From: jprocter Date: Fri, 7 Dec 2012 15:49:04 +0000 (+0000) Subject: Anne reinstated general stockholm parser code but extended to support pseudoknot... X-Git-Tag: Jalview_2_9~221^2^2~8^2~27 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d380a9fd147e32f905a775237576507b6d11444d;p=jalview.git Anne reinstated general stockholm parser code but extended to support pseudoknot annotation lines. This will need merging with Natasha's upgraded io.StockholmFile class --- diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 86cb4ae..987cdcd 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -20,23 +20,29 @@ */ package jalview.io; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; + import java.io.*; import java.util.*; + import javax.xml.parsers.ParserConfigurationException; import org.xml.sax.SAXException; -import com.stevesoft.pat.*; +import com.stevesoft.pat.Regex; import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; -import fr.orsay.lri.varna.factories.RNAFactory; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.datamodel.*; -import jalview.analysis.Rna; + + // import org.apache.log4j.*; @@ -85,485 +91,459 @@ public class StockholmFile extends AlignFile * If there is an error with the input file * @throws ExceptionUnmatchedClosingParentheses */ - public void parse() + public void parse() throws Exception { - FileReader fr = null; - fr = new FileReader(inFile); - - BufferedReader r = new BufferedReader (fr); - result = RNAFactory.loadSecStrStockholm(r); - System.out.println("this is the secondary scructure:" +result.size()); - SequenceI[] seqs = new SequenceI[result.size()]; - System.out.println(type); //the type is "File" - System.out.println(inFile );//inFile is the path - for(int i=0;i|\\])", ")"); + + // 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(); + // logger.debug("Number of sequences: " + this.noSeqs); + Enumeration accs = seqs.keys(); + while (accs.hasMoreElements()) + { + String acc = (String) accs.nextElement(); + // logger.debug("Processing sequence " + acc); + String seq = (String) seqs.remove(acc); + 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); + // seqO.addDBRef(dbref); + } + } + if (accAnnotations != null && accAnnotations.containsKey("SS")) + { + Vector v = (Vector) accAnnotations.get("SS"); + + for (int i = 0; i < v.size(); i++) + { + AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i); + seqO.addAlignmentAnnotation(an); + //annotations.add(an); + } + } + + 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); + Enumeration j = content.keys(); + while (j.hasMoreElements()) + { + String desc = j.nextElement().toString(); + 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, 0f, 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("Could not parse sequence line: " + line); + } + String ns = (String) 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 + * #=GF TN 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(); + } + 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 number DE + * DEscription DR ; ; Database Reference OS + * OrganiSm (species) OC Organism Classification (clade, etc.) + * LO 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); + } + } + 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 seq = new String(s.stringMatched(3)); + String description = null; + // Check for additional information about the current annotation + // We use a simple string tokenizer here for speed + StringTokenizer sep = new StringTokenizer(seq, " \t"); + description = sep.nextToken(); + if (sep.hasMoreTokens()) + { + seq = sep.nextToken(); + } + else + { + seq = description; + description = new String(); + } + // sequence id with from-to fields + + 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); + } + //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(description); + if (ns == null) + { + ns = ""; + } + ns += seq; + content.put(description, ns); + + if(type.equals("SS")){ + Hashtable strucAnn; + if (seqAnn.containsKey(acc)) + { + strucAnn = (Hashtable) seqAnn.get(acc); + } + else + { + strucAnn = new Hashtable(); + } + + Vector newStruc=new Vector(); + parseAnnotationRow(newStruc, type,ns); + + strucAnn.put(type, newStruc); + seqAnn.put(acc, strucAnn); + } + } + else { - annot[j] =rna.substring(j,j+1); - + System.err + .println("Warning - couldn't parse sequence annotation row line:\n" + + line); + // throw new IOException("Error parsing " + line); + } } - - for(int k=0;k 0) { - ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f); - + if (treeName == null) + { + treeName = "Tree " + (1 + getTreeCount()); } - AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann); - - seqs[i].addAlignmentAnnotation(align); - seqs[i].setRNA(result.get(i)); - this.annotations.addElement(align); + addNewickTree(treeName, treeString.toString()); } - this.setSeqs(seqs); - - } -// r = new Regex("# STOCKHOLM ([\\d\\.]+)"); - // if (!r.search(nextLine())) -// { -// throw new IOException( -// "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'"); -// } -// 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(); -// // logger.debug("Number of sequences: " + this.noSeqs); -// Enumeration accs = seqs.keys(); -// while (accs.hasMoreElements()) -// { -// String acc = (String) accs.nextElement(); -// // logger.debug("Processing sequence " + acc); -// String seq = (String) seqs.remove(acc); -// 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); -// // seqO.addDBRef(dbref); -// } -// } -// if (accAnnotations != null && accAnnotations.containsKey("SS")) -// { -// Vector v = (Vector) accAnnotations.get("SS"); -// -// for (int i = 0; i < v.size(); i++) -// { -// AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i); -// seqO.addAlignmentAnnotation(an); -// //annotations.add(an); -// } -// } -// -// 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); -// Enumeration j = content.keys(); -// while (j.hasMoreElements()) -// { -// String desc = j.nextElement().toString(); -// 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, 0f, 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("Could not parse sequence line: " + line); -// } -// String ns = (String) 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 -// * #=GF TN 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(); -// } -// 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 number DE -// * DEscription DR ; ; Database Reference OS -// * OrganiSm (species) OC Organism Classification (clade, etc.) -// * LO 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); -// } -// } -// 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 seq = new String(s.stringMatched(3)); -// String description = null; -// // Check for additional information about the current annotation -// // We use a simple string tokenizer here for speed -// StringTokenizer sep = new StringTokenizer(seq, " \t"); -// description = sep.nextToken(); -// if (sep.hasMoreTokens()) -// { -// seq = sep.nextToken(); -// } -// else -// { -// seq = description; -// description = new String(); -// } -// // sequence id with from-to fields -// -// 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); -// } -// //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(description); -// if (ns == null) -// { -// ns = ""; -// } -// ns += seq; -// content.put(description, ns); -// -// if(type.equals("SS")){ -// Hashtable strucAnn; -// if (seqAnn.containsKey(acc)) -// { -// strucAnn = (Hashtable) seqAnn.get(acc); -// } -// else -// { -// strucAnn = new Hashtable(); -// } -// -// Vector newStruc=new Vector(); -// parseAnnotationRow(newStruc, type,ns); -// -// 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("Unknown annotation detected: " + annType -// + " " + annContent); -// } -// } -// } -// if (treeString.length() > 0) -// { -// if (treeName == null) -// { -// treeName = "Tree " + (1 + getTreeCount()); -// } -// addNewickTree(treeName, treeString.toString()); -// } -// } -// + } + protected static AlignmentAnnotation parseAnnotationRow(Vector annotation, String label, String annots) { @@ -746,4 +726,4 @@ public class StockholmFile extends AlignFile dataName = dataName.substring(1,e).trim(); return dataName; } -} \ No newline at end of file +}