X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHmmerCommand.java;h=9db0ae19601e2135f00f90c221477cf0f01cf522;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=dfd53954fa41de9182503148bcbfe1d89c4b0909;hpb=ff638b98db095ffd7dc792f5d91fe5a0de6fc2ba;p=jalview.git diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java index dfd5395..9db0ae1 100644 --- a/src/jalview/hmmer/HmmerCommand.java +++ b/src/jalview/hmmer/HmmerCommand.java @@ -1,17 +1,21 @@ package jalview.hmmer; import jalview.analysis.SeqsetUtils; +import jalview.analysis.SeqsetUtils.SequenceInfo; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.Annotation; import jalview.datamodel.HiddenMarkovModel; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.JvOptionPane; import jalview.gui.Preferences; +import jalview.io.FastaFile; import jalview.io.HMMFile; import jalview.io.StockholmFile; import jalview.util.FileUtils; @@ -24,9 +28,11 @@ import java.io.File; import java.io.IOException; import java.io.InputStreamReader; import java.io.PrintWriter; +import java.nio.file.Paths; import java.util.ArrayList; import java.util.Hashtable; import java.util.List; +import java.util.Map; /** * Base class for hmmbuild, hmmalign and hmmsearch @@ -44,6 +50,53 @@ public abstract class HmmerCommand implements Runnable protected final List params; + /* + * constants for i18n lookup of passed parameter names + */ + static final String DATABASE_KEY = "label.database"; + + static final String THIS_ALIGNMENT_KEY = "label.this_alignment"; + + static final String USE_ACCESSIONS_KEY = "label.use_accessions"; + + static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs"; + + static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results"; + + static final String NUMBER_OF_ITERATIONS = "label.number_of_iterations"; + + static final String TRIM_TERMINI_KEY = "label.trim_termini"; + + static final String RETURN_N_NEW_SEQ = "label.check_for_new_sequences"; + + static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff"; + + static final String CUTOFF_NONE = "label.default"; + + static final String CUTOFF_SCORE = "label.score"; + + static final String CUTOFF_EVALUE = "label.evalue"; + + static final String REPORTING_SEQ_EVALUE_KEY = "label.reporting_seq_evalue"; + + static final String REPORTING_DOM_EVALUE_KEY = "label.reporting_dom_evalue"; + + static final String REPORTING_SEQ_SCORE_KEY = "label.reporting_seq_score"; + + static final String REPORTING_DOM_SCORE_KEY = "label.reporting_dom_score"; + + static final String INCLUSION_SEQ_EVALUE_KEY = "label.inclusion_seq_evalue"; + + static final String INCLUSION_DOM_EVALUE_KEY = "label.inclusion_dom_evalue"; + + static final String INCLUSION_SEQ_SCORE_KEY = "label.inclusion_seq_score"; + + static final String INCLUSION_DOM_SCORE_KEY = "label.inclusion_dom_score"; + + static final String ARG_TRIM = "--trim"; + + static final String INCLUSION_THRESHOLD_KEY = "label.inclusion_threshold"; + /** * Constructor * @@ -77,7 +130,7 @@ public abstract class HmmerCommand implements Runnable * * @param seqs */ - protected Hashtable stashSequences(SequenceI[] seqs) + protected Map stashSequences(SequenceI[] seqs) { return SeqsetUtils.uniquify(seqs, true); } @@ -85,12 +138,12 @@ public abstract class HmmerCommand implements Runnable /** * Restores the sequence data lost by uniquifying * - * @param hashtable + * @param sequencesHash * @param seqs */ - protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs) + protected void recoverSequences(Map sequencesHash, SequenceI[] seqs) { - SeqsetUtils.deuniquify(hashtable, seqs); + SeqsetUtils.deuniquify(sequencesHash, seqs); } /** @@ -104,13 +157,19 @@ public abstract class HmmerCommand implements Runnable public boolean runCommand(List commands) throws IOException { - List args = Platform.isWindows() ? wrapWithCygwin(commands) + List args = Platform.isWindowsAndNotJS() ? wrapWithCygwin(commands) : commands; try { ProcessBuilder pb = new ProcessBuilder(args); pb.redirectErrorStream(true); // merge syserr to sysout + if (Platform.isWindowsAndNotJS()) + { + String path = pb.environment().get("Path"); + path = jalview.bin.Cache.getProperty("CYGWIN_PATH") + ";" + path; + pb.environment().put("Path", path); + } final Process p = pb.start(); new Thread(new Runnable() { @@ -138,8 +197,8 @@ public abstract class HmmerCommand implements Runnable int exitValue = p.exitValue(); if (exitValue != 0) { - Cache.log.error("Command failed, return code = " + exitValue); - Cache.log.error("Command/args were: " + args.toString()); + Console.error("Command failed, return code = " + exitValue); + Console.error("Command/args were: " + args.toString()); } return exitValue == 0; // 0 is success, by convention } catch (Exception e) @@ -162,11 +221,12 @@ public abstract class HmmerCommand implements Runnable Cache.getProperty(Preferences.CYGWIN_PATH)); if (bash == null) { - Cache.log.error("Cygwin shell not found"); + Console.error("Cygwin shell not found"); return commands; } List wrapped = new ArrayList<>(); + // wrapped.add("C:\Users\tva\run"); wrapped.add(bash.getAbsolutePath()); wrapped.add("-c"); @@ -185,7 +245,7 @@ public abstract class HmmerCommand implements Runnable /** * Exports an alignment, and reference (RF) annotation if present, to the - * specified file, in Stockholm format + * specified file, in Stockholm format, removing all HMM sequences * * @param seqs * @param toFile @@ -193,13 +253,15 @@ public abstract class HmmerCommand implements Runnable * @throws IOException */ public void exportStockholm(SequenceI[] seqs, File toFile, - AnnotatedCollectionI annotated) throws IOException + AnnotatedCollectionI annotated) + throws IOException { if (seqs == null) { return; } AlignmentI newAl = new Alignment(seqs); + if (!newAl.isAligned()) { newAl.padGaps(); @@ -233,6 +295,17 @@ public abstract class HmmerCommand implements Runnable } } + for (SequenceI seq : newAl.getSequencesArray()) + { + if (seq.getAnnotation() != null) + { + for (AlignmentAnnotation ann : seq.getAnnotation()) + { + seq.removeAlignmentAnnotation(ann); + } + } + } + StockholmFile file = new StockholmFile(newAl); String output = file.print(seqs, false); PrintWriter writer = new PrintWriter(toFile); @@ -247,18 +320,22 @@ public abstract class HmmerCommand implements Runnable * @param cmd * command short name e.g. hmmalign * @return + * @throws IOException */ protected String getCommandPath(String cmd) + throws IOException { String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH); + // ensure any symlink to the directory is resolved: + binariesFolder = Paths.get(binariesFolder).toRealPath().toString(); File file = FileUtils.getExecutable(cmd, binariesFolder); if (file == null && af != null) { - JvOptionPane.showInternalMessageDialog(af, - MessageManager.getString("warn.hmm_command_failed")); + JvOptionPane.showInternalMessageDialog(af, MessageManager + .formatMessage("label.executable_not_found", cmd)); } - return file == null ? null : getFilePath(file); + return file == null ? null : getFilePath(file, true); } /** @@ -280,6 +357,73 @@ public abstract class HmmerCommand implements Runnable } } + // TODO is needed? + /** + * Exports a sequence to the specified file + * + * @param hmm + * @param hmmFile + * @throws IOException + */ + public void exportSequence(SequenceI seq, File seqFile) throws IOException + { + if (seq != null) + { + FastaFile file = new FastaFile(); + PrintWriter writer = new PrintWriter(seqFile); + writer.print(file.print(new SequenceI[] { seq }, false)); + writer.close(); + } + } + + /** + * Answers the HMM profile for the profile sequence the user selected (default + * is just the first HMM sequence in the alignment) + * + * @return + */ + protected HiddenMarkovModel getHmmProfile() + { + String alignToParamName = MessageManager.getString("label.use_hmm"); + for (ArgumentI arg : params) + { + String name = arg.getName(); + if (name.equals(alignToParamName)) + { + String seqName = arg.getValue(); + SequenceI hmmSeq = alignment.findName(seqName); + if (hmmSeq.hasHMMProfile()) + { + return hmmSeq.getHMM(); + } + } + } + return null; + } + + /** + * Answers the query sequence the user selected (default is just the first + * sequence in the alignment) + * + * @return + */ + protected SequenceI getSequence() + { + String alignToParamName = MessageManager + .getString("label.use_sequence"); + for (ArgumentI arg : params) + { + String name = arg.getName(); + if (name.equals(alignToParamName)) + { + String seqName = arg.getValue(); + SequenceI seq = alignment.findName(seqName); + return seq; + } + } + return null; + } + /** * Answers an absolute path to the given file, in a format suitable for * processing by a hmmer command. On a Windows platform, the native Windows file @@ -287,12 +431,15 @@ public abstract class HmmerCommand implements Runnable * X with /cygdrive/x. * * @param resultFile + * @param isInCygwin + * True if file is to be read/written from within the Cygwin + * shell. Should be false for any imports. * @return */ - protected String getFilePath(File resultFile) + protected String getFilePath(File resultFile, boolean isInCygwin) { String path = resultFile.getAbsolutePath(); - if (Platform.isWindows()) + if (Platform.isWindowsAndNotJS() && isInCygwin) { // the first backslash escapes '\' for the regular expression argument path = path.replaceAll("\\" + File.separator, "/"); @@ -306,4 +453,87 @@ public abstract class HmmerCommand implements Runnable return path; } + + /** + * A helper method that deletes any HMM consensus sequence from the given + * collection, and from the parent alignment if ac is a subgroup + * + * @param ac + */ + void deleteHmmSequences(AnnotatedCollectionI ac) + { + List hmmSeqs = ac.getHmmSequences(); + for (SequenceI hmmSeq : hmmSeqs) + { + if (ac instanceof SequenceGroup) + { + ((SequenceGroup) ac).deleteSequence(hmmSeq, false); + AnnotatedCollectionI context = ac.getContext(); + if (context != null && context instanceof AlignmentI) + { + ((AlignmentI) context).deleteSequence(hmmSeq); + } + } + else + { + ((AlignmentI) ac).deleteSequence(hmmSeq); + } + } + } + + /** + * Sets the names of any duplicates within the given sequences to include their + * respective lengths. Deletes any duplicates that have the same name after this + * step + * + * @param seqs + */ + void renameDuplicates(AlignmentI al) + { + + SequenceI[] seqs = al.getSequencesArray(); + List wasRenamed = new ArrayList<>(); + + for (SequenceI seq : seqs) + { + wasRenamed.add(false); + } + + for (int i = 0; i < seqs.length; i++) + { + for (int j = 0; j < seqs.length; j++) + { + if (seqs[i].getName().equals(seqs[j].getName()) && i != j + && !wasRenamed.get(j)) + { + + wasRenamed.set(i, true); + String range = "/" + seqs[j].getStart() + "-" + seqs[j].getEnd(); + // setting sequence name to include range - to differentiate between + // sequences of the same name. Currently have to include the range twice + // because the range is removed (once) when setting the name + // TODO come up with a better way of doing this + seqs[j].setName(seqs[j].getName() + range + range); + } + + } + if (wasRenamed.get(i)) + { + String range = "/" + seqs[i].getStart() + "-" + seqs[i].getEnd(); + seqs[i].setName(seqs[i].getName() + range + range); + } + } + + for (int i = 0; i < seqs.length; i++) + { + for (int j = 0; j < seqs.length; j++) + { + if (seqs[i].getName().equals(seqs[j].getName()) && i != j) + { + al.deleteSequence(j); + } + } + } + } + }