X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=4697262a7143db6b8fb022a0c98fe26b910801e6;hb=7ae11f7f7f00549c6fb3af9ee193dc103a3c8de8;hp=606540f5b4196d2eac2beab31f685da364d9239b;hpb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 606540f..4697262 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -28,12 +28,14 @@ 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; @@ -205,7 +207,7 @@ public class StockholmFile extends AlignFile String version; // String id; Hashtable seqAnn = new Hashtable(); // Sequence related annotations - LinkedHashMap seqs = new LinkedHashMap(); + LinkedHashMap seqs = new LinkedHashMap<>(); Regex p, r, rend, s, x; // Temporary line for processing RNA annotation // String RNAannot = ""; @@ -332,17 +334,14 @@ 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 +526,9 @@ 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)); } } @@ -666,7 +668,7 @@ public class StockholmFile extends AlignFile strucAnn = new Hashtable(); } - Vector newStruc = new Vector(); + Vector newStruc = new Vector<>(); parseAnnotationRow(newStruc, type, ns); for (AlignmentAnnotation alan : newStruc) { @@ -718,7 +720,7 @@ public class StockholmFile extends AlignFile private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource) { DBRefEntry dbrf = null; - List dbrs = new ArrayList(); + List dbrs = new ArrayList<>(); String seqdb = "Unknown", sdbac = "" + dbr; int st = -1, en = -1, p; if ((st = sdbac.indexOf("/")) > -1) @@ -755,6 +757,12 @@ 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 +938,11 @@ 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) { @@ -942,8 +955,10 @@ public class StockholmFile extends AlignFile int maxid = 0; int in = 0; Hashtable dataRef = null; + boolean isAA = s[in].isProtein(); while ((in < s.length) && (s[in] != null)) { + String tmp = printId(s[in], jvSuffix); max = Math.max(max, s[in].getLength()); @@ -953,17 +968,33 @@ public class StockholmFile extends AlignFile } if (s[in].getDBRefs() != null) { - for (int idb = 0; idb < s[in].getDBRefs().length; idb++) + if (dataRef == null) + { + dataRef = new Hashtable(); + } + List primrefs = s[in].getPrimaryDBRefs(); + if (primrefs.size() >= 1) + { + dataRef.put(tmp, dbref_to_ac_record(primrefs.get(0))); + } + else { - if (dataRef == null) + for (int idb = 0; idb < s[in].getDBRefs().length; idb++) { - dataRef = new Hashtable(); + DBRefEntry dbref = s[in].getDBRefs()[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; + } } - - String datAs1 = s[in].getDBRefs()[idb].getSource().toString() - + " ; " - + s[in].getDBRefs()[idb].getAccessionId().toString(); - dataRef.put(tmp, datAs1); } } in++; @@ -996,7 +1027,8 @@ public class StockholmFile extends AlignFile String type = (String) 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)); @@ -1127,7 +1159,13 @@ public class StockholmFile extends AlignFile String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character.toString(sequenceI.getCharAt(k))) - : annot.displayCharacter; + : (annot.displayCharacter == null + ? String.valueOf(annot.secondaryStructure) + : annot.displayCharacter); + if (ch == null) + { + ch = " "; + } if (key != null && key.equals("SS")) { char ssannotchar = ' '; @@ -1149,11 +1187,7 @@ public class StockholmFile extends AlignFile } if (charset) { - if (ssannotchar == ' ' && isrna) - { - ssannotchar = '.'; - } - return ssannotchar; + return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar; } }