X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=e4d9f60a6e13c7aa965984f6d40590a0ac274104;hb=8ddacd61ecb5a5259b011df1194475f70e50f457;hp=9d21a400c6c1920c2560ac0c761e55dbbd5ac100;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 9d21a40..e4d9f60 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -23,7 +23,7 @@ */ package jalview.io; -import jalview.datamodel.AlignmentI; +import jalview.analysis.Rna; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; @@ -32,7 +32,9 @@ import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.schemes.ResidueProperties; import jalview.util.Format; +import jalview.util.MessageManager; import java.io.BufferedReader; import java.io.FileReader; @@ -40,8 +42,9 @@ import java.io.IOException; import java.util.ArrayList; import java.util.Enumeration; import java.util.Hashtable; +import java.util.LinkedHashMap; import java.util.List; -import java.util.StringTokenizer; +import java.util.Map; import java.util.Vector; import com.stevesoft.pat.Regex; @@ -70,8 +73,12 @@ import fr.orsay.lri.varna.models.rna.RNA; */ public class StockholmFile extends AlignFile { - // static Logger logger = Logger.getLogger("jalview.io.StockholmFile"); - protected ArrayList result; + private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "("); + + private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")"); + + public static final Regex DETECT_BRACKETS = new Regex( + "(<|>|\\[|\\]|\\(|\\)|\\{|\\})"); StringBuffer out; // output buffer @@ -89,7 +96,8 @@ public class StockholmFile extends AlignFile this.al = al; } - public StockholmFile(String inFile, String type) throws IOException + public StockholmFile(String inFile, DataSourceType type) + throws IOException { super(inFile, type); } @@ -99,6 +107,7 @@ public class StockholmFile extends AlignFile super(source); } + @Override public void initData() { super.initData(); @@ -116,7 +125,7 @@ public class StockholmFile extends AlignFile fr = new FileReader(inFile); BufferedReader r = new BufferedReader(fr); - result = null; + List result = null; try { result = RNAFactory.loadSecStrStockholm(r); @@ -153,9 +162,8 @@ public class StockholmFile extends AlignFile for (int k = 0; k < rna.length(); k++) { - ann[k] = new Annotation(annot[k], "", - jalview.schemes.ResidueProperties.getRNASecStrucState( - annot[k]).charAt(0), 0f); + ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState( + annot[k]).charAt(0), 0f); } AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.", @@ -176,6 +184,7 @@ public class StockholmFile extends AlignFile * @throws IOException * If there is an error with the input file */ + @Override public void parse() throws IOException { StringBuffer treeString = new StringBuffer(); @@ -185,7 +194,7 @@ public class StockholmFile extends AlignFile String version; // String id; Hashtable seqAnn = new Hashtable(); // Sequence related annotations - Hashtable seqs = new Hashtable(); + LinkedHashMap seqs = new LinkedHashMap(); Regex p, r, rend, s, x; // Temporary line for processing RNA annotation // String RNAannot = ""; @@ -198,7 +207,8 @@ public class StockholmFile extends AlignFile if (!r.search(nextLine())) { throw new IOException( - "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'"); + MessageManager + .getString("exception.stockholm_invalid_format")); } else { @@ -258,12 +268,11 @@ public class StockholmFile extends AlignFile } } // logger.debug("Number of sequences: " + this.noSeqs); - Enumeration accs = seqs.keys(); - while (accs.hasMoreElements()) + for (Map.Entry skey : seqs.entrySet()) { - String acc = (String) accs.nextElement(); // logger.debug("Processing sequence " + acc); - String seq = (String) seqs.remove(acc); + String acc = skey.getKey(); + String seq = skey.getValue(); if (maxLength < seq.length()) { maxLength = seq.length(); @@ -356,6 +365,11 @@ public class StockholmFile extends AlignFile // add alignment annotation for this feature String key = type2id(type); + + /* + * have we added annotation rows for this type ? + */ + boolean annotsAdded = false; if (key != null) { if (accAnnotations != null @@ -364,9 +378,11 @@ public class StockholmFile extends AlignFile Vector vv = (Vector) accAnnotations.get(key); for (int ii = 0; ii < vv.size(); ii++) { + annotsAdded = true; AlignmentAnnotation an = (AlignmentAnnotation) vv .elementAt(ii); seqO.addAlignmentAnnotation(an); + annotations.add(an); } } } @@ -375,6 +391,11 @@ public class StockholmFile extends AlignFile while (j.hasMoreElements()) { String desc = j.nextElement().toString(); + if ("annotations".equals(desc) && annotsAdded) + { + // don't add features if we already added an annotation row + continue; + } String ns = content.get(desc).toString(); char[] byChar = ns.toCharArray(); for (int k = 0; k < byChar.length; k++) @@ -416,9 +437,11 @@ public class StockholmFile extends AlignFile if (!x.search(line)) { // logger.error("Could not parse sequence line: " + line); - throw new IOException("Could not parse sequence line: " + line); + throw new IOException(MessageManager.formatMessage( + "exception.couldnt_parse_sequence_line", + new String[] { line })); } - String ns = (String) seqs.get(x.stringMatched(1)); + String ns = seqs.get(x.stringMatched(1)); if (ns == null) { ns = ""; @@ -528,7 +551,8 @@ public class StockholmFile extends AlignFile } else { - throw new IOException("Error parsing " + line); + // throw new IOException("Error parsing " + line); + System.err.println(">> missing annotation: " + line); } } else if (annType.equals("GC")) @@ -558,22 +582,11 @@ public class StockholmFile extends AlignFile { 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 + String oseq = s.stringMatched(3); + /* + * copy of annotation field that may be processed into whitespace chunks + */ + String seq = new String(oseq); Hashtable ann; // Get an object with all the annotations for this sequence @@ -588,8 +601,12 @@ public class StockholmFile extends AlignFile ann = new Hashtable(); seqAnn.put(acc, ann); } + + // // start of block for appending annotation lines for wrapped + // stokchholm file // 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")) @@ -617,15 +634,18 @@ public class StockholmFile extends AlignFile content = new Hashtable(); features.put(this.id2type(type), content); } - String ns = (String) content.get(description); + String ns = (String) content.get("annotation"); + if (ns == null) { ns = ""; } + // finally, append the annotation line ns += seq; - content.put(description, ns); + content.put("annotation", ns); + // // end of wrapped annotation block. + // // Now a new row is created with the current set of data - // if(type.equals("SS")){ Hashtable strucAnn; if (seqAnn.containsKey(acc)) { @@ -636,8 +656,13 @@ public class StockholmFile extends AlignFile strucAnn = new Hashtable(); } - Vector newStruc = new Vector(); + Vector newStruc = new Vector(); parseAnnotationRow(newStruc, type, ns); + for (AlignmentAnnotation alan : newStruc) + { + alan.visible = false; + } + // new annotation overwrites any existing annotation... strucAnn.put(type, newStruc); seqAnn.put(acc, strucAnn); @@ -653,8 +678,9 @@ public class StockholmFile extends AlignFile } else { - throw new IOException("Unknown annotation detected: " + annType - + " " + annContent); + throw new IOException(MessageManager.formatMessage( + "exception.unknown_annotation_detected", new String[] { + annType, annContent })); } } } @@ -767,9 +793,8 @@ public class StockholmFile extends AlignFile { 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.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); } @@ -777,20 +802,14 @@ public class StockholmFile extends AlignFile } protected static AlignmentAnnotation parseAnnotationRow( - Vector annotation, String label, String annots) + 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; + // convert1 = OPEN_PAREN.replaceAll(annots); + // convert2 = CLOSE_PAREN.replaceAll(convert1); + // annots = convert2; String type = label; if (label.contains("_cons")) @@ -814,36 +833,42 @@ public class StockholmFile extends AlignFile // be written out if (ss) { - if (detectbrackets.search(pos)) + // if (" .-_".indexOf(pos) == -1) { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getRNASecStrucState(pos).charAt(0); - } - else - { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getDssp3state(pos).charAt(0); - } + if (DETECT_BRACKETS.search(pos)) + { + ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0); + ann.displayCharacter = "" + pos.charAt(0); + } + else + { + ann.secondaryStructure = ResidueProperties.getDssp3state(pos) + .charAt(0); - if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C') - { - ann.displayCharacter = ""; // null; // " "; - } - else - { - ann.displayCharacter = " " + ann.displayCharacter; + if (ann.secondaryStructure == pos.charAt(0)) + { + ann.displayCharacter = ""; // null; // " "; + } + else + { + ann.displayCharacter = " " + ann.displayCharacter; + } + } } + } els[i] = ann; } AlignmentAnnotation annot = null; - Enumeration e = annotation.elements(); + Enumeration e = annotation.elements(); while (e.hasMoreElements()) { - annot = (AlignmentAnnotation) e.nextElement(); + annot = e.nextElement(); if (annot.label.equals(type)) + { break; + } annot = null; } if (annot == null) @@ -864,8 +889,13 @@ public class StockholmFile extends AlignFile return annot; } - public String print(SequenceI[] s) + @Override + public String print(SequenceI[] s, boolean jvSuffix) { + out = new StringBuffer(); + out.append("# STOCKHOLM 1.0"); + out.append(newline); + // find max length of id int max = 0; int maxid = 0; @@ -873,7 +903,7 @@ public class StockholmFile extends AlignFile Hashtable dataRef = null; while ((in < s.length) && (s[in] != null)) { - String tmp = printId(s[in]); + String tmp = printId(s[in], jvSuffix); if (s[in].getSequence().length > max) { max = s[in].getSequence().length; @@ -883,16 +913,18 @@ public class StockholmFile extends AlignFile { maxid = tmp.length(); } - if (s[in].getDBRef() != null) + if (s[in].getDBRefs() != null) { - for (int idb = 0; idb < s[in].getDBRef().length; idb++) + for (int idb = 0; idb < s[in].getDBRefs().length; idb++) { if (dataRef == null) + { dataRef = new Hashtable(); + } - String datAs1 = s[in].getDBRef()[idb].getSource().toString() + String datAs1 = s[in].getDBRefs()[idb].getSource().toString() + " ; " - + s[in].getDBRef()[idb].getAccessionId().toString(); + + s[in].getDBRefs()[idb].getAccessionId().toString(); dataRef.put(tmp, datAs1); } } @@ -942,66 +974,44 @@ public class StockholmFile extends AlignFile // output annotations while (i < s.length && s[i] != null) { - if (s[i].getDatasetSequence() != null) + AlignmentAnnotation[] alAnot = s[i].getAnnotation(); + if (alAnot != 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++) { - for (int j = 0; j < alAnot.length; j++) + + String key = type2id(alAnot[j].label); + boolean isrna = alAnot[j].isValidStruc(); + + if (isrna) + { + // hardwire to secondary structure if there is RNA secondary + // structure on the annotation + key = "SS"; + } + if (key == null) { - if (ds.getSequenceFeatures() != null) - { - feature = ds.getSequenceFeatures()[0].type; - } - String key = type2id(feature); - if (key == null) - continue; + 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("#=GR "); + out.append(new Format("%-" + maxid + "s").form("#=GR " + + printId(s[i], jvSuffix) + " " + key + " ")); + ann = alAnot[j].annotations; + String seq = ""; + for (int k = 0; k < ann.length; k++) + { + seq += outputCharacter(key, k, isrna, ann, s[i]); } + out.append(seq); + out.append(newline); } } - out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " ")); + out.append(new Format("%-" + maxid + "s") + .form(printId(s[i], jvSuffix) + " ")); out.append(s[i].getSequenceAsString()); out.append(newline); i++; @@ -1014,57 +1024,108 @@ public class StockholmFile extends AlignFile for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++) { aa = al.getAlignmentAnnotation()[ia]; - if (aa.autoCalculated || !aa.visible) + if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null) { continue; } String seq = ""; String label; - + String key = ""; if (aa.label.equals("seq")) + { label = "seq_cons"; + } else - label = type2id(aa.label.toLowerCase()) + "_cons"; - + { + key = type2id(aa.label.toLowerCase()); + if (key == null) + { + label = aa.label; + } + else + { + label = key + "_cons"; + } + } if (label == null) + { label = aa.label; + } + label = label.replace(" ", "_"); out.append(new Format("%-" + maxid + "s").form("#=GC " + label + " ")); + boolean isrna = aa.isValidStruc(); 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); - } + seq += outputCharacter(key, j, isrna, aa.annotations, null); } out.append(seq); out.append(newline); } } + + out.append("//"); + out.append(newline); + return out.toString(); } + /** + * add an annotation character to the output row + * + * @param seq + * @param key + * @param k + * @param isrna + * @param ann + * @param sequenceI + */ + private char outputCharacter(String key, int k, boolean isrna, + Annotation[] ann, SequenceI sequenceI) + { + char seq = ' '; + Annotation annot = ann[k]; + String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character + .toString(sequenceI.getCharAt(k))) : annot.displayCharacter; + if (key != null && key.equals("SS")) + { + if (annot == null) + { + // sensible gap character + return ' '; + } + else + { + // valid secondary structure AND no alternative label (e.g. ' B') + if (annot.secondaryStructure > ' ' && ch.length() < 2) + { + return annot.secondaryStructure; + } + } + } + + if (ch.length() == 0) + { + seq = '.'; + } + else if (ch.length() == 1) + { + seq = ch.charAt(0); + } + else if (ch.length() > 1) + { + seq = ch.charAt(1); + } + return seq; + } + public String print() { out = new StringBuffer(); out.append("# STOCKHOLM 1.0"); out.append(newline); - print(getSeqsAsArray()); + print(getSeqsAsArray(), false); out.append("//"); out.append(newline); @@ -1072,6 +1133,7 @@ public class StockholmFile extends AlignFile } private static Hashtable typeIds = null; + static { if (typeIds == null) @@ -1122,7 +1184,7 @@ public class StockholmFile extends AlignFile } if (key != null) { - return (String) key; + return key; } System.err.println("Warning : Unknown Stockholm annotation type: " + type);