+/*
+ * 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
+ * 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.
+ *
+ * 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
+ */
package jalview.analysis;
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
+import java.util.*;
+
+import jalview.datamodel.*;
/**
* <p>Title: </p>
*/
public class SeqsetUtils
{
- /**
- * Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
- * @param seq SequenceI
- * @return Hashtable
- */
- public static Hashtable SeqCharacterHash(SequenceI seq) {
+
+ /**
+ * Store essential properties of a sequence in a hashtable for later recovery
+ * Keys are Name, Start, End, SeqFeatures, PdbId
+ * @param seq SequenceI
+ * @return Hashtable
+ */
+ public static Hashtable 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()));
- sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
- sqinfo.put("PdbId", (seq.getPDBId()!=null) ? seq.getPDBId() : new String("") );
+ 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 < sfarray.length; i++)
+ {
+ sfeat.add(sfarray[i]);
+ }
+ }
+ 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", ""));
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
+ * @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, Hashtable 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");
- java.util.Vector sfeatures = (java.util.Vector) sqinfo.get("SeqFeatures");
- String pdbid = (String) sqinfo.get("PdbId");
- if (oldname==null)
+ 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.equals(""))
+ }
+ if (pdbid != null && pdbid.size() > 0)
+ {
sq.setPDBId(pdbid);
+ }
- if ((start!=null) && (end!=null)) {
+ if ( (start != null) && (end != null))
+ {
sq.setStart(start.intValue());
sq.setEnd(end.intValue());
}
- if (sfeatures!=null)
- sq.setSequenceFeatures(sfeatures);
+
+ if ( (sfeatures != null) && (sfeatures.size() > 0))
+ {
+ 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);
+ }
+
return namePresent;
}
* @param i int
* @return String
*/
- public static String unique_name(int i) {
- return new String("Sequence"+i);
+ public static String unique_name(int i)
+ {
+ return new String("Sequence" + 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
+ */
public static Hashtable 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];
- if (!write_names)
+ //String[] un_names = new String[sequences.length];
for (int i = 0; i < sequences.length; i++)
{
- String safename = new String("Sequence" + i);
+ String safename = unique_name(i);
map.put(safename, SeqCharacterHash(sequences[i]));
+
if (write_names)
+ {
sequences[i].setName(safename);
+ }
}
+
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(Hashtable map, SequenceI[] sequences)
{
- // recover unsafe sequence names for a sequence set
- boolean allfound = true;
- for (int i = 0; i < sequences.length; i++)
+ 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 < j; i++)
{
- if (map.containsKey(sequences[i].getName()))
+ unmatched.add(sequences[i]);
+ }
+ while (keys.hasMoreElements())
+ {
+ Object key = keys.nextElement();
+ if (key instanceof String)
{
- Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
- SeqCharacterUnhash(sequences[i], sqinfo);
+ if ( (msq = matcher.findIdMatch( (String) key)) != null)
+ {
+ Hashtable sqinfo = (Hashtable) map.get(key);
+ unmatched.remove(msq);
+ SeqCharacterUnhash(msq, sqinfo);
+ }
+ else
+ {
+ System.err.println("Can't find '" + ( (String) key) +
+ "' in uniquified alignment");
+ }
}
- else
+ }
+ 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()))
{
- allfound = false;
+ ;
}
+ return false;
}
- return allfound;
+
+ return true;
}
+ /**
+ * 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 < j; i++)
+ {
+ String tempseq = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ sequences[i].getSequenceAsString());
+
+ if (tempseq.length() == 0)
+ {
+ ungapped[i] = false;
+ }
+ else
+ {
+ ungapped[i] = true;
+ msflen++;
+ }
+ }
+ if (msflen == 0)
+ {
+ return null; // no minimal set
+ }
+ // compose minimal set
+ SequenceI[] mset = new SequenceI[msflen];
+ for (int i = 0, j = sequences.length, k = 0; i < j; i++)
+ {
+ if (ungapped[i])
+ {
+ mset[k++] = sequences[i];
+ }
+ }
+ ungapped = null;
+ return mset;
+ }
}