X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=fabd0c69d178e483ab7c651245d888c183976d26;hb=af65be61ff37a024b694150efed2c6c9b81382ef;hp=f5ca6512ecdeaecfd9506c86a90e8e0bd508b76a;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index f5ca651..fabd0c6 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,46 +1,44 @@
/*
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
-/**
- * Title:
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
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
+ * Keys are Name, Start, End, SeqFeatures, PdbId
+ *
+ * @param seq
+ * SequenceI
* @return Hashtable
*/
public static Hashtable SeqCharacterHash(SequenceI seq)
@@ -53,29 +51,35 @@ public class SeqsetUtils
{
sqinfo.put("Description", seq.getDescription());
}
- Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
- if (sfarray != null && sfarray.length > 0)
+
+ Vector sfeat = new Vector();
+ List sfs = seq.getFeatures().getAllFeatures();
+ sfeat.addAll(sfs);
+
+ if (seq.getDatasetSequence() == null)
{
- for (int i = 0; i < sfarray.length; i++)
- {
- sfeat.add(sfarray[i]);
- }
+ sqinfo.put("SeqFeatures", sfeat);
+ sqinfo.put("PdbId",
+ (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+ : new Vector());
+ }
+ else
+ {
+ sqinfo.put("datasetSequence",
+ (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+ : new Sequence("THISISAPLACEHOLDER", ""));
}
- 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
+ * 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)
@@ -88,9 +92,9 @@ public class SeqsetUtils
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");
+ 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)
@@ -106,25 +110,28 @@ public class SeqsetUtils
sq.setPDBId(pdbid);
}
- if ( (start != null) && (end != null))
+ if ((start != null) && (end != null))
{
sq.setStart(start.intValue());
sq.setEnd(end.intValue());
}
- if ( (sfeatures != null) && (sfeatures.size() > 0))
+ if (sfeatures != null && !sfeatures.isEmpty())
{
- SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
- sq.setSequenceFeatures(sfarray);
+ sq.setSequenceFeatures(sfeatures);
}
if (description != null)
{
sq.setDescription(description);
}
- if ( (seqds != null) &&
- ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
- seqds.getLength() == 0))
+ if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
+ && seqds.getLength() == 0))
{
+ if (sfeatures != null)
+ {
+ System.err.println(
+ "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+ }
sq.setDatasetSequence(seqds);
}
@@ -132,8 +139,11 @@ public class SeqsetUtils
}
/**
- * 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)
@@ -142,18 +152,26 @@ public class SeqsetUtils
}
/**
- * 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 Hashtable uniquify(SequenceI[] sequences,
+ boolean write_names)
{
- // Generate a safely named sequence set and a hash to recover the sequence 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];
+ // String[] un_names = new String[sequences.length];
for (int i = 0; i < sequences.length; i++)
{
@@ -170,46 +188,74 @@ public class SeqsetUtils
}
/**
- * 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(Hashtable 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,
+ boolean quiet)
+ {
jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
- sequences);
+ sequences);
SequenceI msq = null;
Enumeration keys = map.keys();
Vector unmatched = new Vector();
for (int i = 0, j = sequences.length; i < j; i++)
{
- unmatched.add(sequences[i]);
+ unmatched.addElement(sequences[i]);
}
while (keys.hasMoreElements())
{
Object key = keys.nextElement();
if (key instanceof String)
{
- if ( (msq = matcher.findIdMatch( (String) key)) != null)
+ if ((msq = matcher.findIdMatch((String) key)) != null)
{
Hashtable sqinfo = (Hashtable) map.get(key);
- unmatched.remove(msq);
+ 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");
+ }
}
}
}
- 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 i = unmatched.elements(); i
+ .hasMoreElements(); System.out
+ .println(((SequenceI) i.nextElement()).getName()))
{
;
}
@@ -220,9 +266,11 @@ public class SeqsetUtils
}
/**
- * 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)
@@ -233,8 +281,8 @@ public class SeqsetUtils
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)
{