- public StockholmFile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public StockholmFile(FileParse source) throws IOException\r
- {\r
- super(source);\r
- }\r
-\r
- public void initData()\r
- {\r
- super.initData();\r
- }\r
- /**\r
- * Parse a file in Stockholm format into Jalview's data model using VARNA\r
- * \r
- * @throws IOException\r
- * If there is an error with the input file\r
- */\r
- public void parse_with_VARNA(java.io.File inFile) throws IOException\r
- {\r
- FileReader fr = null;\r
- fr = new FileReader(inFile);\r
-\r
- BufferedReader r = new BufferedReader(fr);\r
- result = null;\r
- try\r
- {\r
- result = RNAFactory.loadSecStrStockholm(r);\r
- } catch (ExceptionUnmatchedClosingParentheses umcp)\r
- {\r
- errormessage = "Unmatched parentheses in annotation. Aborting ("\r
- + umcp.getMessage() + ")";\r
- throw new IOException(umcp);\r
- }\r
- // DEBUG System.out.println("this is the secondary scructure:"\r
- // +result.size());\r
- SequenceI[] seqs = new SequenceI[result.size()];\r
- String id=null;\r
- for (int i = 0; i < result.size(); i++)\r
- {\r
- // DEBUG System.err.println("Processing i'th sequence in Stockholm file")\r
- RNA current = result.get(i);\r
-\r
- String seq = current.getSeq();\r
- String rna = current.getStructDBN(true);\r
- // DEBUG System.out.println(seq);\r
- // DEBUG System.err.println(rna);\r
- int begin = 0;\r
- int end = seq.length() - 1;\r
- id = safeName(getDataName());\r
- seqs[i] = new Sequence(id, seq, begin, end);\r
- String[] annot = new String[rna.length()];\r
- Annotation[] ann = new Annotation[rna.length()];\r
- for (int j = 0; j < rna.length(); j++)\r
- {\r
- annot[j] = rna.substring(j, j + 1);\r
-\r
- }\r
-\r
- for (int k = 0; k < rna.length(); k++)\r
- {\r
- ann[k] = new Annotation(annot[k], "",\r
- jalview.schemes.ResidueProperties.getRNASecStrucState(\r
- annot[k]).charAt(0), 0f);\r
-\r
- }\r
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",\r
- current.getID(), ann);\r
-\r
- seqs[i].addAlignmentAnnotation(align);\r
- seqs[i].setRNA(result.get(i));\r
- this.annotations.addElement(align);\r
- }\r
- this.setSeqs(seqs);\r
-\r
- }\r
-\r
- \r
- /**\r
- * Parse a file in Stockholm format into Jalview's data model. The file has to\r
- * be passed at construction time\r
- * \r
- * @throws IOException\r
- * If there is an error with the input file\r
- */\r
- public void parse() throws IOException\r
- {\r
- StringBuffer treeString = new StringBuffer();\r
- String treeName = null;\r
- // --------------- Variable Definitions -------------------\r
- String line;\r
- String version;\r
- // String id;\r
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
- Hashtable seqs = new Hashtable();\r
- Regex p, r, rend, s, x;\r
- // Temporary line for processing RNA annotation\r
- // String RNAannot = "";\r
-\r
- // ------------------ Parsing File ----------------------\r
- // First, we have to check that this file has STOCKHOLM format, i.e. the\r
- // first line must match\r
- \r
- \r
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
- if (!r.search(nextLine()))\r
- {\r
- throw new IOException(\r
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
- }\r
- else\r
- {\r
- version = r.stringMatched(1);\r
- \r
- // logger.debug("Stockholm version: " + version);\r
- }\r
-\r
- // We define some Regexes here that will be used regularily later\r
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
- // id/from/to\r
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
-\r
- // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
-\r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
-\r
- rend.optimize();\r
- p.optimize();\r
- s.optimize();\r
- r.optimize();\r
- x.optimize();\r
- openparen.optimize();\r
- closeparen.optimize();\r
- \r
- while ((line = nextLine()) != null)\r
- {\r
- if (line.length() == 0)\r
- {\r
- continue;\r
- }\r
- if (rend.search(line))\r
- {\r
- // End of the alignment, pass stuff back\r
- this.noSeqs = seqs.size();\r
- \r
- String seqdb,dbsource = null;\r
- Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam\r
- Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam\r
- if (getAlignmentProperty("AC") != null)\r
- {\r
- String dbType = getAlignmentProperty("AC").toString();\r
- if (pf.search(dbType))\r
- {\r
- // PFAM Alignment - so references are typically from Uniprot\r
- dbsource = "PFAM";\r
- }\r
- else if (rf.search(dbType))\r
- {\r
- dbsource = "RFAM";\r
- }\r
- }\r
- // logger.debug("Number of sequences: " + this.noSeqs);\r
- Enumeration accs = seqs.keys();\r
- while (accs.hasMoreElements())\r
- {\r
- String acc = (String) accs.nextElement();\r
- // logger.debug("Processing sequence " + acc);\r
- String seq = (String) seqs.remove(acc);\r
- if (maxLength < seq.length())\r
- {\r
- maxLength = seq.length();\r
- }\r
- int start = 1;\r
- int end = -1;\r
- String sid = acc;\r
- /*\r
- * Retrieve hash of annotations for this accession Associate\r
- * Annotation with accession\r
- */\r
- Hashtable accAnnotations = null;\r
- \r
- if (seqAnn != null && seqAnn.containsKey(acc))\r
- {\r
- accAnnotations = (Hashtable) seqAnn.remove(acc);\r
- //TODO: add structures to sequence\r
- }\r
- \r
- // Split accession in id and from/to\r
- if (p.search(acc))\r
- {\r
- sid = p.stringMatched(1);\r
- start = Integer.parseInt(p.stringMatched(2));\r
- end = Integer.parseInt(p.stringMatched(3));\r
- }\r
- // logger.debug(sid + ", " + start + ", " + end);\r
- \r
- Sequence seqO = new Sequence(sid, seq, start, end);\r
- // Add Description (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
- {\r
- String desc = (String) accAnnotations.get("DE");\r
- seqO.setDescription((desc == null) ? "" : desc);\r
- }\r
- // Add DB References (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
- {\r
- String dbr = (String) accAnnotations.get("DR");\r
- if (dbr != null && dbr.indexOf(";") > -1)\r
- {\r
- String src = dbr.substring(0, dbr.indexOf(";"));\r
- String acn = dbr.substring(dbr.indexOf(";") + 1);\r
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
- }\r
- } \r
-\r
- if (accAnnotations != null && accAnnotations.containsKey("AC"))\r
- {\r
- if (dbsource != null)\r
- {\r
- String dbr = (String) accAnnotations.get("AC");\r
- if (dbr != null)\r
- {\r
- // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession\r
- guessDatabaseFor(seqO, dbr, dbsource);\r
- \r
- }\r
- }\r
- // else - do what ? add the data anyway and prompt the user to specify what references these are ?\r
- }\r
- \r
- Hashtable features = null;\r
- // We need to adjust the positions of all features to account for gaps\r
- try\r
- {\r
- features = (Hashtable) accAnnotations.remove("features");\r
- } catch (java.lang.NullPointerException e)\r
- {\r
- // loggerwarn("Getting Features for " + acc + ": " +\r
- // e.getMessage());\r
- // continue;\r
- }\r
- // if we have features\r
- if (features != null)\r
- {\r
- int posmap[] = seqO.findPositionMap();\r
- Enumeration i = features.keys();\r
- while (i.hasMoreElements())\r
- {\r
- // TODO: parse out secondary structure annotation as annotation\r
- // row\r
- // TODO: parse out scores as annotation row\r
- // TODO: map coding region to core jalview feature types\r
- String type = i.nextElement().toString();\r
- Hashtable content = (Hashtable) features.remove(type);\r
-\r
- // add alignment annotation for this feature\r
- String key = type2id(type);\r
- if (key != null)\r
- {\r
- if (accAnnotations != null\r
- && accAnnotations.containsKey(key))\r
- {\r
- Vector vv = (Vector) accAnnotations.get(key);\r
- for (int ii = 0; ii < vv.size(); ii++)\r
- {\r
- AlignmentAnnotation an = (AlignmentAnnotation) vv\r
- .elementAt(ii);\r
- seqO.addAlignmentAnnotation(an);\r
- }\r
- }\r
- }\r
-\r
- Enumeration j = content.keys();\r
- while (j.hasMoreElements())\r
- {\r
- String desc = j.nextElement().toString();\r
- String ns = content.get(desc).toString();\r
- char[] byChar = ns.toCharArray();\r
- for (int k = 0; k < byChar.length; k++)\r
- {\r
- char c = byChar[k];\r
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
- // uses\r
- // '.'\r
- // for\r
- // feature\r
- // background\r
- {\r
- int new_pos = posmap[k]; // look up nearest seqeunce\r
- // position to this column\r
- SequenceFeature feat = new SequenceFeature(type, desc,\r
- new_pos, new_pos, 0f, null);\r
- \r
- seqO.addSequenceFeature(feat);\r
- }\r
- }\r
- }\r
- \r
- }\r
- \r
- }\r
- // garbage collect\r
- \r
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
- // + ": " + seq);\r
- this.seqs.addElement(seqO);\r
- }\r
- return; // finished parsing this segment of source\r
- }\r
- else if (!r.search(line))\r
- {\r
- // System.err.println("Found sequence line: " + line);\r
- \r
- // Split sequence in sequence and accession parts\r
- if (!x.search(line))\r
- {\r
- // logger.error("Could not parse sequence line: " + line);\r
- throw new IOException("Could not parse sequence line: " + line);\r
- }\r
- String ns = (String) seqs.get(x.stringMatched(1));\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += x.stringMatched(2);\r
- \r
- seqs.put(x.stringMatched(1), ns);\r
- }\r
- else\r
- {\r
- String annType = r.stringMatched(1);\r
- String annContent = r.stringMatched(2);\r
- \r
- // System.err.println("type:" + annType + " content: " + annContent);\r
- \r
- if (annType.equals("GF"))\r
- {\r
- /*\r
- * Generic per-File annotation, free text Magic features: #=GF NH\r
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
- * \r
- * Compulsory fields: ------------------\r
- * \r
- * AC Accession number: Accession number in form PFxxxxx.version or\r
- * PBxxxxxx. ID Identification: One word name for family. DE\r
- * Definition: Short description of family. AU Author: Authors of the\r
- * entry. SE Source of seed: The source suggesting the seed members\r
- * belong to one family. GA Gathering method: Search threshold to\r
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
- * and domain score of match in the full alignment. NC Noise Cutoff:\r
- * Highest sequence score and domain score of match not in full\r
- * alignment. TP Type: Type of family -- presently Family, Domain,\r
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
- * Alignment Method The order ls and fs hits are aligned to the model\r
- * to build the full align. // End of alignment.\r
- * \r
- * Optional fields: ----------------\r
- * \r
- * DC Database Comment: Comment about database reference. DR Database\r
- * Reference: Reference to external database. RC Reference Comment:\r
- * Comment about literature reference. RN Reference Number: Reference\r
- * Number. RM Reference Medline: Eight digit medline UI number. RT\r
- * Reference Title: Reference Title. RA Reference Author: Reference\r
- * Author RL Reference Location: Journal location. PI Previous\r
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
- * NL Location: Location of nested domains - sequence ID, start and\r
- * end of insert.\r
- * \r
- * Obsolete fields: ----------- AL Alignment method of seed: The\r
- * method used to align the seed members.\r
- */\r
- // Let's save the annotations, maybe we'll be able to do something\r
- // with them later...\r
- Regex an = new Regex("(\\w+)\\s*(.*)");\r
- if (an.search(annContent))\r
- {\r
- if (an.stringMatched(1).equals("NH"))\r
- {\r
- treeString.append(an.stringMatched(2));\r
- }\r
- else if (an.stringMatched(1).equals("TN"))\r
- {\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (getTreeCount() + 1);\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- treeName = an.stringMatched(2);\r
- treeString = new StringBuffer();\r
- }\r
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GS"))\r
- {\r
- // Generic per-Sequence annotation, free text\r
- /*\r
- * Pfam uses these features: Feature Description ---------------------\r
- * ----------- AC <accession> ACcession number DE <freetext>\r
- * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
- * LO <look> Look (Color, etc.)\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String content = s.stringMatched(3);\r
- // TODO: store DR in a vector.\r
- // TODO: store AC according to generic file db annotation.\r
- Hashtable ann;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- ann = new Hashtable();\r
- }\r
- ann.put(type, content);\r
- seqAnn.put(acc, ann);\r
- }\r
- else\r
- {\r
- throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else if (annType.equals("GC"))\r
- {\r
- // Generic per-Column annotation, exactly 1 char per column\r
- // always need a label.\r
- if (x.search(annContent))\r
- {\r
- // parse out and create alignment annotation directly.\r
- parseAnnotationRow(annotations, x.stringMatched(1),\r
- x.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GR"))\r
- {\r
- // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
- // column\r
- /*\r
- * Feature Description Markup letters ------- -----------\r
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
- * or after) [0-2]\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String seq = new String(s.stringMatched(3));\r
- String description = null;\r
- // Check for additional information about the current annotation\r
- // We use a simple string tokenizer here for speed\r
- StringTokenizer sep = new StringTokenizer(seq, " \t");\r
- description = sep.nextToken();\r
- if (sep.hasMoreTokens())\r
- {\r
- seq = sep.nextToken();\r
- }\r
- else\r
- {\r
- seq = description;\r
- description = new String();\r
- }\r
- // sequence id with from-to fields\r
- \r
- Hashtable ann;\r
- // Get an object with all the annotations for this sequence\r
- if (seqAnn.containsKey(acc))\r
- {\r
- // logger.debug("Found annotations for " + acc);\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new annotations holder for " + acc);\r
- ann = new Hashtable();\r
- seqAnn.put(acc, ann);\r
- }\r
- // TODO test structure, call parseAnnotationRow with vector from\r
- // hashtable for specific sequence\r
- Hashtable features;\r
- // Get an object with all the content for an annotation\r
- if (ann.containsKey("features"))\r
- {\r
- // logger.debug("Found features for " + acc);\r
- features = (Hashtable) ann.get("features");\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new features holder for " + acc);\r
- features = new Hashtable();\r
- ann.put("features", features);\r
- }\r
- \r
- Hashtable content;\r
- if (features.containsKey(this.id2type(type)))\r
- {\r
- // logger.debug("Found content for " + this.id2type(type));\r
- content = (Hashtable) features.get(this.id2type(type));\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new content holder for " +\r
- // this.id2type(type));\r
- content = new Hashtable();\r
- features.put(this.id2type(type), content);\r
- }\r
- String ns = (String) content.get(description);\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += seq;\r
- content.put(description, ns);\r
- \r
-// if(type.equals("SS")){\r
- Hashtable strucAnn;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- strucAnn = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- strucAnn = new Hashtable();\r
- }\r
- \r
- Vector newStruc=new Vector();\r
- parseAnnotationRow(newStruc, type,ns);\r
- \r
- strucAnn.put(type, newStruc);\r
- seqAnn.put(acc, strucAnn);\r
- }\r
-// }\r
- else\r
- {\r
- System.err\r
- .println("Warning - couldn't parse sequence annotation row line:\n"\r
- + line);\r
- // throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else\r
- {\r
- throw new IOException("Unknown annotation detected: " + annType\r
- + " " + annContent);\r
- }\r
- }\r
- }\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (1 + getTreeCount());\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- }\r
-\r
-/**\r
- * Demangle an accession string and guess the originating sequence database for a given sequence\r
- * @param seqO sequence to be annotated\r
- * @param dbr Accession string for sequence\r
- * @param dbsource source database for alignment (PFAM or RFAM)\r
- */\r
- private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)\r
- {\r
- DBRefEntry dbrf=null;\r
- List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();\r
- String seqdb="Unknown",sdbac=""+dbr;\r
- int st=-1,en=-1,p;\r
- if ((st=sdbac.indexOf("/"))>-1)\r
- {\r
- String num,range=sdbac.substring(st+1);\r
- sdbac = sdbac.substring(0,st);\r
- if ((p=range.indexOf("-"))>-1)\r
- {\r
- p++;\r
- if (p<range.length())\r
- {\r
- num = range.substring(p).trim();\r
- try {\r
- en = Integer.parseInt(num);\r
- } catch (NumberFormatException x)\r
- {\r
- // could warn here that index is invalid\r
- en = -1;\r
- }\r
- }\r
- } else {\r
- p=range.length();\r
- }\r
- num=range.substring(0,p).trim();\r
- try {\r
- st = Integer.parseInt(num);\r
- } catch (NumberFormatException x)\r
- {\r
- // could warn here that index is invalid\r
- st = -1;\r
- }\r
- }\r
- if (dbsource.equals("PFAM")) {\r
- seqdb = "UNIPROT";\r
- if (sdbac.indexOf(".")>-1)\r
- {\r
- // strip of last subdomain\r
- sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
- if (dbr!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- } else {\r
- seqdb = "EMBL"; // total guess - could be ENA, or something else these days\r
- if (sdbac.indexOf(".")>-1)\r
- {\r
- // strip off last subdomain\r
- sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- \r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- if (st!=-1 && en!=-1)\r
- {\r
- for (DBRefEntry d:dbrs)\r
- {\r
- jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);\r
- jalview.datamodel.Mapping mping = new Mapping(mp);\r
- d.setMap(mping);\r
- }\r
- }\r
- }\r
-\r
- protected static AlignmentAnnotation parseAnnotationRow(\r
- Vector annotation, String label, String annots)\r
- {\r
- String convert1, convert2 = null;\r
-\r
- // Convert all bracket types to parentheses\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
-\r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
-\r
- convert1 = openparen.replaceAll(annots);\r
- convert2 = closeparen.replaceAll(convert1);\r
- annots = convert2;\r
-\r
- String type = label;\r
- if (label.contains("_cons"))\r
- {\r
- type = (label.indexOf("_cons") == label.length() - 5) ? label\r
- .substring(0, label.length() - 5) : label;\r
- }\r
- boolean ss = false;\r
- type = id2type(type);\r
- if (type.equals("secondary structure"))\r
- {\r
- ss = true;\r
- }\r
- // decide on secondary structure or not.\r
- Annotation[] els = new Annotation[annots.length()];\r
- for (int i = 0; i < annots.length(); i++)\r
- {\r
- String pos = annots.substring(i, i + 1);\r
- Annotation ann;\r
- ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
- // be written out\r
- if (ss)\r
- {\r
- if (detectbrackets.search(pos))\r
- {\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getRNASecStrucState(pos).charAt(0);\r
- }\r
- else\r
- {\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getDssp3state(pos).charAt(0);\r
- }\r
-\r
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
- {\r
- ann.displayCharacter = ""; // null; // " ";\r
- }\r
- else\r
- {\r
- ann.displayCharacter = " " + ann.displayCharacter;\r
- }\r
- }\r
-\r
- els[i] = ann;\r
- }\r
- AlignmentAnnotation annot = null;\r
- Enumeration e = annotation.elements();\r
- while (e.hasMoreElements())\r
- {\r
- annot = (AlignmentAnnotation) e.nextElement();\r
- if (annot.label.equals(type))\r
- break;\r
- annot = null;\r
- }\r
- if (annot == null)\r
- {\r
- annot = new AlignmentAnnotation(type, type, els);\r
- annotation.addElement(annot);\r
- }\r
- else\r
- {\r
- Annotation[] anns = new Annotation[annot.annotations.length\r
- + els.length];\r
- System.arraycopy(annot.annotations, 0, anns, 0,\r
- annot.annotations.length);\r
- System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
- annot.annotations = anns;\r
- // System.out.println("else: ");\r
- }\r
- return annot;\r
- }\r
-\r
- public String print(SequenceI[] s)