X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=00fbad5af0c96c23c20dd82dcc27d187017a15c9;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=cdcecc0b9fe40cf9d6c61432cce46ab41b4a8b2a;hpb=33c59ebddbc51bbd26bc4c8576ec17c1498b19e8;p=jalview.git
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index cdcecc0..00fbad5 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,7 +1,26 @@
+/*
+ * 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
+ * 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.*;
/**
*
Title:
@@ -17,36 +36,194 @@ import java.util.Hashtable;
*/
public class SeqsetUtils
{
- public static Hashtable uniquify(SequenceI[] sequences)
+
+ /**
+ * 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)
{
- // Generate a safely named sequence set and a hash to recover the sequence names
- Hashtable map = new Hashtable();
- for (int i = 0; i < sequences.length; i++)
+ 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;i0)
+ {
+ sq.setPDBId(pdbid);
+ }
+
+ if ( (start != null) && (end != null))
+ {
+ sq.setStart(start.intValue());
+ sq.setEnd(end.intValue());
+ }
+
+ 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;
}
- public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
+ /**
+ * 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);
+ }
+
+ /**
+ * 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)
{
- // recover unsafe sequence names for a sequence set
- boolean allfound = true;
+ // 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];
+
for (int i = 0; i < sequences.length; i++)
{
- if (map.containsKey(sequences[i].getName()))
+ String safename = unique_name(i);
+ map.put(safename, SeqCharacterHash(sequences[i]));
+
+ if (write_names)
{
- String unsafename = (String) map.get(sequences[i].getName());
- sequences[i].setName(unsafename);
+ sequences[i].setName(safename);
}
- else
- {
- allfound = false;
+ }
+
+
+ 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)
+ {
+ 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; i0) {
+ System.err.println("Did not find matches for :");
+ for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out.println(((SequenceI) i.nextElement()).getName()))
+ ;
+ return false;
+ }
+
+ 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