/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
/*
* This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
*/
package jalview.io;
import java.io.*;
import java.util.*;
import com.stevesoft.pat.*;
import jalview.datamodel.*;
import jalview.analysis.Rna;
// import org.apache.log4j.*;
/**
* This class is supposed to parse a Stockholm format file into Jalview There
* are TODOs in this class: we do not know what the database source and version
* is for the file when parsing the #GS= AC tag which associates accessions with
* sequences. Database references are also not parsed correctly: a separate
* reference string parser must be added to parse the database reference form
* into Jalview's local representation.
*
* @author bsb at sanger.ac.uk
* @version 0.3 + jalview mods
*
*/
public class StockholmFile extends AlignFile
{
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
public StockholmFile()
{
}
public StockholmFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
public StockholmFile(FileParse source) throws IOException
{
super(source);
}
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;
// 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();
// 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());
}
}
private AlignmentAnnotation parseAnnotationRow(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;
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"))
{
ss = true;
}
// decide on secondary structure or not.
Annotation[] els = new Annotation[annots.length()];
for (int i = 0; i < annots.length(); i++)
{
String pos = annots.substring(i, i + 1);
Annotation ann;
ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
// be written out
if (ss)
{
if (detectbrackets.search(pos))
{
ann.secondaryStructure = jalview.schemes.ResidueProperties
.getRNASecStrucState(pos).charAt(0);
}
else
{
ann.secondaryStructure = jalview.schemes.ResidueProperties
.getDssp3state(pos).charAt(0);
}
if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
{
ann.displayCharacter = ""; // null; // " ";
}
else
{
ann.displayCharacter = " " + ann.displayCharacter;
}
}
els[i] = ann;
}
AlignmentAnnotation annot = null;
Enumeration e = annotation.elements();
while (e.hasMoreElements())
{
annot = (AlignmentAnnotation) e.nextElement();
if (annot.label.equals(type))
break;
annot = null;
}
if (annot == null)
{
annot = new AlignmentAnnotation(type, type, els);
annotation.addElement(annot);
}
else
{
Annotation[] anns = new Annotation[annot.annotations.length
+ els.length];
System.arraycopy(annot.annotations, 0, anns, 0,
annot.annotations.length);
System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
annot.annotations = anns;
//System.out.println("else: ");
}
return annot;
}
public static String print(SequenceI[] s)
{
return "not yet implemented";
}
public String print()
{
return print(getSeqsAsArray());
}
private static Hashtable typeIds = null;
static
{
if (typeIds == null)
{
typeIds = new Hashtable();
typeIds.put("SS", "secondary structure");
typeIds.put("SA", "surface accessibility");
typeIds.put("TM", "transmembrane");
typeIds.put("PP", "posterior probability");
typeIds.put("LI", "ligand binding");
typeIds.put("AS", "active site");
typeIds.put("IN", "intron");
typeIds.put("IR", "interacting residue");
typeIds.put("AC", "accession");
typeIds.put("OS", "organism");
typeIds.put("CL", "class");
typeIds.put("DE", "description");
typeIds.put("DR", "reference");
typeIds.put("LO", "look");
typeIds.put("RF", "reference positions");
}
}
private String id2type(String id)
{
if (typeIds.containsKey(id))
{
return (String) typeIds.get(id);
}
System.err.println("Warning : Unknown Stockholm annotation type code "
+ id);
return id;
}
/**
* //ssline is complete secondary structure line private AlignmentAnnotation
* addHelices(Vector annotation, String label, String ssline) {
*
* // 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; }
*/
}