X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=5d645cafe30874f85fe0b58a06619da2571c91c8;hp=9b5a5cdb56420af978d70feebb27cd53faea721f;hb=0ae965fc73680bdc69b06986c060ff17342c4787;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11 diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 9b5a5cd..5d645ca 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -1,19 +1,21 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) - * Copyright (C) 2014 The Jalview Authors + * 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. + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ /* @@ -21,14 +23,38 @@ */ package jalview.io; -import java.io.*; -import java.util.*; - -import com.stevesoft.pat.*; -import jalview.datamodel.*; +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 org.apache.log4j.*; +import jalview.util.MessageManager; /** * This class is supposed to parse a Stockholm format file into Jalview There @@ -39,12 +65,33 @@ import jalview.util.Format; * 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 { - // static Logger logger = Logger.getLogger("jalview.io.StockholmFile"); + 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; @@ -61,7 +108,8 @@ public class StockholmFile extends AlignFile this.al = al; } - public StockholmFile(String inFile, String type) throws IOException + public StockholmFile(String inFile, DataSourceType type) + throws IOException { super(inFile, type); } @@ -71,18 +119,84 @@ public class StockholmFile extends AlignFile 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 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(); @@ -92,24 +206,25 @@ public class StockholmFile extends AlignFile String version; // String id; Hashtable seqAnn = new Hashtable(); // Sequence related annotations - Hashtable seqs = new Hashtable(); + LinkedHashMap 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( - "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'"); + throw new IOException(MessageManager + .getString("exception.stockholm_invalid_format")); } else { version = r.stringMatched(1); + // logger.debug("Stockholm version: " + version); } @@ -125,8 +240,8 @@ public class StockholmFile extends AlignFile Regex openparen = new Regex("(<|\\[)", "("); Regex closeparen = new Regex("(>|\\])", ")"); - // Detect if file is RNA by looking for bracket types - Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))"); + // // Detect if file is RNA by looking for bracket types + // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))"); rend.optimize(); p.optimize(); @@ -147,7 +262,7 @@ public class StockholmFile extends AlignFile // End of the alignment, pass stuff back this.noSeqs = seqs.size(); - String seqdb,dbsource = null; + 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) @@ -164,12 +279,11 @@ public class StockholmFile extends AlignFile } } // logger.debug("Number of sequences: " + this.noSeqs); - Enumeration accs = seqs.keys(); - while (accs.hasMoreElements()) + for (Map.Entry skey : seqs.entrySet()) { - String acc = (String) accs.nextElement(); // logger.debug("Processing sequence " + acc); - String seq = (String) seqs.remove(acc); + String acc = skey.getKey(); + String seq = skey.getValue(); if (maxLength < seq.length()) { maxLength = seq.length(); @@ -205,7 +319,6 @@ public class StockholmFile extends AlignFile String desc = (String) accAnnotations.get("DE"); seqO.setDescription((desc == null) ? "" : desc); } - // Add DB References (if any) if (accAnnotations != null && accAnnotations.containsKey("DR")) { @@ -220,17 +333,18 @@ public class StockholmFile extends AlignFile if (accAnnotations != null && accAnnotations.containsKey("AC")) { - if (dbsource != null) + String dbr = (String) accAnnotations.get("AC"); + if (dbr != null) { - 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 - guessDatabaseFor(seqO, dbr, dbsource); - - } - } - // else - do what ? add the data anyway and prompt the user to specify what references these are ? + // 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; @@ -260,6 +374,11 @@ public class StockholmFile extends AlignFile // 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 @@ -268,9 +387,11 @@ public class StockholmFile extends AlignFile 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); } } } @@ -279,6 +400,11 @@ public class StockholmFile extends AlignFile 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++) @@ -294,7 +420,7 @@ public class StockholmFile extends AlignFile 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); + new_pos, new_pos, null); seqO.addSequenceFeature(feat); } @@ -320,9 +446,11 @@ public class StockholmFile extends AlignFile if (!x.search(line)) { // logger.error("Could not parse sequence line: " + line); - throw new IOException("Could not parse sequence line: " + line); + throw new IOException(MessageManager.formatMessage( + "exception.couldnt_parse_sequence_line", new String[] + { line })); } - String ns = (String) seqs.get(x.stringMatched(1)); + String ns = seqs.get(x.stringMatched(1)); if (ns == null) { ns = ""; @@ -398,6 +526,11 @@ public class StockholmFile extends AlignFile 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)); } } @@ -432,7 +565,8 @@ public class StockholmFile extends AlignFile } else { - throw new IOException("Error parsing " + line); + // throw new IOException("Error parsing " + line); + System.err.println(">> missing annotation: " + line); } } else if (annType.equals("GC")) @@ -462,22 +596,11 @@ public class StockholmFile extends AlignFile { 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 + 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 @@ -492,8 +615,12 @@ public class StockholmFile extends AlignFile 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")) @@ -521,13 +648,18 @@ public class StockholmFile extends AlignFile content = new Hashtable(); features.put(this.id2type(type), content); } - String ns = (String) content.get(description); + String ns = (String) content.get(ANNOTATION); + if (ns == null) { ns = ""; } + // finally, append the annotation line ns += seq; - content.put(description, ns); + 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)) { @@ -538,23 +670,31 @@ public class StockholmFile extends AlignFile strucAnn = new Hashtable(); } - Vector newStruc = new Vector(); + Vector 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" + 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); + throw new IOException(MessageManager.formatMessage( + "exception.unknown_annotation_detected", new String[] + { annType, annContent })); } } } @@ -569,40 +709,49 @@ public class StockholmFile extends AlignFile } /** - * 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) + * 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); } @@ -658,32 +825,36 @@ public class StockholmFile extends AlignFile } protected static AlignmentAnnotation parseAnnotationRow( - Vector annotation, String label, String annots) + Vector annotation, String label, + String annots) { String convert1, convert2 = null; - // Convert all bracket types to parentheses - Regex openparen = new Regex("(<|\\[)", "("); - Regex closeparen = new Regex("(>|\\])", ")"); - - // Detect if file is RNA by looking for bracket types - Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))"); - - convert1 = openparen.replaceAll(annots); - convert2 = closeparen.replaceAll(convert1); - annots = convert2; + // 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; + type = (label.indexOf("_cons") == label.length() - 5) + ? label.substring(0, label.length() - 5) + : label; } - boolean ss = false; + boolean ss = false, posterior = false; type = id2type(type); - if (type.equals("secondary structure")) + + 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()]; @@ -695,36 +866,61 @@ public class StockholmFile extends AlignFile // be written out if (ss) { - if (detectbrackets.search(pos)) - { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getRNASecStrucState(pos).charAt(0); - } - else + // if (" .-_".indexOf(pos) == -1) { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getDssp3state(pos).charAt(0); + 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 (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C') + } + if (posterior && !ann.isWhitespace() + && !Comparison.isGap(pos.charAt(0))) + { + float val = 0; + // symbol encodes values - 0..*==0..10 + if (pos.charAt(0) == '*') { - ann.displayCharacter = ""; // null; // " "; + val = 10; } else { - ann.displayCharacter = " " + ann.displayCharacter; + val = pos.charAt(0) - '0'; + if (val > 9) + { + val = 10; + } } + ann.value = val; } els[i] = ann; } AlignmentAnnotation annot = null; - Enumeration e = annotation.elements(); + Enumeration e = annotation.elements(); while (e.hasMoreElements()) { - annot = (AlignmentAnnotation) e.nextElement(); + annot = e.nextElement(); if (annot.label.equals(type)) + { break; + } annot = null; } if (annot == null) @@ -745,36 +941,67 @@ public class StockholmFile extends AlignFile return annot; } - public String print(SequenceI[] s) + 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; - Hashtable dataRef = null; - while ((in < s.length) && (s[in] != null)) + int slen = s.length; + SequenceI seq; + Hashtable dataRef = null; + boolean isAA = s[in].isProtein(); + while ((in < slen) && ((seq = s[in]) != null)) { - String tmp = printId(s[in]); - if (s[in].getSequence().length > max) - { - max = s[in].getSequence().length; - } + String tmp = printId(seq, jvSuffix); + max = Math.max(max, seq.getLength()); if (tmp.length() > maxid) { maxid = tmp.length(); } - if (s[in].getDBRef() != null) + List seqrefs = seq.getDBRefs(); + int ndb; + if (seqrefs != null && (ndb = seqrefs.size()) > 0) { - for (int idb = 0; idb < s[in].getDBRef().length; idb++) + if (dataRef == null) { - if (dataRef == null) - dataRef = new Hashtable(); - - String datAs1 = s[in].getDBRef()[idb].getSource().toString() - + " ; " - + s[in].getDBRef()[idb].getAccessionId().toString(); - dataRef.put(tmp, datAs1); + dataRef = new Hashtable<>(); + } + List 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++; @@ -800,14 +1027,15 @@ public class StockholmFile extends AlignFile // output database accessions if (dataRef != null) { - Enumeration en = dataRef.keys(); + Enumeration en = dataRef.keys(); while (en.hasMoreElements()) { Object idd = en.nextElement(); - String type = (String) dataRef.remove(idd); - out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS " - + idd.toString() + " ")); - if (type.contains("PFAM") || type.contains("RFAM")) + 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)); @@ -821,131 +1049,179 @@ public class StockholmFile extends AlignFile } // output annotations - while (i < s.length && s[i] != null) + while (i < slen && (seq = s[i]) != null) { - if (s[i].getDatasetSequence() != null) + AlignmentAnnotation[] alAnot = seq.getAnnotation(); + if (alAnot != null) { - SequenceI ds = s[i].getDatasetSequence(); - AlignmentAnnotation[] alAnot; Annotation[] ann; - Annotation annot; - alAnot = s[i].getAnnotation(); - String feature = ""; - if (alAnot != null) + for (int j = 0, nj = alAnot.length; j < nj; j++) { - for (int j = 0; j < alAnot.length; 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) { - if (ds.getSequenceFeatures() != null) - { - feature = ds.getSequenceFeatures()[0].type; - } - String key = type2id(feature); - if (key == null) - continue; + continue; + } - // out.append("#=GR "); - out.append(new Format("%-" + maxid + "s").form("#=GR " - + printId(s[i]) + " " + key + " ")); - ann = alAnot[j].annotations; - String seq = ""; - for (int k = 0; k < ann.length; k++) - { - annot = ann[k]; - String ch = (annot == null) ? Character.toString(s[i] - .getCharAt(k)) : annot.displayCharacter; - if (ch.length() == 0) - { - if (key.equals("SS")) - { - char ll = annot.secondaryStructure; - seq = (Character.toString(ll).equals(" ")) ? seq + "C" - : seq + ll; - } - else - { - seq += "."; - } - } - else if (ch.length() == 1) - { - seq += ch; - } - else if (ch.length() > 1) - { - seq += ch.charAt(1); - } - } - out.append(seq); - out.append(newline); + // 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(s[i]) + " ")); - out.append(s[i].getSequenceAsString()); + out.append(new Format("%-" + maxid + "s") + .form(printId(seq, jvSuffix) + " ")); + out.append(seq.getSequenceAsString()); out.append(newline); i++; } // alignment annotation AlignmentAnnotation aa; - if (al.getAlignmentAnnotation() != null) + AlignmentAnnotation[] an = al.getAlignmentAnnotation(); + if (an != null) { - for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++) + for (int ia = 0, na = an.length; ia < na; ia++) { - aa = al.getAlignmentAnnotation()[ia]; - if (aa.autoCalculated || !aa.visible) + aa = an[ia]; + if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null) { continue; } - String seq = ""; + String sseq = ""; String label; - + String key = ""; if (aa.label.equals("seq")) + { label = "seq_cons"; + } else - label = type2id(aa.label.toLowerCase()) + "_cons"; - - if (label == null) - label = aa.label; - - out.append(new Format("%-" + maxid + "s").form("#=GC " + label - + " ")); - for (int j = 0; j < aa.annotations.length; j++) { - String ch = (aa.annotations[j] == null) ? "-" - : aa.annotations[j].displayCharacter; - if (ch.length() == 0) + key = type2id(aa.label.toLowerCase(Locale.ROOT)); + if (key == null) { - char ll = aa.annotations[j].secondaryStructure; - if (Character.toString(ll).equals(" ")) - seq += "C"; - else - seq += ll; - } - else if (ch.length() == 1) - { - seq += ch; + label = aa.label; } - else if (ch.length() > 1) + else { - seq += ch.charAt(1); + label = key + "_cons"; } } - out.append(seq); + 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()); + print(getSeqsAsArray(), false); out.append("//"); out.append(newline); @@ -953,15 +1229,16 @@ public class StockholmFile extends AlignFile } private static Hashtable typeIds = null; + static { if (typeIds == null) { typeIds = new Hashtable(); - typeIds.put("SS", "secondary structure"); - typeIds.put("SA", "surface accessibility"); + typeIds.put("SS", "Secondary Structure"); + typeIds.put("SA", "Surface Accessibility"); typeIds.put("TM", "transmembrane"); - typeIds.put("PP", "posterior probability"); + typeIds.put("PP", "Posterior Probability"); typeIds.put("LI", "ligand binding"); typeIds.put("AS", "active site"); typeIds.put("IN", "intron"); @@ -972,7 +1249,7 @@ public class StockholmFile extends AlignFile typeIds.put("DE", "description"); typeIds.put("DR", "reference"); typeIds.put("LO", "look"); - typeIds.put("RF", "reference positions"); + typeIds.put("RF", "Reference Positions"); } } @@ -983,8 +1260,8 @@ public class StockholmFile extends AlignFile { return (String) typeIds.get(id); } - System.err.println("Warning : Unknown Stockholm annotation type code " - + id); + System.err.println( + "Warning : Unknown Stockholm annotation type code " + id); return id; } @@ -995,7 +1272,7 @@ public class StockholmFile extends AlignFile while (e.hasMoreElements()) { Object ll = e.nextElement(); - if (typeIds.get(ll).toString().equals(type)) + if (typeIds.get(ll).toString().equalsIgnoreCase(type)) { key = (String) ll; break; @@ -1003,44 +1280,29 @@ public class StockholmFile extends AlignFile } if (key != null) { - return (String) key; + return key; } - System.err.println("Warning : Unknown Stockholm annotation type: " - + type); + System.err.println( + "Warning : Unknown Stockholm annotation type: " + type); return key; } + /** - * //ssline is complete secondary structure line private AlignmentAnnotation - * addHelices(Vector annotation, String label, String ssline) { + * make a friendly ID string. * - * // decide on secondary structure or not. Annotation[] els = new - * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) { - * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new - * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not - * - * ann.secondaryStructure = - * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0); - * - * ann.displayCharacter = "x" + ann.displayCharacter; - * - * System.out.println(ann.displayCharacter); - * - * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e = - * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot = - * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type)) - * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot = - * new AlignmentAnnotation(type, type, els); - * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new - * Annotation[helicesAnnot.annotations.length + els.length]; - * System.arraycopy(helicesAnnot.annotations, 0, anns, 0, - * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns, - * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations = - * anns; } - * - * helicesAnnot.features = Rna.GetBasePairs(ssline); - * Rna.HelixMap(helicesAnnot.features); - * - * - * return helicesAnnot; } + * @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; + } }