X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=5420aff67b8b0b3782175fd1707ba3565a632b2d;hb=81682dafca2e79cf141b134496db0c3a84027806;hp=00fbad5af0c96c23c20dd82dcc27d187017a15c9;hpb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;p=jalview.git
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 00fbad5..5420aff 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,145 +1,207 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
-
-/**
- * Title:
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
+import jalview.bin.Cache;
+import jalview.bin.Console;
+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 java.util.ArrayList;
+import java.util.BitSet;
+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.Optional;
+import java.util.Vector;
+import static java.lang.String.format;
+
+import java.nio.CharBuffer;
+
public class SeqsetUtils
{
+ public static class SequenceInfo {
+ private String name;
+ private int start;
+ private int end;
+ private Optional description = Optional.empty();
+ private Optional> features = Optional.empty();
+ private Optional> pdbId = Optional.empty();
+ private Optional dataset = Optional.empty();
+ private Optional hmm = Optional.empty();
+ private Optional 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)
- sqinfo.put("Description", seq.getDescription());
- Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray=seq.getSequenceFeatures();
- if (sfarray!=null && sfarray.length>0) {
- for (int i=0;i feats = new ArrayList<>(
+ seq.getFeatures().getAllFeatures());
+ sqinfo.features = Optional.of(feats);
+ var pdbEntries = seq.getAllPDBEntries();
+ sqinfo.pdbId = Optional.of(pdbEntries != null ? pdbEntries : new ArrayList<>());
}
- 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",""));
+ if (seq.hasHMMProfile())
+ {
+ sqinfo.hmm = Optional.of(seq.getHMM());
+ }
+ 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
- * @return boolean true if name was not updated from sqinfo Name entry
+ * Filter the sequence through the mask leaving only characters at positions
+ * where the mask value was true. The length of the resulting array is
+ * the cardinality of the mask from 0 to sequence length.
+ *
+ * @param sequence
+ * input sequence
+ * @param mask
+ * mask used to filter the sequence characters
+ * @return input array filtered through the mask
*/
- public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
+ public static char[] filterSequence(char[] sequence, BitSet mask)
{
- 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)
+ mask = mask.get(0, sequence.length);
+ char[] result = new char[mask.cardinality()];
+ for (int i = mask.nextSetBit(0), j = 0; i >= 0;)
{
- namePresent = false;
+ result[j++] = sequence[i];
+ if (i == Integer.MAX_VALUE)
+ // prevents integer overflow of (i + 1)
+ break;
+ i = mask.nextSetBit(i + 1);
}
- else
+ return result;
+ }
+
+ /**
+ * 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, SequenceInfo sqinfo)
+ {
+ if (sqinfo == null)
{
- sq.setName(oldname);
+ return false;
}
- if (pdbid!=null && pdbid.size()>0)
+ if (sqinfo.name != null)
{
- sq.setPDBId(pdbid);
+ sq.setName(sqinfo.name);
}
-
- if ( (start != null) && (end != 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.setStart(start.intValue());
- sq.setEnd(end.intValue());
+ if (sqinfo.features.isPresent())
+ {
+ Console.warn("Setting dataset sequence for a sequence which has " +
+ "sequence features. Dataset sequence features will not be visible.");
+ assert false;
+ }
+ sq.setDatasetSequence(sqinfo.dataset.get());
}
-
- if ((sfeatures != null) && (sfeatures.size()>0))
+ if (sqinfo.hmm.isPresent())
+ sq.setHMM(new HiddenMarkovModel(sqinfo.hmm.get(), sq));
+ if (sqinfo.searchScores.isPresent())
{
- SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
- sq.setSequenceFeatures(sfarray);
- }
- if (description!=null)
- sq.setDescription(description);
- if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {
- 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 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 map = new HashMap<>();
+ // String[] un_names = new String[sequences.length];
for (int i = 0; i < sequences.length; i++)
{
@@ -152,78 +214,136 @@ public class SeqsetUtils
}
}
-
return map;
}
+
+ /**
+ * 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 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[]
+ * 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 map,
+ SequenceI[] sequences, boolean quiet)
{
- jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
+ jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+ sequences);
SequenceI msq = null;
- Enumeration keys = map.keys();
- Vector unmatched = new Vector();
- for (int i=0, j=sequences.length; i keys = map.keySet().iterator();
+ Vector unmatched = new Vector<>();
+ for (int i = 0, j = sequences.length; i < j; i++)
+ {
+ unmatched.addElement(sequences[i]);
+ }
+ while (keys.hasNext())
+ {
+ String key = keys.next();
+ try {
+ if ((msq = matcher.findIdMatch((String) key)) != null)
+ {
+ 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)
+ {
+ Console.warn(format("Can't find '%s' in uniquified alignment",
+ key));
+ }
+ }
+ } catch (ClassCastException ccastex) {
+ if (!quiet)
+ {
+ Console.error("Unexpected object in SeqSet map : "+ key.getClass());
}
}
}
- if (unmatched.size()>0) {
- System.err.println("Did not find matches for :");
- for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out.println(((SequenceI) i.nextElement()).getName()))
- ;
+ if (unmatched.size() > 0 && !quiet)
+ {
+ StringBuilder sb = new StringBuilder("Did not find match for sequences: ");
+ Enumeration i = unmatched.elements();
+ sb.append(i.nextElement().getName());
+ for (; i.hasMoreElements();)
+ {
+ sb.append(", " + i.nextElement().getName());
+ }
+ Console.warn(sb.toString());
return false;
}
return true;
}
+
/**
- * 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) {
- // Identify first row of alignment with residues for prediction
- boolean ungapped[] = new boolean[sequences.length];
- int msflen=0;
- for (int i=0,j=sequences.length; i