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;
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
protected final List<ArgumentI> 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
*
*
* @param seqs
*/
- protected Hashtable stashSequences(SequenceI[] seqs)
+ protected Map<String, SequenceInfo> stashSequences(SequenceI[] seqs)
{
return SeqsetUtils.uniquify(seqs, true);
}
/**
* Restores the sequence data lost by uniquifying
*
- * @param hashtable
+ * @param sequencesHash
* @param seqs
*/
- protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+ protected void recoverSequences(Map<String, SequenceInfo> sequencesHash, SequenceI[] seqs)
{
- SeqsetUtils.deuniquify(hashtable, seqs);
+ SeqsetUtils.deuniquify(sequencesHash, seqs);
}
/**
public boolean runCommand(List<String> commands)
throws IOException
{
- List<String> args = Platform.isWindows() ? wrapWithCygwin(commands)
+ List<String> 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()
{
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)
Cache.getProperty(Preferences.CYGWIN_PATH));
if (bash == null)
{
- Cache.log.error("Cygwin shell not found");
+ Console.error("Cygwin shell not found");
return commands;
}
List<String> wrapped = new ArrayList<>();
+ // wrapped.add("C:\Users\tva\run");
wrapped.add(bash.getAbsolutePath());
wrapped.add("-c");
/**
* 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
* @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();
}
}
+ 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);
* @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);
}
/**
}
}
+ // 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
* 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, "/");
return path;
}
+
+ /**
+ * A helper method that deletes any HMM consensus sequence from the given
+ * collection, and from the parent alignment if <code>ac</code> is a subgroup
+ *
+ * @param ac
+ */
+ void deleteHmmSequences(AnnotatedCollectionI ac)
+ {
+ List<SequenceI> 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<Boolean> 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);
+ }
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff