-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-/*\r
- * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import javax.xml.parsers.ParserConfigurationException;\r
-\r
-import org.xml.sax.SAXException;\r
-\r
-import com.stevesoft.pat.*;\r
-\r
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
-import fr.orsay.lri.varna.factories.RNAFactory;\r
-import fr.orsay.lri.varna.models.rna.RNA;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.Rna;\r
-\r
-// import org.apache.log4j.*;\r
-\r
-/**\r
- * This class is supposed to parse a Stockholm format file into Jalview There\r
- * are TODOs in this class: we do not know what the database source and version\r
- * is for the file when parsing the #GS= AC tag which associates accessions with\r
- * sequences. Database references are also not parsed correctly: a separate\r
- * reference string parser must be added to parse the database reference form\r
- * into Jalview's local representation.\r
- * \r
- * @author bsb at sanger.ac.uk\r
- * @version 0.3 + jalview mods\r
- * \r
- */\r
-public class StockholmFile extends AlignFile\r
-{\r
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
- protected ArrayList<RNA> result;\r
- public String id;\r
- \r
- public StockholmFile()\r
- {\r
- }\r
-\r
- public StockholmFile(String inFile, String type) throws Exception \r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public StockholmFile(FileParse source) throws Exception \r
- {\r
- super(source);\r
- }\r
-\r
- public void initData()\r
- {\r
- super.initData();\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
- * @throws ExceptionUnmatchedClosingParentheses \r
- */\r
- public void parse()\r
- {\r
- FileReader fr = null;\r
- fr = new FileReader(inFile); \r
-\r
- BufferedReader r = new BufferedReader (fr);\r
- result = RNAFactory.loadSecStrStockholm(r);\r
- System.out.println("this is the secondary scructure:" +result.size());\r
- SequenceI[] seqs = new SequenceI[result.size()];\r
- System.out.println(type); //the type is "File"\r
- System.out.println(inFile );//inFile is the path\r
- for(int i=0;i<result.size();i++)\r
- {\r
- RNA current = result.get(i);\r
- \r
- System.out.println(current.getSeq());\r
- //System.out.println(result.get(i).getStructBPSEQ());\r
- System.out.println(result.get(i).getStructDBN(true));\r
- System.out.println(i);\r
- String rna =current.getStructDBN(true);\r
- String seq = current.getSeq();\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], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);\r
- \r
- }\r
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",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 = 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
-// // 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
-//\r
-// this.noSeqs = seqs.size();\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\r
-// * Associate 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
-// // seqO.addDBRef(dbref);\r
-// }\r
-// } \r
-// if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
-// {\r
-// Vector v = (Vector) accAnnotations.get("SS");\r
-// \r
-// for (int i = 0; i < v.size(); i++)\r
-// {\r
-// AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
-// seqO.addAlignmentAnnotation(an);\r
-// //annotations.add(an);\r
-// }\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
-// 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 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
-//
-// 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
- protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
- 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.indexOf("_cons") == label.length() - 5) ? label\r
- .substring(0, label.length() - 5) : label;\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 static String print(SequenceI[] s)\r
- {\r
- return "not yet implemented";\r
- }\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-\r
- private static Hashtable typeIds = null;\r
- static\r
- {\r
- if (typeIds == null)\r
- {\r
- typeIds = new Hashtable();\r
- typeIds.put("SS", "secondary structure");\r
- typeIds.put("SA", "surface accessibility");\r
- typeIds.put("TM", "transmembrane");\r
- typeIds.put("PP", "posterior probability");\r
- typeIds.put("LI", "ligand binding");\r
- typeIds.put("AS", "active site");\r
- typeIds.put("IN", "intron");\r
- typeIds.put("IR", "interacting residue");\r
- typeIds.put("AC", "accession");\r
- typeIds.put("OS", "organism");\r
- typeIds.put("CL", "class");\r
- typeIds.put("DE", "description");\r
- typeIds.put("DR", "reference");\r
- typeIds.put("LO", "look");\r
- typeIds.put("RF", "reference positions");\r
-\r
- }\r
- }\r
-\r
- protected static String id2type(String id)\r
- {\r
- if (typeIds.containsKey(id))\r
- {\r
- return (String) typeIds.get(id);\r
- }\r
- System.err.println("Warning : Unknown Stockholm annotation type code "\r
- + id);\r
- return id;\r
- }\r
- /**\r
- * //ssline is complete secondary structure line private AlignmentAnnotation\r
- * addHelices(Vector annotation, String label, String ssline) {\r
- * \r
- * // decide on secondary structure or not. Annotation[] els = new\r
- * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {\r
- * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new\r
- * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
- * \r
- * ann.secondaryStructure =\r
- * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);\r
- * \r
- * ann.displayCharacter = "x" + ann.displayCharacter;\r
- * \r
- * System.out.println(ann.displayCharacter);\r
- * \r
- * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =\r
- * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =\r
- * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))\r
- * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =\r
- * new AlignmentAnnotation(type, type, els);\r
- * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new\r
- * Annotation[helicesAnnot.annotations.length + els.length];\r
- * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,\r
- * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,\r
- * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =\r
- * anns; }\r
- * \r
- * helicesAnnot.features = Rna.GetBasePairs(ssline);\r
- * Rna.HelixMap(helicesAnnot.features);\r
- * \r
- * \r
- * return helicesAnnot; }\r
- * \r
- */\r
- /**\r
- * make a friendly ID string.\r
- * \r
- * @param dataName\r
- * @return truncated dataName to after last '/'\r
- */\r
- private String safeName(String dataName)\r
- {\r
- int b = 0;\r
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )\r
- { \r
- dataName = dataName.substring(b + 1).trim();\r
- \r
- }\r
- int e = (dataName.length() - dataName.indexOf("."))+1;\r
- dataName = dataName.substring(1,e).trim();\r
- return dataName;\r
- }\r
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+/*
+ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
+ */
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
+
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.Rna;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
+/**
+ * This class is supposed to parse a Stockholm format file into Jalview There
+ * are TODOs in this class: we do not know what the database source and version
+ * is for the file when parsing the #GS= AC tag which associates accessions with
+ * sequences. Database references are also not parsed correctly: a separate
+ * reference string parser must be added to parse the database reference form
+ * into Jalview's local representation.
+ *
+ * @author bsb at sanger.ac.uk
+ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
+ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as
+ * stockholm)
+ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
+ * @version 0.3 + jalview mods
+ *
+ */
+public class StockholmFile extends AlignFile
+{
+ private static final String ANNOTATION = "annotation";
+
+ // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ //
+ // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+
+ public static final Regex DETECT_BRACKETS = new Regex(
+ "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
+
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using
+ // NOT_RNASS first.
+ public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+
+ // use the following regex to decide an annotations (whole) line is NOT an RNA
+ // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
+ private static final Regex NOT_RNASS = new Regex(
+ "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$");
+
+ StringBuffer out; // output buffer
+
+ AlignmentI al;
+
+ public StockholmFile()
+ {
+ }
+
+ /**
+ * Creates a new StockholmFile object for output.
+ */
+ public StockholmFile(AlignmentI al)
+ {
+ this.al = al;
+ }
+
+ public StockholmFile(String inFile, DataSourceType type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public StockholmFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ @Override
+ public void initData()
+ {
+ super.initData();
+ }
+
+ /**
+ * Parse a file in Stockholm format into Jalview's data model using VARNA
+ *
+ * @throws IOException
+ * If there is an error with the input file
+ */
+ public void parse_with_VARNA(java.io.File inFile) throws IOException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ List<RNA> result = null;
+ try
+ {
+ result = RNAFactory.loadSecStrStockholm(r);
+ } catch (ExceptionUnmatchedClosingParentheses umcp)
+ {
+ errormessage = "Unmatched parentheses in annotation. Aborting ("
+ + umcp.getMessage() + ")";
+ throw new IOException(umcp);
+ }
+ // DEBUG System.out.println("this is the secondary scructure:"
+ // +result.size());
+ SequenceI[] seqs = new SequenceI[result.size()];
+ String id = null;
+ for (int i = 0; i < result.size(); i++)
+ {
+ // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
+ RNA current = result.get(i);
+
+ String seq = current.getSeq();
+ String rna = current.getStructDBN(true);
+ // DEBUG System.out.println(seq);
+ // DEBUG System.err.println(rna);
+ int begin = 0;
+ int end = seq.length() - 1;
+ id = safeName(getDataName());
+ seqs[i] = new Sequence(id, seq, begin, end);
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = rna.substring(j, j + 1);
+
+ }
+
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
+
+ }
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+ this.annotations.addElement(align);
+ }
+ this.setSeqs(seqs);
+
+ }
+
+ /**
+ * Parse a file in Stockholm format into Jalview's data model. The file has to
+ * be passed at construction time
+ *
+ * @throws IOException
+ * If there is an error with the input file
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ StringBuffer treeString = new StringBuffer();
+ String treeName = null;
+ // --------------- Variable Definitions -------------------
+ String line;
+ String version;
+ // String id;
+ Hashtable seqAnn = new Hashtable(); // Sequence related annotations
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
+ Regex p, r, rend, s, x;
+ // Temporary line for processing RNA annotation
+ // String RNAannot = "";
+
+ // ------------------ Parsing File ----------------------
+ // First, we have to check that this file has STOCKHOLM format, i.e. the
+ // first line must match
+
+ r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+ if (!r.search(nextLine()))
+ {
+ throw new IOException(MessageManager
+ .getString("exception.stockholm_invalid_format"));
+ }
+ else
+ {
+ version = r.stringMatched(1);
+
+ // logger.debug("Stockholm version: " + version);
+ }
+
+ // We define some Regexes here that will be used regularily later
+ rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
+ p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
+ // id/from/to
+ s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
+ r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
+ x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
+
+ // Convert all bracket types to parentheses (necessary for passing to VARNA)
+ Regex openparen = new Regex("(<|\\[)", "(");
+ Regex closeparen = new Regex("(>|\\])", ")");
+
+ // // Detect if file is RNA by looking for bracket types
+ // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+
+ rend.optimize();
+ p.optimize();
+ s.optimize();
+ r.optimize();
+ x.optimize();
+ openparen.optimize();
+ closeparen.optimize();
+
+ while ((line = nextLine()) != null)
+ {
+ if (line.length() == 0)
+ {
+ continue;
+ }
+ if (rend.search(line))
+ {
+ // End of the alignment, pass stuff back
+ this.noSeqs = seqs.size();
+
+ String dbsource = null;
+ Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
+ Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+ if (getAlignmentProperty("AC") != null)
+ {
+ String dbType = getAlignmentProperty("AC").toString();
+ if (pf.search(dbType))
+ {
+ // PFAM Alignment - so references are typically from Uniprot
+ dbsource = "PFAM";
+ }
+ else if (rf.search(dbType))
+ {
+ dbsource = "RFAM";
+ }
+ }
+ // logger.debug("Number of sequences: " + this.noSeqs);
+ for (Map.Entry<String, String> skey : seqs.entrySet())
+ {
+ // logger.debug("Processing sequence " + acc);
+ String acc = skey.getKey();
+ String seq = skey.getValue();
+ if (maxLength < seq.length())
+ {
+ maxLength = seq.length();
+ }
+ int start = 1;
+ int end = -1;
+ String sid = acc;
+ /*
+ * Retrieve hash of annotations for this accession Associate
+ * Annotation with accession
+ */
+ Hashtable accAnnotations = null;
+
+ if (seqAnn != null && seqAnn.containsKey(acc))
+ {
+ accAnnotations = (Hashtable) seqAnn.remove(acc);
+ // TODO: add structures to sequence
+ }
+
+ // Split accession in id and from/to
+ if (p.search(acc))
+ {
+ sid = p.stringMatched(1);
+ start = Integer.parseInt(p.stringMatched(2));
+ end = Integer.parseInt(p.stringMatched(3));
+ }
+ // logger.debug(sid + ", " + start + ", " + end);
+
+ Sequence seqO = new Sequence(sid, seq, start, end);
+ // Add Description (if any)
+ if (accAnnotations != null && accAnnotations.containsKey("DE"))
+ {
+ String desc = (String) accAnnotations.get("DE");
+ seqO.setDescription((desc == null) ? "" : desc);
+ }
+ // Add DB References (if any)
+ if (accAnnotations != null && accAnnotations.containsKey("DR"))
+ {
+ String dbr = (String) accAnnotations.get("DR");
+ if (dbr != null && dbr.indexOf(";") > -1)
+ {
+ String src = dbr.substring(0, dbr.indexOf(";"));
+ String acn = dbr.substring(dbr.indexOf(";") + 1);
+ jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
+ }
+ }
+
+ if (accAnnotations != null && accAnnotations.containsKey("AC"))
+ {
+ String dbr = (String) accAnnotations.get("AC");
+ if (dbr != null)
+ {
+ // we could get very clever here - but for now - just try to
+ // guess accession type from type of sequence, source of alignment
+ // plus
+ // structure
+ // of accession
+ guessDatabaseFor(seqO, dbr, dbsource);
+ }
+ // else - do what ? add the data anyway and prompt the user to
+ // specify what references these are ?
+ }
+
+ Hashtable features = null;
+ // We need to adjust the positions of all features to account for gaps
+ try
+ {
+ features = (Hashtable) accAnnotations.remove("features");
+ } catch (java.lang.NullPointerException e)
+ {
+ // loggerwarn("Getting Features for " + acc + ": " +
+ // e.getMessage());
+ // continue;
+ }
+ // if we have features
+ if (features != null)
+ {
+ int posmap[] = seqO.findPositionMap();
+ Enumeration i = features.keys();
+ while (i.hasMoreElements())
+ {
+ // TODO: parse out secondary structure annotation as annotation
+ // row
+ // TODO: parse out scores as annotation row
+ // TODO: map coding region to core jalview feature types
+ String type = i.nextElement().toString();
+ Hashtable content = (Hashtable) features.remove(type);
+
+ // add alignment annotation for this feature
+ String key = type2id(type);
+
+ /*
+ * have we added annotation rows for this type ?
+ */
+ boolean annotsAdded = false;
+ if (key != null)
+ {
+ if (accAnnotations != null
+ && accAnnotations.containsKey(key))
+ {
+ Vector vv = (Vector) accAnnotations.get(key);
+ for (int ii = 0; ii < vv.size(); ii++)
+ {
+ annotsAdded = true;
+ AlignmentAnnotation an = (AlignmentAnnotation) vv
+ .elementAt(ii);
+ seqO.addAlignmentAnnotation(an);
+ annotations.add(an);
+ }
+ }
+ }
+
+ Enumeration j = content.keys();
+ while (j.hasMoreElements())
+ {
+ String desc = j.nextElement().toString();
+ if (ANNOTATION.equals(desc) && annotsAdded)
+ {
+ // don't add features if we already added an annotation row
+ continue;
+ }
+ String ns = content.get(desc).toString();
+ char[] byChar = ns.toCharArray();
+ for (int k = 0; k < byChar.length; k++)
+ {
+ char c = byChar[k];
+ if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
+ // uses
+ // '.'
+ // for
+ // feature
+ // background
+ {
+ int new_pos = posmap[k]; // look up nearest seqeunce
+ // position to this column
+ SequenceFeature feat = new SequenceFeature(type, desc,
+ new_pos, new_pos, null);
+
+ seqO.addSequenceFeature(feat);
+ }
+ }
+ }
+
+ }
+
+ }
+ // garbage collect
+
+ // logger.debug("Adding seq " + acc + " from " + start + " to " + end
+ // + ": " + seq);
+ this.seqs.addElement(seqO);
+ }
+ return; // finished parsing this segment of source
+ }
+ else if (!r.search(line))
+ {
+ // System.err.println("Found sequence line: " + line);
+
+ // Split sequence in sequence and accession parts
+ if (!x.search(line))
+ {
+ // logger.error("Could not parse sequence line: " + line);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.couldnt_parse_sequence_line", new String[]
+ { line }));
+ }
+ String ns = seqs.get(x.stringMatched(1));
+ if (ns == null)
+ {
+ ns = "";
+ }
+ ns += x.stringMatched(2);
+
+ seqs.put(x.stringMatched(1), ns);
+ }
+ else
+ {
+ String annType = r.stringMatched(1);
+ String annContent = r.stringMatched(2);
+
+ // System.err.println("type:" + annType + " content: " + annContent);
+
+ if (annType.equals("GF"))
+ {
+ /*
+ * Generic per-File annotation, free text Magic features: #=GF NH
+ * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
+ * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
+ *
+ * Compulsory fields: ------------------
+ *
+ * AC Accession number: Accession number in form PFxxxxx.version or
+ * PBxxxxxx. ID Identification: One word name for family. DE
+ * Definition: Short description of family. AU Author: Authors of the
+ * entry. SE Source of seed: The source suggesting the seed members
+ * belong to one family. GA Gathering method: Search threshold to
+ * build the full alignment. TC Trusted Cutoff: Lowest sequence score
+ * and domain score of match in the full alignment. NC Noise Cutoff:
+ * Highest sequence score and domain score of match not in full
+ * alignment. TP Type: Type of family -- presently Family, Domain,
+ * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
+ * Alignment Method The order ls and fs hits are aligned to the model
+ * to build the full align. // End of alignment.
+ *
+ * Optional fields: ----------------
+ *
+ * DC Database Comment: Comment about database reference. DR Database
+ * Reference: Reference to external database. RC Reference Comment:
+ * Comment about literature reference. RN Reference Number: Reference
+ * Number. RM Reference Medline: Eight digit medline UI number. RT
+ * Reference Title: Reference Title. RA Reference Author: Reference
+ * Author RL Reference Location: Journal location. PI Previous
+ * identifier: Record of all previous ID lines. KW Keywords: Keywords.
+ * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
+ * NL Location: Location of nested domains - sequence ID, start and
+ * end of insert.
+ *
+ * Obsolete fields: ----------- AL Alignment method of seed: The
+ * method used to align the seed members.
+ */
+ // Let's save the annotations, maybe we'll be able to do something
+ // with them later...
+ Regex an = new Regex("(\\w+)\\s*(.*)");
+ if (an.search(annContent))
+ {
+ if (an.stringMatched(1).equals("NH"))
+ {
+ treeString.append(an.stringMatched(2));
+ }
+ else if (an.stringMatched(1).equals("TN"))
+ {
+ if (treeString.length() > 0)
+ {
+ if (treeName == null)
+ {
+ treeName = "Tree " + (getTreeCount() + 1);
+ }
+ addNewickTree(treeName, treeString.toString());
+ }
+ treeName = an.stringMatched(2);
+ treeString = new StringBuffer();
+ }
+ // TODO: JAL-3532 - this is where GF comments and database
+ // references are lost
+ // suggest overriding this method for Stockholm files to catch and
+ // properly
+ // process CC, DR etc into multivalued properties
+ setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
+ }
+ }
+ else if (annType.equals("GS"))
+ {
+ // Generic per-Sequence annotation, free text
+ /*
+ * Pfam uses these features: Feature Description ---------------------
+ * ----------- AC <accession> ACcession number DE <freetext>
+ * DEscription DR <db>; <accession>; Database Reference OS <organism>
+ * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
+ * LO <look> Look (Color, etc.)
+ */
+ if (s.search(annContent))
+ {
+ String acc = s.stringMatched(1);
+ String type = s.stringMatched(2);
+ String content = s.stringMatched(3);
+ // TODO: store DR in a vector.
+ // TODO: store AC according to generic file db annotation.
+ Hashtable ann;
+ if (seqAnn.containsKey(acc))
+ {
+ ann = (Hashtable) seqAnn.get(acc);
+ }
+ else
+ {
+ ann = new Hashtable();
+ }
+ ann.put(type, content);
+ seqAnn.put(acc, ann);
+ }
+ else
+ {
+ // throw new IOException("Error parsing " + line);
+ System.err.println(">> missing annotation: " + line);
+ }
+ }
+ else if (annType.equals("GC"))
+ {
+ // Generic per-Column annotation, exactly 1 char per column
+ // always need a label.
+ if (x.search(annContent))
+ {
+ // parse out and create alignment annotation directly.
+ parseAnnotationRow(annotations, x.stringMatched(1),
+ x.stringMatched(2));
+ }
+ }
+ else if (annType.equals("GR"))
+ {
+ // Generic per-Sequence AND per-Column markup, exactly 1 char per
+ // column
+ /*
+ * Feature Description Markup letters ------- -----------
+ * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
+ * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
+ * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
+ * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
+ * or after) [0-2]
+ */
+ if (s.search(annContent))
+ {
+ String acc = s.stringMatched(1);
+ String type = s.stringMatched(2);
+ String oseq = s.stringMatched(3);
+ /*
+ * copy of annotation field that may be processed into whitespace chunks
+ */
+ String seq = new String(oseq);
+
+ Hashtable ann;
+ // Get an object with all the annotations for this sequence
+ if (seqAnn.containsKey(acc))
+ {
+ // logger.debug("Found annotations for " + acc);
+ ann = (Hashtable) seqAnn.get(acc);
+ }
+ else
+ {
+ // logger.debug("Creating new annotations holder for " + acc);
+ ann = new Hashtable();
+ seqAnn.put(acc, ann);
+ }
+
+ // // start of block for appending annotation lines for wrapped
+ // stokchholm file
+ // TODO test structure, call parseAnnotationRow with vector from
+ // hashtable for specific sequence
+
+ Hashtable features;
+ // Get an object with all the content for an annotation
+ if (ann.containsKey("features"))
+ {
+ // logger.debug("Found features for " + acc);
+ features = (Hashtable) ann.get("features");
+ }
+ else
+ {
+ // logger.debug("Creating new features holder for " + acc);
+ features = new Hashtable();
+ ann.put("features", features);
+ }
+
+ Hashtable content;
+ if (features.containsKey(this.id2type(type)))
+ {
+ // logger.debug("Found content for " + this.id2type(type));
+ content = (Hashtable) features.get(this.id2type(type));
+ }
+ else
+ {
+ // logger.debug("Creating new content holder for " +
+ // this.id2type(type));
+ content = new Hashtable();
+ features.put(this.id2type(type), content);
+ }
+ String ns = (String) content.get(ANNOTATION);
+
+ if (ns == null)
+ {
+ ns = "";
+ }
+ // finally, append the annotation line
+ ns += seq;
+ content.put(ANNOTATION, ns);
+ // // end of wrapped annotation block.
+ // // Now a new row is created with the current set of data
+
+ Hashtable strucAnn;
+ if (seqAnn.containsKey(acc))
+ {
+ strucAnn = (Hashtable) seqAnn.get(acc);
+ }
+ else
+ {
+ strucAnn = new Hashtable();
+ }
+
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
+ parseAnnotationRow(newStruc, type, ns);
+ for (AlignmentAnnotation alan : newStruc)
+ {
+ alan.visible = false;
+ }
+ // new annotation overwrites any existing annotation...
+
+ strucAnn.put(type, newStruc);
+ seqAnn.put(acc, strucAnn);
+ }
+ // }
+ else
+ {
+ System.err.println(
+ "Warning - couldn't parse sequence annotation row line:\n"
+ + line);
+ // throw new IOException("Error parsing " + line);
+ }
+ }
+ else
+ {
+ throw new IOException(MessageManager.formatMessage(
+ "exception.unknown_annotation_detected", new String[]
+ { annType, annContent }));
+ }
+ }
+ }
+ if (treeString.length() > 0)
+ {
+ if (treeName == null)
+ {
+ treeName = "Tree " + (1 + getTreeCount());
+ }
+ addNewickTree(treeName, treeString.toString());
+ }
+ }
+
+ /**
+ * Demangle an accession string and guess the originating sequence database
+ * for a given sequence
+ *
+ * @param seqO
+ * sequence to be annotated
+ * @param dbr
+ * Accession string for sequence
+ * @param dbsource
+ * source database for alignment (PFAM or RFAM)
+ */
+ private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
+ {
+ DBRefEntry dbrf = null;
+ List<DBRefEntry> dbrs = new ArrayList<>();
+ String seqdb = "Unknown", sdbac = "" + dbr;
+ int st = -1, en = -1, p;
+ if ((st = sdbac.indexOf("/")) > -1)
+ {
+ String num, range = sdbac.substring(st + 1);
+ sdbac = sdbac.substring(0, st);
+ if ((p = range.indexOf("-")) > -1)
+ {
+ p++;
+ if (p < range.length())
+ {
+ num = range.substring(p).trim();
+ try
+ {
+ en = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ en = -1;
+ }
+ }
+ }
+ else
+ {
+ p = range.length();
+ }
+ num = range.substring(0, p).trim();
+ try
+ {
+ st = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ st = -1;
+ }
+ }
+ if (dbsource == null)
+ {
+ // make up an origin based on whether the sequence looks like it is
+ // nucleotide
+ // or protein
+ dbsource = (seqO.isProtein()) ? "PFAM" : "RFAM";
+ }
+ if (dbsource.equals("PFAM"))
+ {
+ seqdb = "UNIPROT";
+ if (sdbac.indexOf(".") > -1)
+ {
+ // strip of last subdomain
+ sdbac = sdbac.substring(0, sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+ sdbac);
+ if (dbrf != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+ dbr);
+ if (dbr != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ else
+ {
+ seqdb = "EMBL"; // total guess - could be ENA, or something else these
+ // days
+ if (sdbac.indexOf(".") > -1)
+ {
+ // strip off last subdomain
+ sdbac = sdbac.substring(0, sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+ sdbac);
+ if (dbrf != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+ dbr);
+ if (dbrf != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ if (st != -1 && en != -1)
+ {
+ for (DBRefEntry d : dbrs)
+ {
+ jalview.util.MapList mp = new jalview.util.MapList(
+ new int[]
+ { seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1,
+ 1);
+ jalview.datamodel.Mapping mping = new Mapping(mp);
+ d.setMap(mping);
+ }
+ }
+ }
+
+ protected static AlignmentAnnotation parseAnnotationRow(
+ Vector<AlignmentAnnotation> annotation, String label,
+ String annots)
+ {
+ String convert1, convert2 = null;
+
+ // convert1 = OPEN_PAREN.replaceAll(annots);
+ // convert2 = CLOSE_PAREN.replaceAll(convert1);
+ // annots = convert2;
+
+ String type = label;
+ if (label.contains("_cons"))
+ {
+ type = (label.indexOf("_cons") == label.length() - 5)
+ ? label.substring(0, label.length() - 5)
+ : label;
+ }
+ boolean ss = false, posterior = false;
+ type = id2type(type);
+
+ boolean isrnass = false;
+ if (type.equalsIgnoreCase("secondary structure"))
+ {
+ ss = true;
+ isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+ // here (it's easier for dealing with
+ // other non-alpha-non-brace chars)
+ }
+ if (type.equalsIgnoreCase("posterior probability"))
+ {
+ posterior = true;
+ }
+ // decide on secondary structure or not.
+ Annotation[] els = new Annotation[annots.length()];
+ for (int i = 0; i < annots.length(); i++)
+ {
+ String pos = annots.substring(i, i + 1);
+ Annotation ann;
+ ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
+ // be written out
+ if (ss)
+ {
+ // if (" .-_".indexOf(pos) == -1)
+ {
+ if (isrnass && RNASS_BRACKETS.indexOf(pos) >= 0)
+ {
+ ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
+ ann.displayCharacter = "" + pos.charAt(0);
+ }
+ else
+ {
+ ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
+ .charAt(0);
+
+ if (ann.secondaryStructure == pos.charAt(0))
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
+ }
+ }
+
+ }
+ if (posterior && !ann.isWhitespace()
+ && !Comparison.isGap(pos.charAt(0)))
+ {
+ float val = 0;
+ // symbol encodes values - 0..*==0..10
+ if (pos.charAt(0) == '*')
+ {
+ val = 10;
+ }
+ else
+ {
+ val = pos.charAt(0) - '0';
+ if (val > 9)
+ {
+ val = 10;
+ }
+ }
+ ann.value = val;
+ }
+
+ els[i] = ann;
+ }
+ AlignmentAnnotation annot = null;
+ Enumeration<AlignmentAnnotation> e = annotation.elements();
+ while (e.hasMoreElements())
+ {
+ annot = e.nextElement();
+ if (annot.label.equals(type))
+ {
+ break;
+ }
+ annot = null;
+ }
+ if (annot == null)
+ {
+ annot = new AlignmentAnnotation(type, type, els);
+ annotation.addElement(annot);
+ }
+ else
+ {
+ Annotation[] anns = new Annotation[annot.annotations.length
+ + els.length];
+ System.arraycopy(annot.annotations, 0, anns, 0,
+ annot.annotations.length);
+ System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
+ annot.annotations = anns;
+ // System.out.println("else: ");
+ }
+ return annot;
+ }
+
+ private String dbref_to_ac_record(DBRefEntry ref)
+ {
+ return ref.getSource().toString() + " ; "
+ + ref.getAccessionId().toString();
+ }
+
+ @Override
+ public String print(SequenceI[] s, boolean jvSuffix)
+ {
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
+
+ // find max length of id
+ int max = 0;
+ int maxid = 0;
+ int in = 0;
+ int slen = s.length;
+ SequenceI seq;
+ Hashtable<String, String> dataRef = null;
+ boolean isAA = s[in].isProtein();
+ while ((in < slen) && ((seq = s[in]) != null))
+ {
+ String tmp = printId(seq, jvSuffix);
+ max = Math.max(max, seq.getLength());
+
+ if (tmp.length() > maxid)
+ {
+ maxid = tmp.length();
+ }
+ List<DBRefEntry> seqrefs = seq.getDBRefs();
+ int ndb;
+ if (seqrefs != null && (ndb = seqrefs.size()) > 0)
+ {
+ if (dataRef == null)
+ {
+ dataRef = new Hashtable<>();
+ }
+ List<DBRefEntry> primrefs = seq.getPrimaryDBRefs();
+ if (primrefs.size() >= 1)
+ {
+ dataRef.put(tmp, dbref_to_ac_record(primrefs.get(0)));
+ }
+ else
+ {
+ for (int idb = 0; idb < seq.getDBRefs().size(); idb++)
+ {
+ DBRefEntry dbref = seq.getDBRefs().get(idb);
+ dataRef.put(tmp, dbref_to_ac_record(dbref));
+ // if we put in a uniprot or EMBL record then we're done:
+ if (isAA && DBRefSource.UNIPROT
+ .equals(DBRefUtils.getCanonicalName(dbref.getSource())))
+ {
+ break;
+ }
+ if (!isAA && DBRefSource.EMBL
+ .equals(DBRefUtils.getCanonicalName(dbref.getSource())))
+ {
+ break;
+ }
+ }
+ }
+ }
+ in++;
+ }
+ maxid += 9;
+ int i = 0;
+
+ // output database type
+ if (al.getProperties() != null)
+ {
+ if (!al.getProperties().isEmpty())
+ {
+ Enumeration key = al.getProperties().keys();
+ Enumeration val = al.getProperties().elements();
+ while (key.hasMoreElements())
+ {
+ out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+ out.append(newline);
+ }
+ }
+ }
+
+ // output database accessions
+ if (dataRef != null)
+ {
+ Enumeration<String> en = dataRef.keys();
+ while (en.hasMoreElements())
+ {
+ Object idd = en.nextElement();
+ String type = dataRef.remove(idd);
+ out.append(new Format("%-" + (maxid - 2) + "s")
+ .form("#=GS " + idd.toString() + " "));
+ if (isAA && type.contains("UNIPROT")
+ || (!isAA && type.contains("EMBL")))
+ {
+
+ out.append(" AC " + type.substring(type.indexOf(";") + 1));
+ }
+ else
+ {
+ out.append(" DR " + type + " ");
+ }
+ out.append(newline);
+ }
+ }
+
+ // output annotations
+ while (i < slen && (seq = s[i]) != null)
+ {
+ AlignmentAnnotation[] alAnot = seq.getAnnotation();
+ if (alAnot != null)
+ {
+ Annotation[] ann;
+ for (int j = 0, nj = alAnot.length; j < nj; j++)
+ {
+
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
+
+ if (isrna)
+ {
+ // hardwire to secondary structure if there is RNA secondary
+ // structure on the annotation
+ key = "SS";
+ }
+ if (key == null)
+ {
+
+ continue;
+ }
+
+ // out.append("#=GR ");
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
+ ann = alAnot[j].annotations;
+ String sseq = "";
+ for (int k = 0, nk = ann.length; k < nk; k++)
+ {
+ sseq += outputCharacter(key, k, isrna, ann, seq);
+ }
+ out.append(sseq);
+ out.append(newline);
+ }
+ }
+
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(seq, jvSuffix) + " "));
+ out.append(seq.getSequenceAsString());
+ out.append(newline);
+ i++;
+ }
+
+ // alignment annotation
+ AlignmentAnnotation aa;
+ AlignmentAnnotation[] an = al.getAlignmentAnnotation();
+ if (an != null)
+ {
+ for (int ia = 0, na = an.length; ia < na; ia++)
+ {
+ aa = an[ia];
+ if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
+ {
+ continue;
+ }
+ String sseq = "";
+ String label;
+ String key = "";
+ if (aa.label.equals("seq"))
+ {
+ label = "seq_cons";
+ }
+ else
+ {
+ key = type2id(aa.label.toLowerCase(Locale.ROOT));
+ if (key == null)
+ {
+ label = aa.label;
+ }
+ else
+ {
+ label = key + "_cons";
+ }
+ }
+ if (label == null)
+ {
+ label = aa.label;
+ }
+ label = label.replace(" ", "_");
+
+ out.append(
+ new Format("%-" + maxid + "s").form("#=GC " + label + " "));
+ boolean isrna = aa.isValidStruc();
+ for (int j = 0, nj = aa.annotations.length; j < nj; j++)
+ {
+ sseq += outputCharacter(key, j, isrna, aa.annotations, null);
+ }
+ out.append(sseq);
+ out.append(newline);
+ }
+ }
+
+ out.append("//");
+ out.append(newline);
+
+ return out.toString();
+ }
+
+ /**
+ * add an annotation character to the output row
+ *
+ * @param seq
+ * @param key
+ * @param k
+ * @param isrna
+ * @param ann
+ * @param sequenceI
+ */
+ private char outputCharacter(String key, int k, boolean isrna,
+ Annotation[] ann, SequenceI sequenceI)
+ {
+ char seq = ' ';
+ Annotation annot = ann[k];
+ String ch = (annot == null)
+ ? ((sequenceI == null) ? "-"
+ : Character.toString(sequenceI.getCharAt(k)))
+ : (annot.displayCharacter == null
+ ? String.valueOf(annot.secondaryStructure)
+ : annot.displayCharacter);
+ if (ch == null)
+ {
+ ch = " ";
+ }
+ if (key != null && key.equals("SS"))
+ {
+ char ssannotchar = ' ';
+ boolean charset = false;
+ if (annot == null)
+ {
+ // sensible gap character
+ ssannotchar = ' ';
+ charset = true;
+ }
+ else
+ {
+ // valid secondary structure AND no alternative label (e.g. ' B')
+ if (annot.secondaryStructure > ' ' && ch.length() < 2)
+ {
+ ssannotchar = annot.secondaryStructure;
+ charset = true;
+ }
+ }
+ if (charset)
+ {
+ return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar;
+ }
+ }
+
+ if (ch.length() == 0)
+ {
+ seq = '.';
+ }
+ else if (ch.length() == 1)
+ {
+ seq = ch.charAt(0);
+ }
+ else if (ch.length() > 1)
+ {
+ seq = ch.charAt(1);
+ }
+
+ return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+ : seq;
+ }
+
+ public String print()
+ {
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
+ print(getSeqsAsArray(), false);
+
+ out.append("//");
+ out.append(newline);
+ return out.toString();
+ }
+
+ private static Hashtable typeIds = null;
+
+ static
+ {
+ if (typeIds == null)
+ {
+ typeIds = new Hashtable();
+ typeIds.put("SS", "Secondary Structure");
+ typeIds.put("SA", "Surface Accessibility");
+ typeIds.put("TM", "transmembrane");
+ typeIds.put("PP", "Posterior Probability");
+ typeIds.put("LI", "ligand binding");
+ typeIds.put("AS", "active site");
+ typeIds.put("IN", "intron");
+ typeIds.put("IR", "interacting residue");
+ typeIds.put("AC", "accession");
+ typeIds.put("OS", "organism");
+ typeIds.put("CL", "class");
+ typeIds.put("DE", "description");
+ typeIds.put("DR", "reference");
+ typeIds.put("LO", "look");
+ typeIds.put("RF", "Reference Positions");
+
+ }
+ }
+
+ protected static String id2type(String id)
+ {
+ if (typeIds.containsKey(id))
+ {
+ return (String) typeIds.get(id);
+ }
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type code " + id);
+ return id;
+ }
+
+ protected static String type2id(String type)
+ {
+ String key = null;
+ Enumeration e = typeIds.keys();
+ while (e.hasMoreElements())
+ {
+ Object ll = e.nextElement();
+ if (typeIds.get(ll).toString().equalsIgnoreCase(type))
+ {
+ key = (String) ll;
+ break;
+ }
+ }
+ if (key != null)
+ {
+ return key;
+ }
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type: " + type);
+ return key;
+ }
+
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff