X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=4d8f1367284683ef9b7f9d3e4dce281d2ea7f28c;hb=0184787284a60624bd112260c0318889ade9fd56;hp=fd5fd444f32a67237a57c1d31e5ad87b0911fbce;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index fd5fd44..4d8f136 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,409 +1,1123 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 jalview.datamodel.*;
-import com.stevesoft.pat.*;
-//import org.apache.log4j.*;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+
+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.List;
+import java.util.StringTokenizer;
+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 org.apache.log4j.*;
/**
- * This class is supposed to parse a Stockholm format file into Jalview
+ * 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
+ * @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");
+ // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
+ protected ArrayList result;
+ StringBuffer out; // output buffer
+
+ AlignmentI al;
+
+ public StockholmFile()
+ {
+ }
- public StockholmFile()
+ /**
+ * Creates a new StockholmFile object for output.
+ */
+ public StockholmFile(AlignmentI al)
+ {
+ this.al = al;
+ }
+
+ 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 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);
+ 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);
- public StockholmFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
+ }
+
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.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
+ */
+ 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 = "";
- public void initData()
+ // ------------------ Parsing File ----------------------
+ // First, we have to check that this file has STOCKHOLM format, i.e. the
+ // first line must match
+
+
+ r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+ if (!r.search(nextLine()))
+ {
+ throw new IOException(
+ "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+ }
+ else
+ {
+ version = r.stringMatched(1);
+
+ // logger.debug("Stockholm version: " + version);
+ }
+
+ // We define some Regexes here that will be used regularily later
+ rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
+ p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
+ // id/from/to
+ s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
+ r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
+ x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
+
+ // Convert all bracket types to parentheses (necessary for passing to VARNA)
+ Regex openparen = new Regex("(<|\\[)", "(");
+ Regex closeparen = new Regex("(>|\\])", ")");
+
+ // Detect if file is RNA by looking for bracket types
+ Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+
+ rend.optimize();
+ p.optimize();
+ s.optimize();
+ r.optimize();
+ x.optimize();
+ openparen.optimize();
+ closeparen.optimize();
+
+ while ((line = nextLine()) != null)
+ {
+ if (line.length() == 0)
+ {
+ continue;
+ }
+ if (rend.search(line))
+ {
+ // End of the alignment, pass stuff back
+ this.noSeqs = seqs.size();
+
+ String seqdb,dbsource = null;
+ 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)
+ {
+ String dbType = getAlignmentProperty("AC").toString();
+ if (pf.search(dbType))
+ {
+ // PFAM Alignment - so references are typically from Uniprot
+ dbsource = "PFAM";
+ }
+ else if (rf.search(dbType))
+ {
+ dbsource = "RFAM";
+ }
+ }
+ // logger.debug("Number of sequences: " + this.noSeqs);
+ Enumeration accs = seqs.keys();
+ while (accs.hasMoreElements())
+ {
+ String acc = (String) accs.nextElement();
+ // logger.debug("Processing sequence " + acc);
+ String seq = (String) seqs.remove(acc);
+ if (maxLength < seq.length())
+ {
+ maxLength = seq.length();
+ }
+ int start = 1;
+ int end = -1;
+ String sid = acc;
+ /*
+ * 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);
+ }
+ }
+
+ if (accAnnotations != null && accAnnotations.containsKey("AC"))
+ {
+ if (dbsource != 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 ?
+ }
+
+ Hashtable features = null;
+ // We need to adjust the positions of all features to account for gaps
+ try
+ {
+ features = (Hashtable) accAnnotations.remove("features");
+ } catch (java.lang.NullPointerException e)
+ {
+ // loggerwarn("Getting Features for " + acc + ": " +
+ // e.getMessage());
+ // continue;
+ }
+ // if we have features
+ if (features != null)
+ {
+ int posmap[] = seqO.findPositionMap();
+ Enumeration i = features.keys();
+ while (i.hasMoreElements())
+ {
+ // TODO: parse out secondary structure annotation as annotation
+ // row
+ // TODO: parse out scores as annotation row
+ // TODO: map coding region to core jalview feature types
+ String type = i.nextElement().toString();
+ Hashtable content = (Hashtable) features.remove(type);
+
+ // add alignment annotation for this feature
+ String key = type2id(type);
+ if (key != null)
+ {
+ if (accAnnotations != null
+ && accAnnotations.containsKey(key))
+ {
+ Vector vv = (Vector) accAnnotations.get(key);
+ for (int ii = 0; ii < vv.size(); ii++)
+ {
+ AlignmentAnnotation an = (AlignmentAnnotation) vv
+ .elementAt(ii);
+ seqO.addAlignmentAnnotation(an);
+ }
+ }
+ }
+
+ 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());
+ }
+ }
+
+/**
+ * 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)
{
- super.initData();
+ String num,range=sdbac.substring(st+1);
+ sdbac = sdbac.substring(0,st);
+ if ((p=range.indexOf("-"))>-1)
+ {
+ p++;
+ if (p-1)
+ {
+ // strip of last subdomain
+ 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)
+ {
+ dbrs.add(dbrf);
+ }
+ } 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)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
+ if (dbrf!=null)
+ {
+ dbrs.add(dbrf);
+ }
}
+ if (st!=-1 && en!=-1)
+ {
+ 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.datamodel.Mapping mping = new Mapping(mp);
+ d.setMap(mping);
+ }
+ }
+ }
+
+ protected static AlignmentAnnotation parseAnnotationRow(
+ Vector annotation, String label, String annots)
+ {
+ String convert1, convert2 = null;
- /**
- * 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
+ // 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;
+ if (label.contains("_cons"))
{
- // --------------- 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()))
+ 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))
{
- throw new IOException("This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getRNASecStrucState(pos).charAt(0);
}
else
{
- version = r.stringMatched(1);
- //logger.debug("Stockholm version: " + version);
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getDssp3state(pos).charAt(0);
}
-// 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)
+ if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
{
- if (line.length() == 0) continue;
- if(rend.search(line))
- {
-// End of the alignment, pass stuff back
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
+ }
- 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.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);
- }
- }
- else if (!r.search(line))
- {
- //System.err.println("Found sequence line: " + line);
+ 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;
+ }
- // 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);
+ public String print(SequenceI[] s)
+ {
+ // find max length of id
+ int max = 0;
+ int maxid = 0;
+ int in = 0;
+ Hashtable dataRef = null;
+ while ((in < s.length) && (s[in] != null))
+ {
+ String tmp = printId(s[in]);
+ if (s[in].getSequence().length > max)
+ {
+ max = s[in].getSequence().length;
+ }
+
+ if (tmp.length() > maxid)
+ {
+ maxid = tmp.length();
+ }
+ if (s[in].getDBRef() != null)
+ {
+ for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+ {
+ if (dataRef == null)
+ dataRef = new Hashtable();
+
+ String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+ + " ; "
+ + s[in].getDBRef()[idb].getAccessionId().toString();
+ dataRef.put(tmp, datAs1);
+ }
+ }
+ in++;
+ }
+ maxid += 9;
+ int i = 0;
+
+ // output database type
+ if (al.getProperties() != null)
+ {
+ if (!al.getProperties().isEmpty())
+ {
+ Enumeration key = al.getProperties().keys();
+ Enumeration val = al.getProperties().elements();
+ while (key.hasMoreElements())
+ {
+ out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+ out.append(newline);
+ }
+ }
+ }
+
+ // output database accessions
+ if (dataRef != null)
+ {
+ 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"))
+ {
+
+ out.append(" AC " + type.substring(type.indexOf(";") + 1));
+ }
+ else
+ {
+ out.append(" DR " + type + " ");
+ }
+ out.append(newline);
+ }
+ }
+
+ // output annotations
+ while (i < s.length && s[i] != null)
+ {
+ if (s[i].getDatasetSequence() != 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; j < alAnot.length; j++)
+ {
+ if (ds.getSequenceFeatures() != null)
+ {
+ feature = ds.getSequenceFeatures()[0].type;
+ }
+ String key = type2id(feature);
+
+ if (key == null)
+ 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(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
+ out.append(s[i].getSequenceAsString());
+ out.append(newline);
+ i++;
+ }
+
+ // alignment annotation
+ AlignmentAnnotation aa;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
+ {
+ aa = al.getAlignmentAnnotation()[ia];
+ if (aa.autoCalculated || !aa.visible)
+ {
+ continue;
+ }
+ String seq = "";
+ String label;
+
+ 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)
+ {
+ char ll = aa.annotations[j].secondaryStructure;
+ if (Character.toString(ll).equals(" "))
+ seq += "C";
+ else
+ seq += ll;
+ }
+ else if (ch.length() == 1)
+ {
+ seq += ch;
+ }
+ else if (ch.length() > 1)
+ {
+ seq += ch.charAt(1);
+ }
+ }
+ out.append(seq);
+ out.append(newline);
+ }
+ }
+ return out.toString();
+ }
- seqs.put(x.stringMatched(1), ns);
- }
- else
- {
- String annType = r.stringMatched(1);
- String annContent = r.stringMatched(2);
+ public String print()
+ {
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
+ print(getSeqsAsArray());
+
+ out.append("//");
+ out.append(newline);
+ return out.toString();
+ }
- //System.err.println("type:" + annType + " content: " + annContent);
+ 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");
- 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);
- }
- }
- }
}
+ }
- public static String print(SequenceI[] s)
+ protected static String id2type(String id)
+ {
+ if (typeIds.containsKey(id))
{
- return "not yet implemented";
+ return (String) typeIds.get(id);
}
+ System.err.println("Warning : Unknown Stockholm annotation type code "
+ + id);
+ return id;
+ }
- public String print()
+ protected static String type2id(String type)
+ {
+ String key = null;
+ Enumeration e = typeIds.keys();
+ while (e.hasMoreElements())
{
- return print(getSeqsAsArray());
+ Object ll = e.nextElement();
+ if (typeIds.get(ll).toString().equals(type))
+ {
+ key = (String) ll;
+ break;
+ }
}
-
- private String id2type(String id)
+ if (key != null)
{
- // GR ids
- if (id.equals("SS")) return "secondary structure";
- else if (id.equals("SA")) return "surface accessibility";
- else if (id.equals("TM")) return "transmembrane";
- else if (id.equals("PP")) return "posterior probability";
- else if (id.equals("LI")) return "ligand binding";
- else if (id.equals("AS")) return "active site";
- else if (id.equals("IN")) return "intron";
- else if (id.equals("IR")) return "interacting residue";
- // GS ids
- else if (id.equals("AC")) return "accession";
- else if (id.equals("OS")) return "organism";
- else if (id.equals("CL")) return "class";
- else if (id.equals("DE")) return "description";
- else if (id.equals("DR")) return "reference";
- else if (id.equals("LO")) return "look";
- else return null;
+ return (String) key;
+ }
+ System.err.println("Warning : Unknown Stockholm annotation type: "
+ + type);
+ return key;
+ }
+ /**
+ * 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;
+ }
}