2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
26 import jalview.analysis.Rna;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.DBRefEntry;
31 import jalview.datamodel.Mapping;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceI;
35 import jalview.schemes.ResidueProperties;
36 import jalview.util.Comparison;
37 import jalview.util.Format;
38 import jalview.util.MessageManager;
40 import java.io.BufferedReader;
41 import java.io.FileReader;
42 import java.io.IOException;
43 import java.util.ArrayList;
44 import java.util.Enumeration;
45 import java.util.Hashtable;
46 import java.util.LinkedHashMap;
47 import java.util.List;
49 import java.util.Vector;
51 import com.stevesoft.pat.Regex;
53 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
54 import fr.orsay.lri.varna.factories.RNAFactory;
55 import fr.orsay.lri.varna.models.rna.RNA;
57 // import org.apache.log4j.*;
60 * This class is supposed to parse a Stockholm format file into Jalview There
61 * are TODOs in this class: we do not know what the database source and version
62 * is for the file when parsing the #GS= AC tag which associates accessions with
63 * sequences. Database references are also not parsed correctly: a separate
64 * reference string parser must be added to parse the database reference form
65 * into Jalview's local representation.
67 * @author bsb at sanger.ac.uk
68 * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
69 * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as
71 * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
72 * @version 0.3 + jalview mods
75 public class StockholmFile extends AlignFile
77 private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
79 private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
81 public static final Regex DETECT_BRACKETS = new Regex(
82 "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
84 StringBuffer out; // output buffer
88 public StockholmFile()
93 * Creates a new StockholmFile object for output.
95 public StockholmFile(AlignmentI al)
100 public StockholmFile(String inFile, DataSourceType type)
106 public StockholmFile(FileParse source) throws IOException
112 public void initData()
118 * Parse a file in Stockholm format into Jalview's data model using VARNA
120 * @throws IOException
121 * If there is an error with the input file
123 public void parse_with_VARNA(java.io.File inFile) throws IOException
125 FileReader fr = null;
126 fr = new FileReader(inFile);
128 BufferedReader r = new BufferedReader(fr);
129 List<RNA> result = null;
132 result = RNAFactory.loadSecStrStockholm(r);
133 } catch (ExceptionUnmatchedClosingParentheses umcp)
135 errormessage = "Unmatched parentheses in annotation. Aborting ("
136 + umcp.getMessage() + ")";
137 throw new IOException(umcp);
139 // DEBUG System.out.println("this is the secondary scructure:"
141 SequenceI[] seqs = new SequenceI[result.size()];
143 for (int i = 0; i < result.size(); i++)
145 // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
146 RNA current = result.get(i);
148 String seq = current.getSeq();
149 String rna = current.getStructDBN(true);
150 // DEBUG System.out.println(seq);
151 // DEBUG System.err.println(rna);
153 int end = seq.length() - 1;
154 id = safeName(getDataName());
155 seqs[i] = new Sequence(id, seq, begin, end);
156 String[] annot = new String[rna.length()];
157 Annotation[] ann = new Annotation[rna.length()];
158 for (int j = 0; j < rna.length(); j++)
160 annot[j] = rna.substring(j, j + 1);
164 for (int k = 0; k < rna.length(); k++)
166 ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
167 annot[k]).charAt(0), 0f);
170 AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
171 current.getID(), ann);
173 seqs[i].addAlignmentAnnotation(align);
174 seqs[i].setRNA(result.get(i));
175 this.annotations.addElement(align);
182 * Parse a file in Stockholm format into Jalview's data model. The file has to
183 * be passed at construction time
185 * @throws IOException
186 * If there is an error with the input file
189 public void parse() throws IOException
191 StringBuffer treeString = new StringBuffer();
192 String treeName = null;
193 // --------------- Variable Definitions -------------------
197 Hashtable seqAnn = new Hashtable(); // Sequence related annotations
198 LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
199 Regex p, r, rend, s, x;
200 // Temporary line for processing RNA annotation
201 // String RNAannot = "";
203 // ------------------ Parsing File ----------------------
204 // First, we have to check that this file has STOCKHOLM format, i.e. the
205 // first line must match
207 r = new Regex("# STOCKHOLM ([\\d\\.]+)");
208 if (!r.search(nextLine()))
210 throw new IOException(
212 .getString("exception.stockholm_invalid_format"));
216 version = r.stringMatched(1);
218 // logger.debug("Stockholm version: " + version);
221 // We define some Regexes here that will be used regularily later
222 rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
223 p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
225 s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
226 r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
227 x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
229 // Convert all bracket types to parentheses (necessary for passing to VARNA)
230 Regex openparen = new Regex("(<|\\[)", "(");
231 Regex closeparen = new Regex("(>|\\])", ")");
233 // Detect if file is RNA by looking for bracket types
234 Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
241 openparen.optimize();
242 closeparen.optimize();
244 while ((line = nextLine()) != null)
246 if (line.length() == 0)
250 if (rend.search(line))
252 // End of the alignment, pass stuff back
253 this.noSeqs = seqs.size();
255 String seqdb, dbsource = null;
256 Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
257 Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
258 if (getAlignmentProperty("AC") != null)
260 String dbType = getAlignmentProperty("AC").toString();
261 if (pf.search(dbType))
263 // PFAM Alignment - so references are typically from Uniprot
266 else if (rf.search(dbType))
271 // logger.debug("Number of sequences: " + this.noSeqs);
272 for (Map.Entry<String, String> skey : seqs.entrySet())
274 // logger.debug("Processing sequence " + acc);
275 String acc = skey.getKey();
276 String seq = skey.getValue();
277 if (maxLength < seq.length())
279 maxLength = seq.length();
285 * Retrieve hash of annotations for this accession Associate
286 * Annotation with accession
288 Hashtable accAnnotations = null;
290 if (seqAnn != null && seqAnn.containsKey(acc))
292 accAnnotations = (Hashtable) seqAnn.remove(acc);
293 // TODO: add structures to sequence
296 // Split accession in id and from/to
299 sid = p.stringMatched(1);
300 start = Integer.parseInt(p.stringMatched(2));
301 end = Integer.parseInt(p.stringMatched(3));
303 // logger.debug(sid + ", " + start + ", " + end);
305 Sequence seqO = new Sequence(sid, seq, start, end);
306 // Add Description (if any)
307 if (accAnnotations != null && accAnnotations.containsKey("DE"))
309 String desc = (String) accAnnotations.get("DE");
310 seqO.setDescription((desc == null) ? "" : desc);
312 // Add DB References (if any)
313 if (accAnnotations != null && accAnnotations.containsKey("DR"))
315 String dbr = (String) accAnnotations.get("DR");
316 if (dbr != null && dbr.indexOf(";") > -1)
318 String src = dbr.substring(0, dbr.indexOf(";"));
319 String acn = dbr.substring(dbr.indexOf(";") + 1);
320 jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
324 if (accAnnotations != null && accAnnotations.containsKey("AC"))
326 if (dbsource != null)
328 String dbr = (String) accAnnotations.get("AC");
331 // we could get very clever here - but for now - just try to
332 // guess accession type from source of alignment plus structure
334 guessDatabaseFor(seqO, dbr, dbsource);
338 // else - do what ? add the data anyway and prompt the user to
339 // specify what references these are ?
342 Hashtable features = null;
343 // We need to adjust the positions of all features to account for gaps
346 features = (Hashtable) accAnnotations.remove("features");
347 } catch (java.lang.NullPointerException e)
349 // loggerwarn("Getting Features for " + acc + ": " +
353 // if we have features
354 if (features != null)
356 int posmap[] = seqO.findPositionMap();
357 Enumeration i = features.keys();
358 while (i.hasMoreElements())
360 // TODO: parse out secondary structure annotation as annotation
362 // TODO: parse out scores as annotation row
363 // TODO: map coding region to core jalview feature types
364 String type = i.nextElement().toString();
365 Hashtable content = (Hashtable) features.remove(type);
367 // add alignment annotation for this feature
368 String key = type2id(type);
371 * have we added annotation rows for this type ?
373 boolean annotsAdded = false;
376 if (accAnnotations != null
377 && accAnnotations.containsKey(key))
379 Vector vv = (Vector) accAnnotations.get(key);
380 for (int ii = 0; ii < vv.size(); ii++)
383 AlignmentAnnotation an = (AlignmentAnnotation) vv
385 seqO.addAlignmentAnnotation(an);
391 Enumeration j = content.keys();
392 while (j.hasMoreElements())
394 String desc = j.nextElement().toString();
395 if ("annotations".equals(desc) && annotsAdded)
397 // don't add features if we already added an annotation row
400 String ns = content.get(desc).toString();
401 char[] byChar = ns.toCharArray();
402 for (int k = 0; k < byChar.length; k++)
405 if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
412 int new_pos = posmap[k]; // look up nearest seqeunce
413 // position to this column
414 SequenceFeature feat = new SequenceFeature(type, desc,
415 new_pos, new_pos, 0f, null);
417 seqO.addSequenceFeature(feat);
427 // logger.debug("Adding seq " + acc + " from " + start + " to " + end
429 this.seqs.addElement(seqO);
431 return; // finished parsing this segment of source
433 else if (!r.search(line))
435 // System.err.println("Found sequence line: " + line);
437 // Split sequence in sequence and accession parts
440 // logger.error("Could not parse sequence line: " + line);
441 throw new IOException(MessageManager.formatMessage(
442 "exception.couldnt_parse_sequence_line",
443 new String[] { line }));
445 String ns = seqs.get(x.stringMatched(1));
450 ns += x.stringMatched(2);
452 seqs.put(x.stringMatched(1), ns);
456 String annType = r.stringMatched(1);
457 String annContent = r.stringMatched(2);
459 // System.err.println("type:" + annType + " content: " + annContent);
461 if (annType.equals("GF"))
464 * Generic per-File annotation, free text Magic features: #=GF NH
465 * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
466 * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
468 * Compulsory fields: ------------------
470 * AC Accession number: Accession number in form PFxxxxx.version or
471 * PBxxxxxx. ID Identification: One word name for family. DE
472 * Definition: Short description of family. AU Author: Authors of the
473 * entry. SE Source of seed: The source suggesting the seed members
474 * belong to one family. GA Gathering method: Search threshold to
475 * build the full alignment. TC Trusted Cutoff: Lowest sequence score
476 * and domain score of match in the full alignment. NC Noise Cutoff:
477 * Highest sequence score and domain score of match not in full
478 * alignment. TP Type: Type of family -- presently Family, Domain,
479 * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
480 * Alignment Method The order ls and fs hits are aligned to the model
481 * to build the full align. // End of alignment.
483 * Optional fields: ----------------
485 * DC Database Comment: Comment about database reference. DR Database
486 * Reference: Reference to external database. RC Reference Comment:
487 * Comment about literature reference. RN Reference Number: Reference
488 * Number. RM Reference Medline: Eight digit medline UI number. RT
489 * Reference Title: Reference Title. RA Reference Author: Reference
490 * Author RL Reference Location: Journal location. PI Previous
491 * identifier: Record of all previous ID lines. KW Keywords: Keywords.
492 * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
493 * NL Location: Location of nested domains - sequence ID, start and
496 * Obsolete fields: ----------- AL Alignment method of seed: The
497 * method used to align the seed members.
499 // Let's save the annotations, maybe we'll be able to do something
500 // with them later...
501 Regex an = new Regex("(\\w+)\\s*(.*)");
502 if (an.search(annContent))
504 if (an.stringMatched(1).equals("NH"))
506 treeString.append(an.stringMatched(2));
508 else if (an.stringMatched(1).equals("TN"))
510 if (treeString.length() > 0)
512 if (treeName == null)
514 treeName = "Tree " + (getTreeCount() + 1);
516 addNewickTree(treeName, treeString.toString());
518 treeName = an.stringMatched(2);
519 treeString = new StringBuffer();
521 setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
524 else if (annType.equals("GS"))
526 // Generic per-Sequence annotation, free text
528 * Pfam uses these features: Feature Description ---------------------
529 * ----------- AC <accession> ACcession number DE <freetext>
530 * DEscription DR <db>; <accession>; Database Reference OS <organism>
531 * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
532 * LO <look> Look (Color, etc.)
534 if (s.search(annContent))
536 String acc = s.stringMatched(1);
537 String type = s.stringMatched(2);
538 String content = s.stringMatched(3);
539 // TODO: store DR in a vector.
540 // TODO: store AC according to generic file db annotation.
542 if (seqAnn.containsKey(acc))
544 ann = (Hashtable) seqAnn.get(acc);
548 ann = new Hashtable();
550 ann.put(type, content);
551 seqAnn.put(acc, ann);
555 // throw new IOException("Error parsing " + line);
556 System.err.println(">> missing annotation: " + line);
559 else if (annType.equals("GC"))
561 // Generic per-Column annotation, exactly 1 char per column
562 // always need a label.
563 if (x.search(annContent))
565 // parse out and create alignment annotation directly.
566 parseAnnotationRow(annotations, x.stringMatched(1),
570 else if (annType.equals("GR"))
572 // Generic per-Sequence AND per-Column markup, exactly 1 char per
575 * Feature Description Markup letters ------- -----------
576 * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
577 * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
578 * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
579 * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
582 if (s.search(annContent))
584 String acc = s.stringMatched(1);
585 String type = s.stringMatched(2);
586 String oseq = s.stringMatched(3);
588 * copy of annotation field that may be processed into whitespace chunks
590 String seq = new String(oseq);
593 // Get an object with all the annotations for this sequence
594 if (seqAnn.containsKey(acc))
596 // logger.debug("Found annotations for " + acc);
597 ann = (Hashtable) seqAnn.get(acc);
601 // logger.debug("Creating new annotations holder for " + acc);
602 ann = new Hashtable();
603 seqAnn.put(acc, ann);
606 // // start of block for appending annotation lines for wrapped
608 // TODO test structure, call parseAnnotationRow with vector from
609 // hashtable for specific sequence
612 // Get an object with all the content for an annotation
613 if (ann.containsKey("features"))
615 // logger.debug("Found features for " + acc);
616 features = (Hashtable) ann.get("features");
620 // logger.debug("Creating new features holder for " + acc);
621 features = new Hashtable();
622 ann.put("features", features);
626 if (features.containsKey(this.id2type(type)))
628 // logger.debug("Found content for " + this.id2type(type));
629 content = (Hashtable) features.get(this.id2type(type));
633 // logger.debug("Creating new content holder for " +
634 // this.id2type(type));
635 content = new Hashtable();
636 features.put(this.id2type(type), content);
638 String ns = (String) content.get("annotation");
644 // finally, append the annotation line
646 content.put("annotation", ns);
647 // // end of wrapped annotation block.
648 // // Now a new row is created with the current set of data
651 if (seqAnn.containsKey(acc))
653 strucAnn = (Hashtable) seqAnn.get(acc);
657 strucAnn = new Hashtable();
660 Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
661 parseAnnotationRow(newStruc, type, ns);
662 for (AlignmentAnnotation alan : newStruc)
664 alan.visible = false;
666 // new annotation overwrites any existing annotation...
668 strucAnn.put(type, newStruc);
669 seqAnn.put(acc, strucAnn);
675 .println("Warning - couldn't parse sequence annotation row line:\n"
677 // throw new IOException("Error parsing " + line);
682 throw new IOException(MessageManager.formatMessage(
683 "exception.unknown_annotation_detected", new String[] {
684 annType, annContent }));
688 if (treeString.length() > 0)
690 if (treeName == null)
692 treeName = "Tree " + (1 + getTreeCount());
694 addNewickTree(treeName, treeString.toString());
699 * Demangle an accession string and guess the originating sequence database
700 * for a given sequence
703 * sequence to be annotated
705 * Accession string for sequence
707 * source database for alignment (PFAM or RFAM)
709 private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
711 DBRefEntry dbrf = null;
712 List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
713 String seqdb = "Unknown", sdbac = "" + dbr;
714 int st = -1, en = -1, p;
715 if ((st = sdbac.indexOf("/")) > -1)
717 String num, range = sdbac.substring(st + 1);
718 sdbac = sdbac.substring(0, st);
719 if ((p = range.indexOf("-")) > -1)
722 if (p < range.length())
724 num = range.substring(p).trim();
727 en = Integer.parseInt(num);
728 } catch (NumberFormatException x)
730 // could warn here that index is invalid
739 num = range.substring(0, p).trim();
742 st = Integer.parseInt(num);
743 } catch (NumberFormatException x)
745 // could warn here that index is invalid
749 if (dbsource.equals("PFAM"))
752 if (sdbac.indexOf(".") > -1)
754 // strip of last subdomain
755 sdbac = sdbac.substring(0, sdbac.indexOf("."));
756 dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
763 dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
772 seqdb = "EMBL"; // total guess - could be ENA, or something else these
774 if (sdbac.indexOf(".") > -1)
776 // strip off last subdomain
777 sdbac = sdbac.substring(0, sdbac.indexOf("."));
778 dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
786 dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
793 if (st != -1 && en != -1)
795 for (DBRefEntry d : dbrs)
797 jalview.util.MapList mp = new jalview.util.MapList(new int[] {
798 seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
799 jalview.datamodel.Mapping mping = new Mapping(mp);
805 protected static AlignmentAnnotation parseAnnotationRow(
806 Vector<AlignmentAnnotation> annotation, String label,
809 String convert1, convert2 = null;
811 // convert1 = OPEN_PAREN.replaceAll(annots);
812 // convert2 = CLOSE_PAREN.replaceAll(convert1);
813 // annots = convert2;
816 if (label.contains("_cons"))
818 type = (label.indexOf("_cons") == label.length() - 5) ? label
819 .substring(0, label.length() - 5) : label;
821 boolean ss = false, posterior = false;
822 type = id2type(type);
823 if (type.equalsIgnoreCase("secondary structure"))
827 if (type.equalsIgnoreCase("posterior probability"))
831 // decide on secondary structure or not.
832 Annotation[] els = new Annotation[annots.length()];
833 for (int i = 0; i < annots.length(); i++)
835 String pos = annots.substring(i, i + 1);
837 ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
841 // if (" .-_".indexOf(pos) == -1)
843 if (DETECT_BRACKETS.search(pos))
845 ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
846 ann.displayCharacter = "" + pos.charAt(0);
850 ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
853 if (ann.secondaryStructure == pos.charAt(0))
855 ann.displayCharacter = ""; // null; // " ";
859 ann.displayCharacter = " " + ann.displayCharacter;
865 if (posterior && !ann.isWhitespace()
866 && !Comparison.isGap(pos.charAt(0)))
869 // symbol encodes values - 0..*==0..10
870 if (pos.charAt(0) == '*')
876 val = pos.charAt(0) - '0';
887 AlignmentAnnotation annot = null;
888 Enumeration<AlignmentAnnotation> e = annotation.elements();
889 while (e.hasMoreElements())
891 annot = e.nextElement();
892 if (annot.label.equals(type))
900 annot = new AlignmentAnnotation(type, type, els);
901 annotation.addElement(annot);
905 Annotation[] anns = new Annotation[annot.annotations.length
907 System.arraycopy(annot.annotations, 0, anns, 0,
908 annot.annotations.length);
909 System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
910 annot.annotations = anns;
911 // System.out.println("else: ");
917 public String print(SequenceI[] s, boolean jvSuffix)
919 out = new StringBuffer();
920 out.append("# STOCKHOLM 1.0");
923 // find max length of id
927 Hashtable dataRef = null;
928 while ((in < s.length) && (s[in] != null))
930 String tmp = printId(s[in], jvSuffix);
931 if (s[in].getSequence().length > max)
933 max = s[in].getSequence().length;
936 if (tmp.length() > maxid)
938 maxid = tmp.length();
940 if (s[in].getDBRefs() != null)
942 for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
946 dataRef = new Hashtable();
949 String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
951 + s[in].getDBRefs()[idb].getAccessionId().toString();
952 dataRef.put(tmp, datAs1);
960 // output database type
961 if (al.getProperties() != null)
963 if (!al.getProperties().isEmpty())
965 Enumeration key = al.getProperties().keys();
966 Enumeration val = al.getProperties().elements();
967 while (key.hasMoreElements())
969 out.append("#=GF " + key.nextElement() + " " + val.nextElement());
975 // output database accessions
978 Enumeration en = dataRef.keys();
979 while (en.hasMoreElements())
981 Object idd = en.nextElement();
982 String type = (String) dataRef.remove(idd);
983 out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS "
984 + idd.toString() + " "));
985 if (type.contains("PFAM") || type.contains("RFAM"))
988 out.append(" AC " + type.substring(type.indexOf(";") + 1));
992 out.append(" DR " + type + " ");
998 // output annotations
999 while (i < s.length && s[i] != null)
1001 AlignmentAnnotation[] alAnot = s[i].getAnnotation();
1005 for (int j = 0; j < alAnot.length; j++)
1008 String key = type2id(alAnot[j].label);
1009 boolean isrna = alAnot[j].isValidStruc();
1013 // hardwire to secondary structure if there is RNA secondary
1014 // structure on the annotation
1023 // out.append("#=GR ");
1024 out.append(new Format("%-" + maxid + "s").form("#=GR "
1025 + printId(s[i], jvSuffix) + " " + key + " "));
1026 ann = alAnot[j].annotations;
1028 for (int k = 0; k < ann.length; k++)
1030 seq += outputCharacter(key, k, isrna, ann, s[i]);
1033 out.append(newline);
1037 out.append(new Format("%-" + maxid + "s")
1038 .form(printId(s[i], jvSuffix) + " "));
1039 out.append(s[i].getSequenceAsString());
1040 out.append(newline);
1044 // alignment annotation
1045 AlignmentAnnotation aa;
1046 if (al.getAlignmentAnnotation() != null)
1048 for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
1050 aa = al.getAlignmentAnnotation()[ia];
1051 if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
1058 if (aa.label.equals("seq"))
1064 key = type2id(aa.label.toLowerCase());
1071 label = key + "_cons";
1078 label = label.replace(" ", "_");
1080 out.append(new Format("%-" + maxid + "s").form("#=GC " + label
1082 boolean isrna = aa.isValidStruc();
1083 for (int j = 0; j < aa.annotations.length; j++)
1085 seq += outputCharacter(key, j, isrna, aa.annotations, null);
1088 out.append(newline);
1093 out.append(newline);
1095 return out.toString();
1099 * add an annotation character to the output row
1108 private char outputCharacter(String key, int k, boolean isrna,
1109 Annotation[] ann, SequenceI sequenceI)
1112 Annotation annot = ann[k];
1113 String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
1114 .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
1115 if (key != null && key.equals("SS"))
1119 // sensible gap character
1124 // valid secondary structure AND no alternative label (e.g. ' B')
1125 if (annot.secondaryStructure > ' ' && ch.length() < 2)
1127 return annot.secondaryStructure;
1132 if (ch.length() == 0)
1136 else if (ch.length() == 1)
1140 else if (ch.length() > 1)
1147 public String print()
1149 out = new StringBuffer();
1150 out.append("# STOCKHOLM 1.0");
1151 out.append(newline);
1152 print(getSeqsAsArray(), false);
1155 out.append(newline);
1156 return out.toString();
1159 private static Hashtable typeIds = null;
1163 if (typeIds == null)
1165 typeIds = new Hashtable();
1166 typeIds.put("SS", "Secondary Structure");
1167 typeIds.put("SA", "Surface Accessibility");
1168 typeIds.put("TM", "transmembrane");
1169 typeIds.put("PP", "Posterior Probability");
1170 typeIds.put("LI", "ligand binding");
1171 typeIds.put("AS", "active site");
1172 typeIds.put("IN", "intron");
1173 typeIds.put("IR", "interacting residue");
1174 typeIds.put("AC", "accession");
1175 typeIds.put("OS", "organism");
1176 typeIds.put("CL", "class");
1177 typeIds.put("DE", "description");
1178 typeIds.put("DR", "reference");
1179 typeIds.put("LO", "look");
1180 typeIds.put("RF", "Reference Positions");
1185 protected static String id2type(String id)
1187 if (typeIds.containsKey(id))
1189 return (String) typeIds.get(id);
1191 System.err.println("Warning : Unknown Stockholm annotation type code "
1196 protected static String type2id(String type)
1199 Enumeration e = typeIds.keys();
1200 while (e.hasMoreElements())
1202 Object ll = e.nextElement();
1203 if (typeIds.get(ll).toString().equalsIgnoreCase(type))
1213 System.err.println("Warning : Unknown Stockholm annotation type: "
1219 * make a friendly ID string.
1222 * @return truncated dataName to after last '/'
1224 private String safeName(String dataName)
1227 while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
1229 dataName = dataName.substring(b + 1).trim();
1232 int e = (dataName.length() - dataName.indexOf(".")) + 1;
1233 dataName = dataName.substring(1, e).trim();