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 java.io.BufferedReader;
import java.io.File;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
/**
* Base class for hmmbuild, hmmalign and hmmsearch
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 = "None";
+ static final String CUTOFF_NONE = "label.default";
+
+ static final String CUTOFF_SCORE = "label.score";
+
+ static final String CUTOFF_EVALUE = "label.evalue";
- static final String CUTOFF_SCORE = "Score";
+ static final String REPORTING_SEQ_EVALUE_KEY = "label.reporting_seq_evalue";
- static final String CUTOFF_EVALUE = "E-Value";
+ static final String REPORTING_DOM_EVALUE_KEY = "label.reporting_dom_evalue";
- static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+ static final String REPORTING_SEQ_SCORE_KEY = "label.reporting_seq_score";
- static final String DOM_EVALUE_KEY = "label.dom_evalue";
+ static final String REPORTING_DOM_SCORE_KEY = "label.reporting_dom_score";
- static final String SEQ_SCORE_KEY = "label.seq_score";
+ static final String INCLUSION_SEQ_EVALUE_KEY = "label.inclusion_seq_evalue";
- static final String DOM_SCORE_KEY = "label.dom_score";
+ 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.isWindows())
+ if (Platform.isWindowsAndNotJS())
{
String path = pb.environment().get("Path");
path = jalview.bin.Cache.getProperty("CYGWIN_PATH") + ";" + path;
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;
}
* @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);
}
/**
- * Exports the given alignment withotu any anotations to a fasta file
- *
- * @param seqs
- * @param toFile
- */
- public void exportFasta(AlignmentI al, File toFile)
- {
- FastaFile file = new FastaFile();
-
- String output = file.print(al.getSequencesArray(), false);
- PrintWriter writer;
- try
- {
- writer = new PrintWriter(toFile);
- writer.println(output);
- writer.close();
- } catch (FileNotFoundException e)
- {
- e.printStackTrace();
- }
-
- }
-
- /**
* Answers the full path to the given hmmer executable, or null if file cannot
* be found or is not executable
*
}
/**
- * Answers the HMM profile for the profile sequence the user selected (default
- * is just the first HMM sequence in the alignment)
+ * Answers the query sequence the user selected (default is just the first
+ * sequence in the alignment)
*
* @return
*/
protected String getFilePath(File resultFile, boolean isInCygwin)
{
String path = resultFile.getAbsolutePath();
- if (Platform.isWindows() && isInCygwin)
+ if (Platform.isWindowsAndNotJS() && isInCygwin)
{
// the first backslash escapes '\' for the regular expression argument
path = path.replaceAll("\\" + File.separator, "/");
}
}
}
+
+ /**
+ * 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