/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.datamodel.SequenceI;\r
-\r
-import java.util.Hashtable;\r
-\r
-\r
+ * 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 java.util.*;
+
+import jalview.datamodel.*;
+
/**
* <p>Title: </p>
*
*
* @author not attributable
* @version 1.0
- */\r
-public class SeqsetUtils {\r
- /**
- * Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
- * @param seq SequenceI
- * @return Hashtable
- */\r
- public static Hashtable SeqCharacterHash(SequenceI seq) {\r
- Hashtable sqinfo = new Hashtable();\r
- sqinfo.put("Name", seq.getName());\r
- sqinfo.put("Start", new Integer(seq.getStart()));\r
- sqinfo.put("End", new Integer(seq.getEnd()));\r
- sqinfo.put("SeqFeatures", seq.getSequenceFeatures());\r
- sqinfo.put("PdbId",\r
- (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));\r
-\r
- return sqinfo;\r
- }\r
-\r
- /**
- * 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
- */\r
- public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {\r
- boolean namePresent = true;\r
- String oldname = (String) sqinfo.get("Name");\r
- Integer start = (Integer) sqinfo.get("Start");\r
- Integer end = (Integer) sqinfo.get("End");\r
- java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(\r
- "SeqFeatures");\r
- String pdbid = (String) sqinfo.get("PdbId");\r
-\r
- if (oldname == null) {\r
- namePresent = false;\r
- } else {\r
- sq.setName(oldname);\r
- }\r
-\r
- if (!pdbid.equals("")) {\r
- sq.setPDBId(pdbid);\r
- }\r
-\r
- if ((start != null) && (end != null)) {\r
- sq.setStart(start.intValue());\r
- sq.setEnd(end.intValue());\r
- }\r
-\r
- if (sfeatures != null) {\r
- sq.setSequenceFeatures(sfeatures);\r
- }\r
-\r
- return namePresent;\r
- }\r
-\r
- /**
- * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
- * @param i int
- * @return String
- */\r
- public static String unique_name(int i) {\r
- return new String("Sequence" + i);\r
- }\r
-\r
- public static Hashtable uniquify(SequenceI[] sequences, boolean write_names) {\r
- // Generate a safely named sequence set and a hash to recover the sequence names\r
- Hashtable map = new Hashtable();\r
- String[] un_names = new String[sequences.length];\r
-\r
- if (!write_names) {\r
- for (int i = 0; i < sequences.length; i++) {\r
- String safename = new String("Sequence" + i);\r
- map.put(safename, SeqCharacterHash(sequences[i]));\r
-\r
- if (write_names) {\r
- sequences[i].setName(safename);\r
- }\r
- }\r
- }\r
-\r
- return map;\r
- }\r
-\r
- public static boolean deuniquify(Hashtable map, SequenceI[] sequences) {\r
- // recover unsafe sequence names for a sequence set\r
- boolean allfound = true;\r
-\r
- for (int i = 0; i < sequences.length; i++) {\r
- if (map.containsKey(sequences[i].getName())) {\r
- Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());\r
- SeqCharacterUnhash(sequences[i], sqinfo);\r
- } else {\r
- allfound = false;\r
- }\r
- }\r
-\r
- return allfound;\r
- }\r
-}\r
+ */
+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)
+ {
+ 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<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 true if name was not updated from sqinfo Name entry
+ */
+ 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");
+ 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))
+ {
+ 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;
+ }
+
+ /**
+ * 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)
+ {
+ // 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++)
+ {
+ 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)
+ {
+ 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++)
+ unmatched.add(sequences[i]);
+ while (keys.hasMoreElements()) {
+ Object key = keys.nextElement();
+ if (key instanceof String) {
+ 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");
+ }
+ }
+ }
+ 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()))
+ ;
+ 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<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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff