/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Vector;
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
public class SeqsetUtils
{
+ public static class SequenceInfo {
+ private String name;
+ private int start;
+ private int end;
+ private Optional<String> description = Optional.empty();
+ private Optional<List<SequenceFeature>> features = Optional.empty();
+ private Optional<List<PDBEntry>> pdbId = Optional.empty();
+ private Optional<SequenceI> dataset = Optional.empty();
+ private Optional<HiddenMarkovModel> hmm = Optional.empty();
+ private Optional<AlignmentAnnotation[]> searchScores = Optional.empty();
+
+ private SequenceInfo(String name, int start, int end) {
+ this.name = name;
+ this.start = start;
+ this.end = end;
+ }
+ }
/**
* Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
- * @param seq SequenceI
+ * Keys are Name, Start, End, SeqFeatures, PdbId, HMM
+ *
+ * @param seq
+ * SequenceI
* @return Hashtable
*/
- public static Hashtable SeqCharacterHash(SequenceI seq)
+ public static SequenceInfo SeqCharacterHash(SequenceI seq)
{
- Hashtable sqinfo = new Hashtable();
- sqinfo.put("Name", seq.getName());
- sqinfo.put("Start", new Integer(seq.getStart()));
- sqinfo.put("End", new Integer(seq.getEnd()));
- if (seq.getDescription() != null)
+ SequenceInfo sqinfo = new SequenceInfo(seq.getName(), seq.getStart(), seq.getEnd());
+ sqinfo.description = Optional.ofNullable(seq.getDescription());
+ sqinfo.dataset = Optional.ofNullable(seq.getDatasetSequence());
+ if (!sqinfo.dataset.isPresent())
{
- sqinfo.put("Description", seq.getDescription());
+ ArrayList<SequenceFeature> feats = new ArrayList<>(
+ seq.getFeatures().getAllFeatures());
+ sqinfo.features = Optional.of(feats);
+ sqinfo.pdbId = Optional.of(Objects.requireNonNullElse(
+ seq.getAllPDBEntries(), new ArrayList<>()));
}
- Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
- if (sfarray != null && sfarray.length > 0)
+ if (seq.hasHMMProfile())
{
- for (int i = 0; i < sfarray.length; i++)
- {
- sfeat.add(sfarray[i]);
- }
+ sqinfo.hmm = Optional.of(seq.getHMM());
}
- sqinfo.put("SeqFeatures", sfeat);
- sqinfo.put("PdbId",
- (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
- sqinfo.put("datasetSequence",
- (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
- new Sequence("THISISAPLACEHOLDER", ""));
+ sqinfo.searchScores = Optional.ofNullable(seq.getAnnotation("Search Scores"));
return sqinfo;
}
/**
- * Recover essential properties of a sequence from a hashtable
- * TODO: replace these methods with something more elegant.
- * @param sq SequenceI
- * @param sqinfo Hashtable
+ * Recover essential properties of a sequence from a hashtable TODO: replace
+ * these methods with something more elegant.
+ *
+ * @param sq
+ * SequenceI
+ * @param sqinfo
+ * Hashtable
* @return boolean true if name was not updated from sqinfo Name entry
*/
- public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
+ public static boolean SeqCharacterUnhash(SequenceI sq, SequenceInfo sqinfo)
{
- boolean namePresent = true;
if (sqinfo == null)
{
return false;
}
- String oldname = (String) sqinfo.get("Name");
- Integer start = (Integer) sqinfo.get("Start");
- Integer end = (Integer) sqinfo.get("End");
- Vector sfeatures = (Vector) sqinfo.get(
- "SeqFeatures");
- Vector pdbid = (Vector) sqinfo.get("PdbId");
- String description = (String) sqinfo.get("Description");
- Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
- if (oldname == null)
- {
- namePresent = false;
- }
- else
- {
- sq.setName(oldname);
- }
- if (pdbid != null && pdbid.size() > 0)
- {
- sq.setPDBId(pdbid);
- }
-
- if ( (start != null) && (end != null))
- {
- sq.setStart(start.intValue());
- sq.setEnd(end.intValue());
- }
-
- if ( (sfeatures != null) && (sfeatures.size() > 0))
+ if (sqinfo.name != null)
{
- SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
- sq.setSequenceFeatures(sfarray);
+ sq.setName(sqinfo.name);
}
- if (description != null)
+ sq.setStart(sqinfo.start);
+ sq.setEnd(sqinfo.end);
+ if (sqinfo.pdbId.isPresent() && !sqinfo.pdbId.get().isEmpty())
+ sq.setPDBId(new Vector<>(sqinfo.pdbId.get()));
+ if (sqinfo.features.isPresent() && !sqinfo.features.get().isEmpty())
+ sq.setSequenceFeatures(sqinfo.features.get());
+ if (sqinfo.description.isPresent())
+ sq.setDescription(sqinfo.description.get());
+ if (sqinfo.dataset.isPresent())
{
- sq.setDescription(description);
+ assert sqinfo.features.isEmpty() :
+ "Setting dataset sequence for a sequence which has sequence features. " +
+ "Dataset sequence features will not be visible.";
+ sq.setDatasetSequence(sqinfo.dataset.get());
}
- if ( (seqds != null) &&
- ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
- seqds.getLength() == 0))
+ if (sqinfo.hmm.isPresent())
+ sq.setHMM(new HiddenMarkovModel(sqinfo.hmm.get(), sq));
+ if (sqinfo.searchScores.isPresent())
{
- sq.setDatasetSequence(seqds);
+ for (AlignmentAnnotation score : sqinfo.searchScores.get())
+ {
+ sq.addAlignmentAnnotation(score);
+ }
}
-
- return namePresent;
+ return sqinfo.name != null;
}
/**
- * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
- * @param i int
+ * Form of the unique name used in uniquify for the i'th sequence in an
+ * ordered vector of sequences.
+ *
+ * @param i
+ * int
* @return String
*/
public static String unique_name(int i)
{
- return new String("Sequence" + i);
+ return String.format("Sequence%d", i);
}
/**
- * Generates a hash of SeqCharacterHash properties for each sequence
- * in a sequence set, and optionally renames the sequences to an
- * unambiguous 'safe' name.
- * @param sequences SequenceI[]
- * @param write_names boolean set this to rename each of the sequences to its unique_name(index) name
- * @return Hashtable to be passed to @see deuniquify to recover original names (and properties) for renamed sequences
+ * Generates a hash of SeqCharacterHash properties for each sequence in a
+ * sequence set, and optionally renames the sequences to an unambiguous 'safe'
+ * name.
+ *
+ * @param sequences
+ * SequenceI[]
+ * @param write_names
+ * boolean set this to rename each of the sequences to its
+ * unique_name(index) name
+ * @return Hashtable to be passed to
+ * @see deuniquify to recover original names (and properties) for renamed
+ * sequences
*/
- public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
+ public static Map<String, SequenceInfo> uniquify(SequenceI[] sequences,
+ boolean write_names)
{
- // Generate a safely named sequence set and a hash to recover the sequence names
- Hashtable map = new Hashtable();
- //String[] un_names = new String[sequences.length];
+ // Generate a safely named sequence set and a hash to recover the sequence
+ // names
+ HashMap<String, SequenceInfo> map = new HashMap<>();
+ // String[] un_names = new String[sequences.length];
for (int i = 0; i < sequences.length; i++)
{
}
/**
- * recover unsafe sequence names and original properties for a sequence
- * set using a map generated by @see uniquify(sequences,true)
- * @param map Hashtable
- * @param sequences SequenceI[]
+ * recover unsafe sequence names and original properties for a sequence set
+ * using a map generated by
+ *
+ * @see uniquify(sequences,true)
+ * @param map
+ * Hashtable
+ * @param sequences
+ * SequenceI[]
+ * @return boolean
+ */
+ public static boolean deuniquify(Map<String, SequenceInfo> map,
+ SequenceI[] sequences)
+ {
+ return deuniquify(map, sequences, true);
+ }
+
+ /**
+ * recover unsafe sequence names and original properties for a sequence set
+ * using a map generated by
+ *
+ * @see uniquify(sequences,true)
+ * @param map
+ * Hashtable
+ * @param sequences
+ * SequenceI[]
+ * @param quiet
+ * when false, don't complain about sequences without any data in the
+ * map.
* @return boolean
*/
- public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
+ public static boolean deuniquify(Map<String, SequenceInfo> map,
+ SequenceI[] sequences, boolean quiet)
{
jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
- sequences);
+ sequences);
SequenceI msq = null;
- Enumeration keys = map.keys();
- Vector unmatched = new Vector();
+ Iterator<String> keys = map.keySet().iterator();
+ Vector<SequenceI> unmatched = new Vector<>();
for (int i = 0, j = sequences.length; i < j; i++)
{
- unmatched.add(sequences[i]);
+ unmatched.addElement(sequences[i]);
}
- while (keys.hasMoreElements())
+ while (keys.hasNext())
{
- Object key = keys.nextElement();
- if (key instanceof String)
- {
- if ( (msq = matcher.findIdMatch( (String) key)) != null)
+ String key = keys.next();
+ try {
+ if ((msq = matcher.findIdMatch((String) key)) != null)
{
- Hashtable sqinfo = (Hashtable) map.get(key);
- unmatched.remove(msq);
+ SequenceInfo sqinfo = map.get(key);
+ unmatched.removeElement(msq);
SeqCharacterUnhash(msq, sqinfo);
}
else
{
- System.err.println("Can't find '" + ( (String) key) +
- "' in uniquified alignment");
+ if (!quiet)
+ {
+ System.err.println("Can't find '" + ((String) key)
+ + "' in uniquified alignment");
+ }
+ }
+ } catch (ClassCastException ccastex) {
+ if (!quiet)
+ {
+ System.err.println("Unexpected object in SeqSet map : "+key.getClass());
}
}
}
- if (unmatched.size() > 0)
+ if (unmatched.size() > 0 && !quiet)
{
System.err.println("Did not find matches for :");
- for (Enumeration i = unmatched.elements(); i.hasMoreElements();
- System.out.println( ( (SequenceI) i.nextElement()).getName()))
+ for (Enumeration<SequenceI> i = unmatched.elements();
+ i.hasMoreElements();)
{
- ;
+ System.out.println(((SequenceI) i.nextElement()).getName());
}
return false;
}
}
/**
- * returns a subset of the sequenceI seuqences,
- * including only those that contain at least one residue.
- * @param sequences SequenceI[]
+ * returns a subset of the sequenceI seuqences, including only those that
+ * contain at least one residue.
+ *
+ * @param sequences
+ * SequenceI[]
* @return SequenceI[]
*/
public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
for (int i = 0, j = sequences.length; i < j; i++)
{
String tempseq = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- sequences[i].getSequenceAsString());
+ jalview.util.Comparison.GapChars,
+ sequences[i].getSequenceAsString());
if (tempseq.length() == 0)
{
git://source.jalview.org / jalview.git / blobdiff