X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=27be358ec23e7fc901a0cd1b0753137f31906cab;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=7ca07c8f78a4398f781cfa910e456b56c018e138;hpb=5f3ef8297b73e71bf3afb7ecc75d16879b8c330d;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 7ca07c8..27be358 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. * @@ -23,6 +23,7 @@ */ package jalview.io; +import jalview.analysis.Rna; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; @@ -31,6 +32,7 @@ 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; @@ -40,7 +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.Map; import java.util.StringTokenizer; import java.util.Vector; @@ -70,8 +74,12 @@ 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("(>|\\])", ")"); + + private static final Regex DETECT_BRACKETS = new Regex( + "(<|>|\\[|\\]|\\(|\\))"); StringBuffer out; // output buffer @@ -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 = ""; @@ -197,7 +206,9 @@ 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")); } else { @@ -257,12 +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(); @@ -416,9 +426,11 @@ public class StockholmFile extends AlignFile if (!x.search(line)) { // logger.error("Could not parse sequence line: " + line); - throw new IOException(MessageManager.formatMessage("exception.couldnt_parse_sequence_line", new String[]{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 +540,8 @@ public class StockholmFile extends AlignFile } else { - throw new IOException(MessageManager.formatMessage("exception.error_parsing_line", new String[]{line})); + // throw new IOException("Error parsing " + line); + System.err.println(">> missing annotation: " + line); } } else if (annType.equals("GC")) @@ -657,7 +670,9 @@ public class StockholmFile extends AlignFile } else { - throw new IOException(MessageManager.formatMessage("exception.unknown_annotation_detected", new String[]{annType,annContent})); + throw new IOException(MessageManager.formatMessage( + "exception.unknown_annotation_detected", new String[] { + annType, annContent })); } } } @@ -770,9 +785,8 @@ 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); } @@ -780,19 +794,13 @@ 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); + convert1 = OPEN_PAREN.replaceAll(annots); + convert2 = CLOSE_PAREN.replaceAll(convert1); annots = convert2; String type = label; @@ -817,34 +825,37 @@ public class StockholmFile extends AlignFile // be written out if (ss) { - if (detectbrackets.search(pos)) - { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getRNASecStrucState(pos).charAt(0); - } - else + // if (" .-_".indexOf(pos) == -1) { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getDssp3state(pos).charAt(0); - } + if (DETECT_BRACKETS.search(pos)) + { + ann.secondaryStructure = Rna.getRNASecStrucState(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; @@ -888,18 +899,18 @@ 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); } } @@ -965,6 +976,7 @@ public class StockholmFile extends AlignFile { feature = ds.getSequenceFeatures()[0].type; } + // ?bug - feature may still have previous loop value String key = type2id(feature); if (key == null) @@ -976,33 +988,11 @@ public class StockholmFile extends AlignFile out.append(new Format("%-" + maxid + "s").form("#=GR " + printId(s[i]) + " " + key + " ")); ann = alAnot[j].annotations; + boolean isrna = alAnot[j].isValidStruc(); 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); - } + seq += outputCharacter(key, k, isrna, ann, s[i]); } out.append(seq); out.append(newline); @@ -1023,54 +1013,41 @@ 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 || isrna) - { - 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); @@ -1079,6 +1056,56 @@ public class StockholmFile extends AlignFile 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 if one is available or make one up + return sequenceI == null ? '-' : sequenceI.getCharAt(k); + } + 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; + } + + @Override public String print() { out = new StringBuffer(); @@ -1092,6 +1119,7 @@ public class StockholmFile extends AlignFile } private static Hashtable typeIds = null; + static { if (typeIds == null)