X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=5d645cafe30874f85fe0b58a06619da2571c91c8;hb=3f086e4f77ae2baed4b6290bce9cfd964fbc9446;hp=84e629e043e85055e787ef5d33bc6d4d90d81e58;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 84e629e..5d645ca 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -23,20 +23,6 @@ */ package jalview.io; -import jalview.analysis.Rna; -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.schemes.ResidueProperties; -import jalview.util.Comparison; -import jalview.util.Format; -import jalview.util.MessageManager; - import java.io.BufferedReader; import java.io.FileReader; import java.io.IOException; @@ -45,6 +31,7 @@ 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; @@ -53,8 +40,21 @@ 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.*; +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 jalview.util.MessageManager; /** * This class is supposed to parse a Stockholm format file into Jalview There @@ -76,20 +76,21 @@ public class StockholmFile extends AlignFile { private static final String ANNOTATION = "annotation"; -// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "("); -// -// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")"); + // 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. + // 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( - "^[^<>[\\](){}A-DF-Za-df-z]*$"); + "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$"); StringBuffer out; // output buffer @@ -239,8 +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(); @@ -332,17 +333,15 @@ 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); - - } + // 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 ? @@ -527,6 +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)); } } @@ -755,6 +759,13 @@ public class StockholmFile extends AlignFile st = -1; } } + if (dbsource == null) + { + // make up an origin based on whether the sequence looks like it is + // nucleotide + // or protein + dbsource = (seqO.isProtein()) ? "PFAM" : "RFAM"; + } if (dbsource.equals("PFAM")) { seqdb = "UNIPROT"; @@ -930,6 +941,12 @@ public class StockholmFile extends AlignFile return annot; } + private String dbref_to_ac_record(DBRefEntry ref) + { + return ref.getSource().toString() + " ; " + + ref.getAccessionId().toString(); + } + @Override public String print(SequenceI[] s, boolean jvSuffix) { @@ -944,6 +961,7 @@ public class StockholmFile extends AlignFile int slen = s.length; SequenceI seq; Hashtable dataRef = null; + boolean isAA = s[in].isProtein(); while ((in < slen) && ((seq = s[in]) != null)) { String tmp = printId(seq, jvSuffix); @@ -961,14 +979,29 @@ public class StockholmFile extends AlignFile { dataRef = new Hashtable<>(); } - for (int idb = 0; idb < ndb; idb++) + List primrefs = seq.getPrimaryDBRefs(); + if (primrefs.size() >= 1) { - - DBRefEntry ref = seqrefs.get(idb); - String datAs1 = ref.getSource().toString() - + " ; " - + ref.getAccessionId().toString(); - dataRef.put(tmp, datAs1); + 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++; @@ -998,10 +1031,11 @@ public class StockholmFile extends AlignFile while (en.hasMoreElements()) { Object idd = en.nextElement(); - String type = (String) dataRef.remove(idd); + String type = dataRef.remove(idd); out.append(new Format("%-" + (maxid - 2) + "s") .form("#=GS " + idd.toString() + " ")); - if (type.contains("PFAM") || type.contains("RFAM")) + if (isAA && type.contains("UNIPROT") + || (!isAA && type.contains("EMBL"))) { out.append(" AC " + type.substring(type.indexOf(";") + 1)); @@ -1081,7 +1115,7 @@ public class StockholmFile extends AlignFile } else { - key = type2id(aa.label.toLowerCase()); + key = type2id(aa.label.toLowerCase(Locale.ROOT)); if (key == null) { label = aa.label;