X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=9d21a400c6c1920c2560ac0c761e55dbbd5ac100;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=24bb5212f7e542a04b0460dff15697355c018762;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 24bb521..9d21a40 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -62,7 +62,8 @@ import fr.orsay.lri.varna.models.rna.RNA; * * @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 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 * @@ -71,6 +72,7 @@ public class StockholmFile extends AlignFile { // static Logger logger = Logger.getLogger("jalview.io.StockholmFile"); protected ArrayList result; + StringBuffer out; // output buffer AlignmentI al; @@ -101,6 +103,7 @@ public class StockholmFile extends AlignFile { super.initData(); } + /** * Parse a file in Stockholm format into Jalview's data model using VARNA * @@ -126,7 +129,7 @@ public class StockholmFile extends AlignFile // DEBUG System.out.println("this is the secondary scructure:" // +result.size()); SequenceI[] seqs = new SequenceI[result.size()]; - String id=null; + String id = null; for (int i = 0; i < result.size(); i++) { // DEBUG System.err.println("Processing i'th sequence in Stockholm file") @@ -166,7 +169,6 @@ public class StockholmFile extends AlignFile } - /** * Parse a file in Stockholm format into Jalview's data model. The file has to * be passed at construction time @@ -176,71 +178,70 @@ public class StockholmFile extends AlignFile */ public void parse() throws IOException { - StringBuffer treeString = new StringBuffer(); - String treeName = null; - // --------------- Variable Definitions ------------------- - String line; - String version; + StringBuffer treeString = new StringBuffer(); + String treeName = null; + // --------------- Variable Definitions ------------------- + String line; + String version; // String id; - Hashtable seqAnn = new Hashtable(); // Sequence related annotations - Hashtable seqs = new Hashtable(); - 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( - "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 + Hashtable seqAnn = new Hashtable(); // Sequence related annotations + Hashtable seqs = new Hashtable(); + 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( + "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(); - - String seqdb,dbsource = null; + + String seqdb, 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) @@ -256,59 +257,59 @@ public class StockholmFile extends AlignFile dbsource = "RFAM"; } } - // 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; - /* + // 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); - } - } + */ + 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")) { @@ -316,39 +317,42 @@ public class StockholmFile extends AlignFile { 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 source of alignment plus structure of accession + { + // we could get very clever here - but for now - just try to + // guess accession type from 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 ? + + } + } + // 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); + + 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); @@ -367,338 +371,347 @@ public class StockholmFile extends AlignFile } } - 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); - } + 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()); - } - } + 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); + } -/** - * 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) + 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()); + } + } + + /** + * 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 dbrs=new ArrayList(); - String seqdb="Unknown",sdbac=""+dbr; - int st=-1,en=-1,p; - if ((st=sdbac.indexOf("/"))>-1) + DBRefEntry dbrf = null; + List 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) + String num, range = sdbac.substring(st + 1); + sdbac = sdbac.substring(0, st); + if ((p = range.indexOf("-")) > -1) { p++; - if (p-1) + 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) + 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) + 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) + } + 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) + 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) + + dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, + dbr); + if (dbrf != null) { dbrs.add(dbrf); } } - if (st!=-1 && en!=-1) + if (st != -1 && en != -1) { - for (DBRefEntry d:dbrs) + 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.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); } @@ -1025,7 +1048,7 @@ public class StockholmFile extends AlignFile seq += ch; } else if (ch.length() > 1) - { + { seq += ch.charAt(1); } } @@ -1105,6 +1128,7 @@ public class StockholmFile extends AlignFile + type); return key; } + /** * make a friendly ID string. *