-package jalview.analysis;
-
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-
-/**
- * <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()));
- sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
- sqinfo.put("PdbId", (seq.getPDBId()!=null) ? seq.getPDBId() : new String("") );
- 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
- */
- public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {
- boolean namePresent = true;
- 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)
- namePresent = false;
- else
- sq.setName(oldname);
- if (!pdbid.equals(""))
- sq.setPDBId(pdbid);
-
- if ((start!=null) && (end!=null)) {
- sq.setStart(start.intValue());
- sq.setEnd(end.intValue());
- }
- if (sfeatures!=null)
- sq.setSequenceFeatures(sfeatures);
- 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);
- }
-
- 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)
-
- for (int i = 0; i < sequences.length; i++)
- {
- String safename = new String("Sequence" + i);
- map.put(safename, SeqCharacterHash(sequences[i]));
- if (write_names)
- sequences[i].setName(safename);
- }
- return map;
- }
-
- 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++)
- {
- if (map.containsKey(sequences[i].getName()))
- {
- Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
- SeqCharacterUnhash(sequences[i], sqinfo);
- }
- else
- {
- allfound = false;
- }
- }
- return allfound;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
git://source.jalview.org / jalview.git / blobdiff