*********************.887777765699****97899* +FER1_MESCR MAATtaALSGATMSTAFAPKTP-PMTA.ALPTNVGR..ALFGLKS.SASR +#=GR FER1_MESCR PP 56655799***********755.6666.89******..*******.*987 +FER1_SPIOL MAAT..TTTMMGMATTFVPKPQAPPMMaALPSNTGR..SLFGLKT.GSR- +#=GR FER1_SPIOL PP 8888..8888889**********999978999****..*******.954. +FER3_RAPSA ----..---------------------.--------..-------.---- +#=GR FER3_RAPSA PP .................................................. +FER2_ARATH MAST..ALSSAIVGTSFIRRSPAPISLrSLPSANTQ..SLFGLKS.GTAR +#=GR FER2_ARATH PP 9***..*********************9999*****..*******.**** +FER_BRANA ----..---------------------.--------..-------.---- +#=GR FER_BRANA PP .................................................. +FER1_ARATH MAST..ALSSAIVSTSFLRRQQTPISLrSLPFANTQ..SLFGLKS.STAR +#=GR FER1_ARATH PP 9***..*********************999******..*******.**** +Q93Z60_ARATH MAST..ALSSAIVSTSFLRRQQTPISLrSLPFANTQ..SLFGLKS.STAR +#=GR Q93Z60_ARATH PP 9***..*********************999******..*******.**** +FER1_MAIZE ----..RAPAFFFSSSSLRAAPAPTAV.A-LPAAKV..GIMGRSA.SSRR +#=GR FER1_MAIZE PP ......567899***************.5.567899..*******.*988 +O80429_MAIZE ----..--AATALSMSILRA--PPPCF.SSPLRLRV..AVAKPLA.APMR +#=GR O80429_MAIZE PP ........57899*****95..34555.89******..*******.**** +#=GC PP_cons 8799..8999*********9*999999.999999**..*******.*999 +#=GC RF xxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx..xxxxxxx.xxxx + +FER_CAPAA -------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGS +#=GR FER_CAPAA PP .......89***************************************** +FER_CAPAN GGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGS +#=GR FER_CAPAN PP 9************************************************* +FER1_SOLLC NGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGS +#=GR FER1_SOLLC PP 9************************************************* +Q93XJ9_SOLTU NGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGS +#=GR Q93XJ9_SOLTU PP 9************************************************* +FER1_PEA GDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGS +#=GR FER1_PEA PP ************************************************** +Q7XA98_TRIPR GDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGS +#=GR Q7XA98_TRIPR PP ************************************************** +FER1_MESCR -GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGS +#=GR FER1_MESCR PP .9************************************************ +FER1_SPIOL -GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGS +#=GR FER1_SPIOL PP .55678******************************************** +FER3_RAPSA -------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGS +#=GR FER3_RAPSA PP .......8****************************************** +FER2_ARATH GGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGS +#=GR FER2_ARATH PP ************************************************** +FER_BRANA -------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGS +#=GR FER_BRANA PP .......8****************************************** +FER1_ARATH GGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGS +#=GR FER1_ARATH PP ************************************************** +Q93Z60_ARATH GGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGS +#=GR Q93Z60_ARATH PP ************************************************** +FER1_MAIZE --RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGS +#=GR FER1_MAIZE PP ..9*********************************************** +O80429_MAIZE RQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGS +#=GR O80429_MAIZE PP ************************************************** +#=GC PP_cons *99*********************************************** +#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + +FER_CAPAA CSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEA +#=GR FER_CAPAA PP ************************************************** +FER_CAPAN CSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEA +#=GR FER_CAPAN PP ************************************************** +FER1_SOLLC CSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEE +#=GR FER1_SOLLC PP ************************************************** +Q93XJ9_SOLTU CSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEE +#=GR Q93XJ9_SOLTU PP ************************************************** +FER1_PEA CSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEE +#=GR FER1_PEA PP ************************************************** +Q7XA98_TRIPR CSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEE +#=GR Q7XA98_TRIPR PP ************************************************** +FER1_MESCR CSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEE +#=GR FER1_MESCR PP ************************************************** +FER1_SPIOL CSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEE +#=GR FER1_SPIOL PP ************************************************** +FER3_RAPSA CSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREE +#=GR FER3_RAPSA PP ************************************************** +FER2_ARATH CSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEE +#=GR FER2_ARATH PP ************************************************** +FER_BRANA CSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEE +#=GR FER_BRANA PP ************************************************** +FER1_ARATH CSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEE +#=GR FER1_ARATH PP ************************************************** +Q93Z60_ARATH CSSCAGKVVSGSIDQSDQSFLDD--------------------------- +#=GR Q93Z60_ARATH PP **********************8........................... +FER1_MAIZE CSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEE +#=GR FER1_MAIZE PP ************************************************** +O80429_MAIZE CSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKED +#=GR O80429_MAIZE PP ************************************************** +#=GC PP_cons ************************************************** +#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + +FER_CAPAA ELV- +#=GR FER_CAPAA PP *98. +FER_CAPAN ELV- +#=GR FER_CAPAN PP *98. +FER1_SOLLC ELTA +#=GR FER1_SOLLC PP **96 +Q93XJ9_SOLTU ELTA +#=GR Q93XJ9_SOLTU PP **96 +FER1_PEA DLTA +#=GR FER1_PEA PP **96 +Q7XA98_TRIPR ELTA +#=GR Q7XA98_TRIPR PP **96 +FER1_MESCR ELTA +#=GR FER1_MESCR PP **96 +FER1_SPIOL ELTA +#=GR FER1_SPIOL PP **96 +FER3_RAPSA DMV- +#=GR FER3_RAPSA PP *96. +FER2_ARATH DIV- +#=GR FER2_ARATH PP *96. +FER_BRANA ELV- +#=GR FER_BRANA PP *97. +FER1_ARATH AI-- +#=GR FER1_ARATH PP 87.. +Q93Z60_ARATH ---- +#=GR Q93Z60_ARATH PP .... +FER1_MAIZE ELT- +#=GR FER1_MAIZE PP **8. +O80429_MAIZE DLL- +#=GR O80429_MAIZE PP *95. +#=GC PP_cons *986 +#=GC RF xxxx // diff --git a/src/jalview/hmmer/hmm_buffer.hmm b/src/jalview/hmmer/hmm_buffer.hmm index a4007e7..397e822 100644 --- a/src/jalview/hmmer/hmm_buffer.hmm +++ b/src/jalview/hmmer/hmm_buffer.hmm @@ -3,462 +3,464 @@ NAME null LENG 148 ALPH amino RF no +MM no +CONS no CS no MAP yes -DATE Fri Aug 4 12:03:17 2017 +DATE Mon Aug 7 16:18:25 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 +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 - - + 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 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 - - + 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 - - + 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 - - + 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 - - + 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 - - + 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 - - + 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 - - + 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 - - + 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 - - + 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 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 - 12 2.01604 4.15364 3.23013 2.99255 4.26101 2.66741 4.12859 3.66796 3.09383 3.37186 4.20680 3.19709 3.64453 3.39377 3.41395 1.27425 2.68165 3.13093 5.59931 4.36607 16 - - + 12 2.01604 4.15364 3.23013 2.99255 4.26101 2.66741 4.12859 3.66796 3.09383 3.37186 4.20680 3.19709 3.64453 3.39377 3.41395 1.27425 2.68165 3.13093 5.59931 4.36607 16 - - 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 - 13 2.41396 4.26265 3.40226 2.93569 3.72492 3.24366 3.92462 2.93397 2.83929 2.73560 3.16052 3.25846 3.81309 3.20648 3.16819 2.37913 1.73294 2.65776 5.16309 3.91530 17 - - + 13 2.41396 4.26265 3.40226 2.93569 3.72492 3.24366 3.92462 2.93397 2.83929 2.73560 3.16052 3.25846 3.81309 3.20648 3.16819 2.37913 1.73294 2.65776 5.16309 3.91530 17 - - 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 - 14 2.06589 4.14828 3.30608 3.02868 4.20053 2.92394 4.12227 3.52677 3.06750 3.27902 4.13704 3.22373 3.65849 3.38850 3.37961 1.31011 2.40891 3.04032 5.55736 4.32788 18 - - + 14 2.06589 4.14828 3.30608 3.02868 4.20053 2.92394 4.12227 3.52677 3.06750 3.27902 4.13704 3.22373 3.65849 3.38850 3.37961 1.31011 2.40891 3.04032 5.55736 4.32788 18 - - 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 - 15 2.74009 4.29274 3.92243 3.42912 1.74599 3.72053 3.90473 2.32427 3.32349 2.18956 3.31553 3.65797 4.14118 3.57919 3.55745 2.71376 3.01017 2.38146 4.46330 2.97696 19 - - + 15 2.74009 4.29274 3.92243 3.42912 1.74599 3.72053 3.90473 2.32427 3.32349 2.18956 3.31553 3.65797 4.14118 3.57919 3.55745 2.71376 3.01017 2.38146 4.46330 2.97696 19 - - 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 - 16 2.76094 4.39380 4.31945 3.75589 3.18422 4.12530 4.45889 2.01307 3.63847 1.30728 2.59228 4.05575 4.41925 3.86957 3.85970 3.43754 3.19324 1.94550 5.06650 3.93230 20 - - + 16 2.76094 4.39380 4.31945 3.75589 3.18422 4.12530 4.45889 2.01307 3.63847 1.30728 2.59228 4.05575 4.41925 3.86957 3.85970 3.43754 3.19324 1.94550 5.06650 3.93230 20 - - 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 - 17 2.70295 4.73637 3.16526 2.68917 4.18427 3.37581 3.71759 3.61851 2.27125 3.18722 4.06871 3.11427 2.39752 2.89725 1.66361 2.77186 2.98335 3.28411 5.34221 4.10051 21 - - + 17 2.70295 4.73637 3.16526 2.68917 4.18427 3.37581 3.71759 3.61851 2.27125 3.18722 4.06871 3.11427 2.39752 2.89725 1.66361 2.77186 2.98335 3.28411 5.34221 4.10051 21 - - 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 0.07762 3.90315 2.90945 0.61958 0.77255 0.55549 0.85282 - 18 2.49055 4.81399 3.14505 2.59164 4.19520 3.44406 3.60132 3.55142 1.92611 3.12799 3.98038 3.04037 3.86298 2.75679 1.83484 2.76119 2.76042 3.23493 5.31169 4.06564 22 - - + 18 2.49055 4.81399 3.14505 2.59164 4.19520 3.44406 3.60132 3.55142 1.92611 3.12799 3.98038 3.04037 3.86298 2.75679 1.83484 2.76119 2.76042 3.23493 5.31169 4.06564 22 - - 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 0.06501 3.85742 3.17445 0.61958 0.77255 0.59400 0.80322 - 19 2.43450 4.81939 2.81703 2.39298 4.15804 3.33308 3.59871 3.56807 2.06609 3.14527 3.97247 2.89702 3.36070 2.29211 2.66793 2.54254 2.87166 3.22778 5.35034 4.03520 23 - - + 19 2.43450 4.81939 2.81703 2.39298 4.15804 3.33308 3.59871 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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 - - + 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/FileFormat.java b/src/jalview/io/FileFormat.java index 50d2aa7..11e06a2 100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@ -354,7 +354,7 @@ public enum FileFormat implements FileFormatI return false; } }, - HMMER3("HMMER3", "hmm", false, false) + HMMER3("HMMER3", "hmm", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java index e7f8030..02d92296 100644 --- a/src/jalview/io/HMMFile.java +++ b/src/jalview/io/HMMFile.java @@ -27,9 +27,6 @@ public class HMMFile extends AlignFile // HMM to store file data private HiddenMarkovModel hmm = new HiddenMarkovModel(); - - - // number of possible transitions private final int NUMBER_OF_TRANSITIONS = 7; @@ -48,13 +45,15 @@ public class HMMFile extends AlignFile private static final String TRANSITIONTYPELINE = "m->m m->i m->d i->m i->i d->m d->d"; /** - * Constructor for HMMFile + * Constructor for HMMFile, parses immediately + * * @param source * @throws IOException */ public HMMFile(FileParse source) throws IOException { super(false, source); + parse(); } /** diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index b3ccb45..96a35f9 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -80,8 +80,8 @@ import java.util.Map; * @author jimp * */ -public abstract class AlignmentViewport implements AlignViewportI, - CommandListener, VamsasSource +public abstract class AlignmentViewport + implements AlignViewportI, CommandListener, VamsasSource { final protected ViewportRanges ranges; @@ -98,7 +98,6 @@ public abstract class AlignmentViewport implements AlignViewportI, protected Deque historyList = new ArrayDeque<>(); protected Deque redoList = new ArrayDeque<>(); - /** * alignment displayed in the viewport. Please use get/setter @@ -571,8 +570,6 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle.setSeqNameItalics(default1); } - - @Override public AlignmentI getAlignment() { @@ -668,8 +665,8 @@ public abstract class AlignmentViewport implements AlignViewportI, sg.setColourScheme(cs); if (cs != null) { - sg.getGroupColourScheme() - .alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme().alignmentChanged(sg, + hiddenRepSequences); } } } @@ -678,8 +675,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return residueShading == null ? null : residueShading - .getColourScheme(); + return residueShading == null ? null : residueShading.getColourScheme(); } @Override @@ -837,7 +833,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return information.get(index); } - @Override public AlignmentAnnotation getAlignmentGapAnnotation() { @@ -870,11 +865,11 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator - .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + jalview.workers.ConservationThread.class) == null) { - calculator.registerWorker(new jalview.workers.ConservationThread( - this, ap)); + calculator.registerWorker( + new jalview.workers.ConservationThread(this, ap)); } } @@ -888,7 +883,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null) + if (calculator + .getRegisteredWorkersOfClass(ConsensusThread.class) == null) { calculator.registerWorker(new ConsensusThread(this, ap)); } @@ -919,8 +915,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } if (doConsensus) { - if (calculator - .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + ComplementConsensusThread.class) == null) { calculator .registerWorker(new ComplementConsensusThread(this, ap)); @@ -957,7 +953,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + StrucConsensusThread.class) == null) { calculator.registerWorker(new StrucConsensusThread(this, ap)); } @@ -1300,8 +1297,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (sequenceSetID != null) { - System.err - .println("Warning - overwriting a sequenceSetId for a viewport!"); + System.err.println( + "Warning - overwriting a sequenceSetId for a viewport!"); } sequenceSetID = new String(newid); } @@ -1531,8 +1528,8 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup = new SequenceGroup(); selectionGroup.setEndRes(alignment.getWidth() - 1); } - List tmp = alignment.getHiddenSequences().showAll( - hiddenRepSequences); + List tmp = alignment.getHiddenSequences() + .showAll(hiddenRepSequences); for (SequenceI seq : tmp) { selectionGroup.addSequence(seq, false); @@ -1550,8 +1547,8 @@ public abstract class AlignmentViewport implements AlignViewportI, public void showSequence(int index) { - List tmp = alignment.getHiddenSequences().showSequence( - index, hiddenRepSequences); + List tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -1622,8 +1619,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } int gsize = selectionGroup.getSize(); - SequenceI[] hseqs = selectionGroup.getSequences().toArray( - new SequenceI[gsize]); + SequenceI[] hseqs = selectionGroup.getSequences() + .toArray(new SequenceI[gsize]); hideSequence(hseqs); setSelectionGroup(null); @@ -1713,8 +1710,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean isHiddenRepSequence(SequenceI seq) { - return (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + return (hiddenRepSequences != null + && hiddenRepSequences.containsKey(seq)); } /** @@ -1732,8 +1729,8 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public int adjustForHiddenSeqs(int alignmentIndex) { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); + return alignment.getHiddenSequences() + .adjustForHiddenSeqs(alignmentIndex); } @Override @@ -1805,8 +1802,7 @@ public abstract class AlignmentViewport implements AlignViewportI, return new AlignmentView(alignment, alignment.getHiddenColumns(), selectionGroup, alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns(), - selectedOnly, - markGroups); + selectedOnly, markGroups); } @Override @@ -1852,8 +1848,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns()) { - selection = alignment.getHiddenColumns().getVisibleSequenceStrings( - start, end, seqs); + selection = alignment.getHiddenColumns() + .getVisibleSequenceStrings(start, end, seqs); } else { @@ -1922,8 +1918,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (selectedOnly && selectionGroup != null) { alignment.getHiddenColumns().makeVisibleAnnotation( - selectionGroup.getStartRes(), - selectionGroup.getEndRes(), clone); + selectionGroup.getStartRes(), selectionGroup.getEndRes(), + clone); } else { @@ -2064,7 +2060,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } } - /** * If this is a protein alignment and there are mappings to cDNA, adds the * cDNA consensus annotation and returns true, else returns false. @@ -2127,6 +2122,7 @@ public abstract class AlignmentViewport implements AlignViewportI, information.hasText = true; information.autoCalculated = false; information.sequenceRef = hmmSequence; + information.setCalcId("HMM annotation"); this.information.add(information); hinformation.add(new Profiles(new ProfileI[1])); alignment.addAnnotation(information); @@ -2140,8 +2136,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { gapcounts = new AlignmentAnnotation("Occupancy", MessageManager.getString("label.occupancy_descr"), - new Annotation[1], 0f, - alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, alignment.getHeight(), + AlignmentAnnotation.BAR_GRAPH); gapcounts.hasText = true; gapcounts.autoCalculated = true; gapcounts.scaleColLabel = true; @@ -2159,8 +2155,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { conservation = new AlignmentAnnotation("Conservation", MessageManager.formatMessage("label.conservation_descr", - getConsPercGaps()), new Annotation[1], - 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + getConsPercGaps()), + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; alignment.addAnnotation(conservation); @@ -2646,8 +2642,8 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle = new ViewStyle(settingsForView); if (residueShading != null) { - residueShading.setConservationApplied(settingsForView - .isConservationColourSelected()); + residueShading.setConservationApplied( + settingsForView.isConservationColourSelected()); } } @@ -2815,7 +2811,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return sortAnnotationsBy; } - public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) + public void setSortAnnotationsBy( + SequenceAnnotationOrder sortAnnotationsBy) { this.sortAnnotationsBy = sortAnnotationsBy; } @@ -2893,8 +2890,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return 0; } boolean iAmProtein = !getAlignment().isNucleotide(); - AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement - .getAlignment(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() + : complement.getAlignment(); if (proteinAlignment == null) { return 0; @@ -2925,7 +2922,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ int lastSeq = alignment.getHeight() - 1; List seqMappings = null; - for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + for (int seqNo = ranges + .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -2936,9 +2934,9 @@ public abstract class AlignmentViewport implements AlignViewportI, { continue; } - seqMappings = MappingUtils - .findMappingsForSequenceAndOthers(sequence, mappings, - getCodingComplement().getAlignment().getSequences()); + seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, + mappings, + getCodingComplement().getAlignment().getSequences()); if (!seqMappings.isEmpty()) { break; @@ -3038,6 +3036,5 @@ public abstract class AlignmentViewport implements AlignViewportI, { return searchResults; } - } -- 1.7.10.2