X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=d67448583da70cd393e26069701ec22d933631a8;hb=73e4b463a2257168a1155a96deb0a18a0e4ce162;hp=606540f5b4196d2eac2beab31f685da364d9239b;hpb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 606540f..d674485 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 @@ -146,19 +147,19 @@ public class StockholmFile extends AlignFile + umcp.getMessage() + ")"; throw new IOException(umcp); } - // DEBUG System.out.println("this is the secondary scructure:" + // DEBUG jalview.bin.Console.outPrintln("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") + // DEBUG jalview.bin.Console.errPrintln("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); + // DEBUG jalview.bin.Console.outPrintln(seq); + // DEBUG jalview.bin.Console.errPrintln(rna); int begin = 0; int end = seq.length() - 1; id = safeName(getDataName()); @@ -205,7 +206,7 @@ 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 = ""; @@ -217,8 +218,9 @@ public class StockholmFile extends AlignFile r = new Regex("# STOCKHOLM ([\\d\\.]+)"); if (!r.search(nextLine())) { - throw new IOException(MessageManager - .getString("exception.stockholm_invalid_format")); + throw new IOException( + MessageManager.getString("exception.stockholm_invalid_format") + + " (" + r + ")"); } else { @@ -239,8 +241,8 @@ 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(); @@ -261,7 +263,7 @@ public class StockholmFile extends AlignFile // End of the alignment, pass stuff back this.noSeqs = seqs.size(); - String seqdb, dbsource = null; + String 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) @@ -332,17 +334,15 @@ 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 ? @@ -441,7 +441,7 @@ public class StockholmFile extends AlignFile } else if (!r.search(line)) { - // System.err.println("Found sequence line: " + line); + // jalview.bin.Console.errPrintln("Found sequence line: " + line); // Split sequence in sequence and accession parts if (!x.search(line)) @@ -465,7 +465,7 @@ public class StockholmFile extends AlignFile String annType = r.stringMatched(1); String annContent = r.stringMatched(2); - // System.err.println("type:" + annType + " content: " + annContent); + // jalview.bin.Console.errPrintln("type:" + annType + " content: " + annContent); if (annType.equals("GF")) { @@ -527,6 +527,11 @@ 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)); } } @@ -562,7 +567,7 @@ public class StockholmFile extends AlignFile else { // throw new IOException("Error parsing " + line); - System.err.println(">> missing annotation: " + line); + jalview.bin.Console.errPrintln(">> missing annotation: " + line); } } else if (annType.equals("GC")) @@ -666,7 +671,7 @@ public class StockholmFile extends AlignFile strucAnn = new Hashtable(); } - Vector newStruc = new Vector(); + Vector newStruc = new Vector<>(); parseAnnotationRow(newStruc, type, ns); for (AlignmentAnnotation alan : newStruc) { @@ -680,7 +685,7 @@ public class StockholmFile extends AlignFile // } else { - System.err.println( + jalview.bin.Console.errPrintln( "Warning - couldn't parse sequence annotation row line:\n" + line); // throw new IOException("Error parsing " + line); @@ -718,7 +723,7 @@ 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 +760,13 @@ 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"; @@ -925,11 +937,17 @@ public class StockholmFile extends AlignFile annot.annotations.length); System.arraycopy(els, 0, anns, annot.annotations.length, els.length); annot.annotations = anns; - // System.out.println("else: "); + // jalview.bin.Console.outPrintln("else: "); } 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) { @@ -941,29 +959,50 @@ public class StockholmFile extends AlignFile int max = 0; int maxid = 0; int in = 0; - Hashtable dataRef = null; - while ((in < s.length) && (s[in] != null)) + int slen = s.length; + SequenceI seq; + Hashtable dataRef = null; + boolean isAA = s[in].isProtein(); + while ((in < slen) && ((seq = s[in]) != null)) { - String tmp = printId(s[in], jvSuffix); - max = Math.max(max, s[in].getLength()); + String tmp = printId(seq, jvSuffix); + max = Math.max(max, seq.getLength()); if (tmp.length() > maxid) { maxid = tmp.length(); } - if (s[in].getDBRefs() != null) + List seqrefs = seq.getDBRefs(); + int ndb; + if (seqrefs != null && (ndb = seqrefs.size()) > 0) { - for (int idb = 0; idb < s[in].getDBRefs().length; idb++) + if (dataRef == null) + { + dataRef = new Hashtable<>(); + } + List primrefs = seq.getPrimaryDBRefs(); + if (primrefs.size() >= 1) + { + dataRef.put(tmp, dbref_to_ac_record(primrefs.get(0))); + } + else { - if (dataRef == null) + for (int idb = 0; idb < seq.getDBRefs().size(); idb++) { - dataRef = new Hashtable(); + 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; + } } - - String datAs1 = s[in].getDBRefs()[idb].getSource().toString() - + " ; " - + s[in].getDBRefs()[idb].getAccessionId().toString(); - dataRef.put(tmp, datAs1); } } in++; @@ -989,14 +1028,15 @@ public class StockholmFile extends AlignFile // output database accessions if (dataRef != null) { - Enumeration en = dataRef.keys(); + Enumeration en = dataRef.keys(); 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)); @@ -1009,14 +1049,23 @@ public class StockholmFile extends AlignFile } } - // output annotations - while (i < s.length && s[i] != null) + // output description and annotations + + while (i < slen && (seq = s[i]) != null) { - AlignmentAnnotation[] alAnot = s[i].getAnnotation(); + if (seq.getDescription() != null) + { + // out.append("#=GR "); + out.append(new Format("%-" + maxid + "s").form("#=GS " + + printId(seq, jvSuffix) + " DE " + seq.getDescription())); + out.append(newline); + } + + AlignmentAnnotation[] alAnot = seq.getAnnotation(); if (alAnot != null) { Annotation[] ann; - for (int j = 0; j < alAnot.length; j++) + for (int j = 0, nj = alAnot.length; j < nj; j++) { String key = type2id(alAnot[j].label); @@ -1036,37 +1085,38 @@ public class StockholmFile extends AlignFile // out.append("#=GR "); out.append(new Format("%-" + maxid + "s").form( - "#=GR " + printId(s[i], jvSuffix) + " " + key + " ")); + "#=GR " + printId(seq, jvSuffix) + " " + key + " ")); ann = alAnot[j].annotations; - String seq = ""; - for (int k = 0; k < ann.length; k++) + String sseq = ""; + for (int k = 0, nk = ann.length; k < nk; k++) { - seq += outputCharacter(key, k, isrna, ann, s[i]); + sseq += outputCharacter(key, k, isrna, ann, seq); } - out.append(seq); + out.append(sseq); out.append(newline); } } out.append(new Format("%-" + maxid + "s") - .form(printId(s[i], jvSuffix) + " ")); - out.append(s[i].getSequenceAsString()); + .form(printId(seq, jvSuffix) + " ")); + out.append(seq.getSequenceAsString()); out.append(newline); i++; } // alignment annotation AlignmentAnnotation aa; - if (al.getAlignmentAnnotation() != null) + AlignmentAnnotation[] an = al.getAlignmentAnnotation(); + if (an != null) { - for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++) + for (int ia = 0, na = an.length; ia < na; ia++) { - aa = al.getAlignmentAnnotation()[ia]; + aa = an[ia]; if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null) { continue; } - String seq = ""; + String sseq = ""; String label; String key = ""; if (aa.label.equals("seq")) @@ -1075,7 +1125,7 @@ public class StockholmFile extends AlignFile } else { - key = type2id(aa.label.toLowerCase()); + key = type2id(aa.label.toLowerCase(Locale.ROOT)); if (key == null) { label = aa.label; @@ -1094,11 +1144,11 @@ public class StockholmFile extends AlignFile out.append( new Format("%-" + maxid + "s").form("#=GC " + label + " ")); boolean isrna = aa.isValidStruc(); - for (int j = 0; j < aa.annotations.length; j++) + for (int j = 0, nj = aa.annotations.length; j < nj; j++) { - seq += outputCharacter(key, j, isrna, aa.annotations, null); + sseq += outputCharacter(key, j, isrna, aa.annotations, null); } - out.append(seq); + out.append(sseq); out.append(newline); } } @@ -1127,7 +1177,13 @@ 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 +1205,7 @@ public class StockholmFile extends AlignFile } if (charset) { - if (ssannotchar == ' ' && isrna) - { - ssannotchar = '.'; - } - return ssannotchar; + return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar; } } @@ -1218,7 +1270,7 @@ public class StockholmFile extends AlignFile { return (String) typeIds.get(id); } - System.err.println( + jalview.bin.Console.errPrintln( "Warning : Unknown Stockholm annotation type code " + id); return id; } @@ -1240,7 +1292,7 @@ public class StockholmFile extends AlignFile { return key; } - System.err.println( + jalview.bin.Console.errPrintln( "Warning : Unknown Stockholm annotation type: " + type); return key; }