-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.analysis;\r
-\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-/**\r
- * <p>Title: </p>\r
- *\r
- * <p>Description: </p>\r
- *\r
- * <p>Copyright: Copyright (c) 2004</p>\r
- *\r
- * <p>Company: Dundee University</p>\r
- *\r
- * @author not attributable\r
- * @version 1.0\r
- */\r
-public class SeqsetUtils\r
-{\r
-\r
- /**\r
- * Store essential properties of a sequence in a hashtable for later recovery\r
- * Keys are Name, Start, End, SeqFeatures, PdbId\r
- * @param seq SequenceI\r
- * @return Hashtable\r
- */\r
- public static Hashtable SeqCharacterHash(SequenceI seq)\r
- {\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
- Vector sfeat = new Vector();\r
- jalview.datamodel.SequenceFeature[] sfarray=seq.getSequenceFeatures();\r
- if (sfarray!=null && sfarray.length>0) {\r
- for (int i=0;i<sfarray.length;i++)\r
- sfeat.add(sfarray[i]);\r
- }\r
- sqinfo.put("SeqFeatures", sfeat);\r
- sqinfo.put("PdbId",\r
- (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());\r
- sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));\r
- return sqinfo;\r
- }\r
-\r
- /**\r
- * Recover essential properties of a sequence from a hashtable\r
- * TODO: replace these methods with something more elegant.\r
- * @param sq SequenceI\r
- * @param sqinfo Hashtable\r
- * @return boolean true if name was not updated from sqinfo Name entry\r
- */\r
- public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)\r
- {\r
- boolean namePresent = true;\r
- if (sqinfo==null)\r
- return false;\r
- String oldname = (String) sqinfo.get("Name");\r
- Integer start = (Integer) sqinfo.get("Start");\r
- Integer end = (Integer) sqinfo.get("End");\r
- Vector sfeatures = (Vector) sqinfo.get(\r
- "SeqFeatures");\r
- Vector pdbid = (Vector) sqinfo.get("PdbId");\r
- Sequence seqds = (Sequence) sqinfo.get("datasetSequence");\r
- if (oldname == null)\r
- {\r
- namePresent = false;\r
- }\r
- else\r
- {\r
- sq.setName(oldname);\r
- }\r
- if (pdbid!=null && pdbid.size()>0)\r
- {\r
- sq.setPDBId(pdbid);\r
- }\r
-\r
- if ( (start != null) && (end != null))\r
- {\r
- sq.setStart(start.intValue());\r
- sq.setEnd(end.intValue());\r
- }\r
-\r
- if ((sfeatures != null) && (sfeatures.size()>0))\r
- {\r
- SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();\r
- sq.setSequenceFeatures(sfarray);\r
- }\r
-\r
- if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {\r
- sq.setDatasetSequence(seqds);\r
- }\r
-\r
- return namePresent;\r
- }\r
-\r
- /**\r
- * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.\r
- * @param i int\r
- * @return String\r
- */\r
- public static String unique_name(int i)\r
- {\r
- return new String("Sequence" + i);\r
- }\r
-\r
- /**\r
- * Generates a hash of SeqCharacterHash properties for each sequence\r
- * in a sequence set, and optionally renames the sequences to an\r
- * unambiguous 'safe' name.\r
- * @param sequences SequenceI[]\r
- * @param write_names boolean set this to rename each of the sequences to its unique_name(index) name\r
- * @return Hashtable to be passed to @see deuniquify to recover original names (and properties) for renamed sequences\r
- */\r
- public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)\r
- {\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
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- String safename = unique_name(i);\r
- map.put(safename, SeqCharacterHash(sequences[i]));\r
-\r
- if (write_names)\r
- {\r
- sequences[i].setName(safename);\r
- }\r
- }\r
-\r
-\r
- return map;\r
- }\r
- /**\r
- * recover unsafe sequence names and original properties for a sequence\r
- * set using a map generated by @see uniquify(sequences,true)\r
- * @param map Hashtable\r
- * @param sequences SequenceI[]\r
- * @return boolean\r
- */\r
- public static boolean deuniquify(Hashtable map, SequenceI[] sequences)\r
- {\r
- jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);\r
- SequenceI msq = null;\r
- Enumeration keys = map.keys();\r
- Vector unmatched = new Vector();\r
- for (int i=0, j=sequences.length; i<j; i++)\r
- unmatched.add(sequences[i]);\r
- while (keys.hasMoreElements()) {\r
- Object key = keys.nextElement();\r
- if (key instanceof String) {\r
- if ((msq = matcher.findIdMatch((String) key))!=null) {\r
- Hashtable sqinfo = (Hashtable) map.get(key);\r
- unmatched.remove(msq);\r
- SeqCharacterUnhash(msq, sqinfo);\r
- }\r
- else\r
- {\r
- System.err.println("Can't find '"+((String) key)+"' in uniquified alignment");\r
- }\r
- }\r
- }\r
- if (unmatched.size()>0) {\r
- System.err.println("Did not find matches for :");\r
- for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out.println(((SequenceI) i.nextElement()).getName()))\r
- ;\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
- /**\r
- * returns a subset of the sequenceI seuqences,\r
- * including only those that contain at least one residue.\r
- * @param sequences SequenceI[]\r
- * @return SequenceI[]\r
- */\r
- public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences) {\r
- // Identify first row of alignment with residues for prediction\r
- boolean ungapped[] = new boolean[sequences.length];\r
- int msflen=0;\r
- for (int i=0,j=sequences.length; i<j;i++) {\r
- String tempseq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequences[i].getSequence());\r
- if (tempseq.length()==0)\r
- ungapped[i]=false;\r
- else {\r
- ungapped[i]=true;\r
- msflen++;\r
- }\r
- }\r
- if (msflen==0)\r
- return null; // no minimal set\r
- // compose minimal set\r
- SequenceI[] mset = new SequenceI[msflen];\r
- for (int i=0,j=sequences.length,k=0; i<j;i++) {\r
- if (ungapped[i])\r
- mset[k++] = sequences[i];\r
- }\r
- ungapped = null;\r
- return mset;\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>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @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
+ * @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].getSequence());
+ 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 / commitdiff