/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 javax.xml.parsers.ParserConfigurationException;
import org.xml.sax.SAXException;
import com.stevesoft.pat.*;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.models.rna.RNA;
import jalview.datamodel.*;
import jalview.analysis.Rna;
// import org.apache.log4j.*;
/**
* 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");
protected ArrayList result;
public String id;
public StockholmFile()
{
}
public StockholmFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
public StockholmFile(FileParse source) throws Exception
{
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
* @throws ExceptionUnmatchedClosingParentheses
*/
public void parse()
{
FileReader fr = null;
fr = new FileReader(inFile);
BufferedReader r = new BufferedReader (fr);
result = RNAFactory.loadSecStrStockholm(r);
System.out.println("this is the secondary scructure:" +result.size());
SequenceI[] seqs = new SequenceI[result.size()];
System.out.println(type); //the type is "File"
System.out.println(inFile );//inFile is the path
for(int i=0;i|\\])", ")");
//
// // Detect if file is RNA by looking for bracket types
// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
//
// rend.optimize();
// p.optimize();
// s.optimize();
// r.optimize();
// x.optimize();
// openparen.optimize();
// closeparen.optimize();
//
// while ((line = nextLine()) != null)
// {
// if (line.length() == 0)
// {
// continue;
// }
// if (rend.search(line))
// {
// // End of the alignment, pass stuff back
//
// this.noSeqs = seqs.size();
// // logger.debug("Number of sequences: " + this.noSeqs);
// Enumeration accs = seqs.keys();
// while (accs.hasMoreElements())
// {
// String acc = (String) accs.nextElement();
// // logger.debug("Processing sequence " + acc);
// String seq = (String) seqs.remove(acc);
// if (maxLength < seq.length())
// {
// maxLength = seq.length();
// }
// int start = 1;
// int end = -1;
// String sid = acc;
// /*
// * Retrieve hash of annotations for this accession
// * Associate Annotation with accession
// */
// Hashtable accAnnotations = null;
//
// if (seqAnn != null && seqAnn.containsKey(acc))
// {
// accAnnotations = (Hashtable) seqAnn.remove(acc);
// //TODO: add structures to sequence
// }
//
// // Split accession in id and from/to
// if (p.search(acc))
// {
// sid = p.stringMatched(1);
// start = Integer.parseInt(p.stringMatched(2));
// end = Integer.parseInt(p.stringMatched(3));
// }
// // logger.debug(sid + ", " + start + ", " + end);
//
// Sequence seqO = new Sequence(sid, seq, start, end);
// // Add Description (if any)
// if (accAnnotations != null && accAnnotations.containsKey("DE"))
// {
// String desc = (String) accAnnotations.get("DE");
// seqO.setDescription((desc == null) ? "" : desc);
// }
// // Add DB References (if any)
// if (accAnnotations != null && accAnnotations.containsKey("DR"))
// {
// String dbr = (String) accAnnotations.get("DR");
// if (dbr != null && dbr.indexOf(";") > -1)
// {
// String src = dbr.substring(0, dbr.indexOf(";"));
// String acn = dbr.substring(dbr.indexOf(";") + 1);
// jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
// // seqO.addDBRef(dbref);
// }
// }
// if (accAnnotations != null && accAnnotations.containsKey("SS"))
// {
// Vector v = (Vector) accAnnotations.get("SS");
//
// for (int i = 0; i < v.size(); i++)
// {
// AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);
// seqO.addAlignmentAnnotation(an);
// //annotations.add(an);
// }
// }
//
// Hashtable features = null;
// // We need to adjust the positions of all features to account for gaps
// try
// {
// features = (Hashtable) accAnnotations.remove("features");
// } catch (java.lang.NullPointerException e)
// {
// // loggerwarn("Getting Features for " + acc + ": " +
// // e.getMessage());
// // continue;
// }
// // if we have features
// if (features != null)
// {
// int posmap[] = seqO.findPositionMap();
// Enumeration i = features.keys();
// while (i.hasMoreElements())
// {
// // TODO: parse out secondary structure annotation as annotation
// // row
// // TODO: parse out scores as annotation row
// // TODO: map coding region to core jalview feature types
// String type = i.nextElement().toString();
// Hashtable content = (Hashtable) features.remove(type);
// Enumeration j = content.keys();
// while (j.hasMoreElements())
// {
// String desc = j.nextElement().toString();
// String ns = content.get(desc).toString();
// char[] byChar = ns.toCharArray();
// for (int k = 0; k < byChar.length; k++)
// {
// char c = byChar[k];
// if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
// // uses
// // '.'
// // for
// // feature
// // background
// {
// int new_pos = posmap[k]; // look up nearest seqeunce
// // position to this column
// SequenceFeature feat = new SequenceFeature(type, desc,
// new_pos, new_pos, 0f, null);
//
// seqO.addSequenceFeature(feat);
// }
// }
// }
//
// }
//
// }
// // garbage collect
//
// // logger.debug("Adding seq " + acc + " from " + start + " to " + end
// // + ": " + seq);
// this.seqs.addElement(seqO);
// }
// return; // finished parsing this segment of source
// }
// else if (!r.search(line))
// {
// // System.err.println("Found sequence line: " + line);
//
// // Split sequence in sequence and accession parts
// if (!x.search(line))
// {
// // logger.error("Could not parse sequence line: " + line);
// throw new IOException("Could not parse sequence line: " + line);
// }
// String ns = (String) seqs.get(x.stringMatched(1));
// if (ns == null)
// {
// ns = "";
// }
// ns += x.stringMatched(2);
//
// seqs.put(x.stringMatched(1), ns);
// }
// else
// {
// String annType = r.stringMatched(1);
// String annContent = r.stringMatched(2);
//
// // System.err.println("type:" + annType + " content: " + annContent);
//
// if (annType.equals("GF"))
// {
// /*
// * Generic per-File annotation, free text Magic features: #=GF NH
// * #=GF TN Pfam descriptions: 7. DESCRIPTION OF FIELDS
// *
// * Compulsory fields: ------------------
// *
// * AC Accession number: Accession number in form PFxxxxx.version or
// * PBxxxxxx. ID Identification: One word name for family. DE
// * Definition: Short description of family. AU Author: Authors of the
// * entry. SE Source of seed: The source suggesting the seed members
// * belong to one family. GA Gathering method: Search threshold to
// * build the full alignment. TC Trusted Cutoff: Lowest sequence score
// * and domain score of match in the full alignment. NC Noise Cutoff:
// * Highest sequence score and domain score of match not in full
// * alignment. TP Type: Type of family -- presently Family, Domain,
// * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
// * Alignment Method The order ls and fs hits are aligned to the model
// * to build the full align. // End of alignment.
// *
// * Optional fields: ----------------
// *
// * DC Database Comment: Comment about database reference. DR Database
// * Reference: Reference to external database. RC Reference Comment:
// * Comment about literature reference. RN Reference Number: Reference
// * Number. RM Reference Medline: Eight digit medline UI number. RT
// * Reference Title: Reference Title. RA Reference Author: Reference
// * Author RL Reference Location: Journal location. PI Previous
// * identifier: Record of all previous ID lines. KW Keywords: Keywords.
// * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
// * NL Location: Location of nested domains - sequence ID, start and
// * end of insert.
// *
// * Obsolete fields: ----------- AL Alignment method of seed: The
// * method used to align the seed members.
// */
// // Let's save the annotations, maybe we'll be able to do something
// // with them later...
// Regex an = new Regex("(\\w+)\\s*(.*)");
// if (an.search(annContent))
// {
// if (an.stringMatched(1).equals("NH"))
// {
// treeString.append(an.stringMatched(2));
// }
// else if (an.stringMatched(1).equals("TN"))
// {
// if (treeString.length() > 0)
// {
// if (treeName == null)
// {
// treeName = "Tree " + (getTreeCount() + 1);
// }
// addNewickTree(treeName, treeString.toString());
// }
// treeName = an.stringMatched(2);
// treeString = new StringBuffer();
// }
// setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
// }
// }
// else if (annType.equals("GS"))
// {
// // Generic per-Sequence annotation, free text
// /*
// * Pfam uses these features: Feature Description ---------------------
// * ----------- AC ACcession number DE
// * DEscription DR ; ; Database Reference OS
// * OrganiSm (species) OC Organism Classification (clade, etc.)
// * LO Look (Color, etc.)
// */
// if (s.search(annContent))
// {
// String acc = s.stringMatched(1);
// String type = s.stringMatched(2);
// String content = s.stringMatched(3);
// // TODO: store DR in a vector.
// // TODO: store AC according to generic file db annotation.
// Hashtable ann;
// if (seqAnn.containsKey(acc))
// {
// ann = (Hashtable) seqAnn.get(acc);
// }
// else
// {
// ann = new Hashtable();
// }
// ann.put(type, content);
// seqAnn.put(acc, ann);
// }
// else
// {
// throw new IOException("Error parsing " + line);
// }
// }
// else if (annType.equals("GC"))
// {
// // Generic per-Column annotation, exactly 1 char per column
// // always need a label.
// if (x.search(annContent))
// {
// // parse out and create alignment annotation directly.
// parseAnnotationRow(annotations, x.stringMatched(1),
// x.stringMatched(2));
// }
// }
// else if (annType.equals("GR"))
// {
// // Generic per-Sequence AND per-Column markup, exactly 1 char per
// // column
// /*
// * Feature Description Markup letters ------- -----------
// * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
// * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
// * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
// * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
// * or after) [0-2]
// */
// if (s.search(annContent))
// {
// String acc = s.stringMatched(1);
// String type = s.stringMatched(2);
// String seq = new String(s.stringMatched(3));
// String description = null;
// // Check for additional information about the current annotation
// // We use a simple string tokenizer here for speed
// StringTokenizer sep = new StringTokenizer(seq, " \t");
// description = sep.nextToken();
// if (sep.hasMoreTokens())
// {
// seq = sep.nextToken();
// }
// else
// {
// seq = description;
// description = new String();
// }
// // sequence id with from-to fields
//
// Hashtable ann;
// // Get an object with all the annotations for this sequence
// if (seqAnn.containsKey(acc))
// {
// // logger.debug("Found annotations for " + acc);
// ann = (Hashtable) seqAnn.get(acc);
// }
// else
// {
// // logger.debug("Creating new annotations holder for " + acc);
// ann = new Hashtable();
// seqAnn.put(acc, ann);
// }
// //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence
// Hashtable features;
// // Get an object with all the content for an annotation
// if (ann.containsKey("features"))
// {
// // logger.debug("Found features for " + acc);
// features = (Hashtable) ann.get("features");
// }
// else
// {
// // logger.debug("Creating new features holder for " + acc);
// features = new Hashtable();
// ann.put("features", features);
// }
//
// Hashtable content;
// if (features.containsKey(this.id2type(type)))
// {
// // logger.debug("Found content for " + this.id2type(type));
// content = (Hashtable) features.get(this.id2type(type));
// }
// else
// {
// // logger.debug("Creating new content holder for " +
// // this.id2type(type));
// content = new Hashtable();
// features.put(this.id2type(type), content);
// }
// String ns = (String) content.get(description);
// if (ns == null)
// {
// ns = "";
// }
// ns += seq;
// content.put(description, ns);
//
// if(type.equals("SS")){
// Hashtable strucAnn;
// if (seqAnn.containsKey(acc))
// {
// strucAnn = (Hashtable) seqAnn.get(acc);
// }
// else
// {
// strucAnn = new Hashtable();
// }
//
// Vector newStruc=new Vector();
// parseAnnotationRow(newStruc, type,ns);
//
// strucAnn.put(type, newStruc);
// seqAnn.put(acc, strucAnn);
// }
// }
// else
// {
// System.err
// .println("Warning - couldn't parse sequence annotation row line:\n"
// + line);
// // throw new IOException("Error parsing " + line);
// }
// }
// else
// {
// throw new IOException("Unknown annotation detected: " + annType
// + " " + annContent);
// }
// }
// }
// if (treeString.length() > 0)
// {
// if (treeName == null)
// {
// treeName = "Tree " + (1 + getTreeCount());
// }
// addNewickTree(treeName, treeString.toString());
// }
// }
//
protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,
String label, String annots)
{
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");
}
}
protected static 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; }
*
*/
/**
* make a friendly ID string.
*
* @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;
}
}