X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=9104a5fceff177a6d620d40520ed37c26fb859a4;hb=97d6516fd717d0daddcbc8154c4de29a812982e5;hp=fd5fd444f32a67237a57c1d31e5ad87b0911fbce;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index fd5fd44..9104a5f 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -20,10 +20,13 @@ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk */ package jalview.io; + import java.io.*; import java.util.*; -import jalview.datamodel.*; + import com.stevesoft.pat.*; +import jalview.datamodel.*; + //import org.apache.log4j.*; /** @@ -31,379 +34,534 @@ import com.stevesoft.pat.*; * @author bsb at sanger.ac.uk * @version 0.3 */ -public class StockholmFile extends AlignFile +public class StockholmFile + extends AlignFile { - //static Logger logger = Logger.getLogger("jalview.io.StockholmFile"); - - public StockholmFile() + //static Logger logger = Logger.getLogger("jalview.io.StockholmFile"); + + public StockholmFile() + { + } + + public StockholmFile(String inFile, String type) + throws IOException + { + super(inFile, type); + } + + public void initData() + { + super.initData(); + } + + /** + * 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 + */ + 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 + Hashtable seqs = new Hashtable(); + Regex p, r, rend, s, x; + + // ------------------ 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'"); } - - - public StockholmFile(String inFile, String type) throws IOException + else { - super(inFile, type); + version = r.stringMatched(1); + //logger.debug("Stockholm version: " + version); } - public void initData() +// We define some Regexes here that will be used regularily later + rend = new Regex("\\/\\/"); // Find the end of an alignment + p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in id/from/to + s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype + r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line + x = new Regex("(\\S+)\\s+(\\S+)"); //split id from sequence + + rend.optimize(); + p.optimize(); + s.optimize(); + r.optimize(); + x.optimize(); + + while ( (line = nextLine()) != null) { - super.initData(); - } + if (line.length() == 0) + { + continue; + } + if (rend.search(line)) + { +// End of the alignment, pass stuff back - /** - * 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 - */ - public void parse() throws IOException - { - // --------------- Variable Definitions ------------------- - String line; - String version; - // String id; - Hashtable alAnn = new Hashtable(); // Alignment wide annotations - Hashtable seqAnn = new Hashtable(); // Sequence related annotations - Hashtable seqs = new Hashtable(); - Regex p, r, rend, s, x; - - // ------------------ 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())) + this.noSeqs = seqs.size(); + //logger.debug("Number of sequences: " + this.noSeqs); + Enumeration accs = seqs.keys(); + while (accs.hasMoreElements()) { - throw new IOException("This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'"); + String acc = (String) accs.nextElement(); + //logger.debug("Processing sequence " + acc); + String seq = (String) seqs.get(acc); + if (maxLength < seq.length()) + { + maxLength = seq.length(); + } + int start = 1; + int end = -1; + String sid = acc; + // Retrieve hash of annotations for this accession + Hashtable accAnnotations = null; + + if (seqAnn!=null && seqAnn.containsKey(acc)) + { + accAnnotations = (Hashtable) seqAnn.get(acc); + } + + // 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); + DBRefEntry dbref = new DBRefEntry(jalview.util.DBRefUtils.getCanonicalName(src), acn, ""); + seqO.addDBRef(dbref); + } + } + Hashtable features = null; + // We need to adjust the positions of all features to account for gaps + try + { + features = (Hashtable) accAnnotations.get( + "features"); + } + catch (java.lang.NullPointerException e) + { + //loggerwarn("Getting Features for " + acc + ": " + e.getMessage()); + //continue; + } + // if we have features + if (features != null) + { + 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.get(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 == '-')) + { + int new_pos = seqO.findPosition(k); + SequenceFeature feat = + new SequenceFeature(type, + desc, new_pos, new_pos, 0f, null); + + seqO.addSequenceFeature(feat); + } + } + } + + } + + } + //logger.debug("Adding seq " + acc + " from " + start + " to " + end + ": " + seq); + this.seqs.addElement(seqO); } - else + } + 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) { - version = r.stringMatched(1); - //logger.debug("Stockholm version: " + version); + ns = ""; } + ns += x.stringMatched(2); -// We define some Regexes here that will be used regularily later - rend = new Regex("\\/\\/"); // Find the end of an alignment - p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in id/from/to - s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype - r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line - x = new Regex("(\\S+)\\s+(\\S+)"); //split id from sequence - - rend.optimize(); - p.optimize(); - s.optimize(); - r.optimize(); - x.optimize(); - - while ( (line = nextLine()) != null) + 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")) { - if (line.length() == 0) continue; - if(rend.search(line)) + /* 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")) { -// 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()) + treeString.append(an.stringMatched(2)); + } else + if (an.stringMatched(1).equals("TN")) { + if (treeString.length()>0) + { + if (treeName==null) { - String acc = (String) accs.nextElement(); - //logger.debug("Processing sequence " + acc); - String seq = (String) seqs.get(acc); - if (maxLength < seq.length()) - { - maxLength = seq.length(); - } - int start = 1; - int end = -1; - String sid = acc; - // 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); - Hashtable features = null; - // We need to adjust the positions of all features to account for gaps - try - { - features = (Hashtable) ((Hashtable) seqAnn.get(acc)).get("features"); - } - catch (java.lang.NullPointerException e) - { - //loggerwarn("Getting Features for " + acc + ": " + e.getMessage()); - //continue; - } - // if we have features - if (features != null) - { - Enumeration i = features.keys(); - while(i.hasMoreElements()) - { - String type = i.nextElement().toString(); - Hashtable content = (Hashtable) features.get(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 == '-')) - { - int new_pos = seqO.findPosition(k); - SequenceFeature feat = - new SequenceFeature(type, - desc, new_pos, new_pos, 0f, null); - - seqO.addSequenceFeature(feat); - } - } - } - - } - - } - //logger.debug("Adding seq " + acc + " from " + start + " to " + end + ": " + seq); - this.seqs.addElement(seqO); + treeName = "Tree "+(getTreeCount()+1); } + addNewickTree(treeName, treeString.toString()); + } + treeName = an.stringMatched(2); + treeString = new StringBuffer(); } - else if (!r.search(line)) + 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)) { - //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); + 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. + AlignmentAnnotation annotation = parseAnnotationRow(x.stringMatched(1), x.stringMatched(2)); + annotations.addElement(annotation); + } + } + 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 = s.stringMatched(3); + String description = new String(); + + // Check for additional information about the current annotation + if (x.search(seq)) + { + description = x.stringMatched(1); + seq = x.stringMatched(2); + } + // sequence id with from-to fields - seqs.put(x.stringMatched(1), ns); + 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 { - String annType = r.stringMatched(1); - String annContent = r.stringMatched(2); + //logger.debug("Creating new annotations holder for " + acc); + ann = new Hashtable(); + seqAnn.put(acc, ann); + } - //System.err.println("type:" + annType + " content: " + annContent); + 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); + } - 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)) alAnn.put(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); - - 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")) - { - System.out.println(annContent); - // Generic per-Column annotation, exactly 1 char per column - } - 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 = s.stringMatched(3); - String description = new String(); - - // Check for additional information about the current annotation - if (x.search(seq)) - { - description = x.stringMatched(1); - seq = x.stringMatched(2); - } - // 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); - } - - 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, seq); - } - else - { - throw new IOException("Error parsing " + line); - } - } - else - { - throw new IOException("Unknown annotation detected: " + annType + " " + annContent); - } + 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, seq); + } + else + { + throw new IOException("Error parsing " + line); + } + } + else + { + throw new IOException("Unknown annotation detected: " + annType + " " + + annContent); } + } } - - public static String print(SequenceI[] s) + if (treeString.length()>0) { - return "not yet implemented"; + if (treeName==null) + { + treeName = "Tree "+(1+getTreeCount()); + } + addNewickTree(treeName, treeString.toString()); } - - public String print() + } + + private AlignmentAnnotation parseAnnotationRow(String label, String annots) + { + String type = (label.indexOf("_cons")==label.length()-5) ? label.substring(0, label.length()-5) + : label; + boolean ss = false; + type = id2type(type); + if (type.equals("secondary structure")) { - return print(getSeqsAsArray()); + ss=true; } - - private String id2type(String id) + // decide on secondary structure or not. + Annotation[] els = new Annotation[annots.length()]; + for (int i = 0; i