X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=936d2b9e2fbc11ca61aad9a9f7047ba80fe197b8;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=23c4d2179e8d2934e20a9c3f8291e6a400a26759;hpb=a21b84a669a9620f6943b9b5054e8756cb6f0687;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 23c4d21..936d2b9 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -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 +32,8 @@ 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; @@ -43,7 +46,6 @@ import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; -import java.util.StringTokenizer; import java.util.Vector; import com.stevesoft.pat.Regex; @@ -72,8 +74,14 @@ 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 String ANNOTATION = "annotation"; + + 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 @@ -91,7 +99,8 @@ 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); } @@ -101,6 +110,7 @@ public class StockholmFile extends AlignFile super(source); } + @Override public void initData() { super.initData(); @@ -118,7 +128,7 @@ public class StockholmFile extends AlignFile fr = new FileReader(inFile); BufferedReader r = new BufferedReader(fr); - result = null; + List result = null; try { result = RNAFactory.loadSecStrStockholm(r); @@ -155,9 +165,8 @@ 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.", @@ -178,6 +187,7 @@ 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(); @@ -358,6 +368,11 @@ 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 @@ -366,6 +381,7 @@ 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); @@ -378,6 +394,11 @@ public class StockholmFile extends AlignFile while (j.hasMoreElements()) { String desc = j.nextElement().toString(); + if (ANNOTATION.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++) @@ -393,7 +414,7 @@ public class StockholmFile extends AlignFile int new_pos = posmap[k]; // look up nearest seqeunce // position to this column SequenceFeature feat = new SequenceFeature(type, desc, - new_pos, new_pos, 0f, null); + new_pos, new_pos, null); seqO.addSequenceFeature(feat); } @@ -533,8 +554,7 @@ 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); } } @@ -565,22 +585,11 @@ 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 @@ -595,8 +604,12 @@ 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")) @@ -624,15 +637,18 @@ 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)) { @@ -649,7 +665,8 @@ public class StockholmFile extends AlignFile { alan.visible = false; } - // annotations.addAll(newStruc); + // new annotation overwrites any existing annotation... + strucAnn.put(type, newStruc); seqAnn.put(acc, strucAnn); } @@ -788,20 +805,14 @@ 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")) @@ -809,12 +820,16 @@ public class StockholmFile extends AlignFile type = (label.indexOf("_cons") == label.length() - 5) ? label .substring(0, label.length() - 5) : label; } - boolean ss = false; + boolean ss = false, posterior = false; type = id2type(type); - if (type.equals("secondary structure")) + if (type.equalsIgnoreCase("secondary structure")) { ss = true; } + if (type.equalsIgnoreCase("posterior probability")) + { + posterior = true; + } // decide on secondary structure or not. Annotation[] els = new Annotation[annots.length()]; for (int i = 0; i < annots.length(); i++) @@ -827,16 +842,15 @@ public class StockholmFile extends AlignFile { // if (" .-_".indexOf(pos) == -1) { - if (detectbrackets.search(pos)) + if (DETECT_BRACKETS.search(pos)) { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getRNASecStrucState(pos).charAt(0); + ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0); + ann.displayCharacter = "" + pos.charAt(0); } else { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getDssp3state(pos).charAt(0); - } + ann.secondaryStructure = ResidueProperties.getDssp3state(pos) + .charAt(0); if (ann.secondaryStructure == pos.charAt(0)) { @@ -846,17 +860,37 @@ public class StockholmFile extends AlignFile { ann.displayCharacter = " " + ann.displayCharacter; } + } } } + if (posterior && !ann.isWhitespace() + && !Comparison.isGap(pos.charAt(0))) + { + float val = 0; + // symbol encodes values - 0..*==0..10 + if (pos.charAt(0) == '*') + { + val = 10; + } + else + { + val = pos.charAt(0) - '0'; + if (val > 9) + { + val = 10; + } + } + ann.value = val; + } 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; @@ -881,8 +915,13 @@ 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; @@ -890,7 +929,7 @@ 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; @@ -961,47 +1000,44 @@ 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; - } - // ?bug - feature may still have previous loop value - 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; - boolean isrna = alAnot[j].isValidStruc(); - 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("#=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++; @@ -1054,6 +1090,10 @@ public class StockholmFile extends AlignFile out.append(newline); } } + + out.append("//"); + out.append(newline); + return out.toString(); } @@ -1078,8 +1118,8 @@ public class StockholmFile extends AlignFile { if (annot == null) { - // sensible gap character if one is available or make one up - return sequenceI == null ? '-' : sequenceI.getCharAt(k); + // sensible gap character + return ' '; } else { @@ -1111,7 +1151,7 @@ public class StockholmFile extends AlignFile out = new StringBuffer(); out.append("# STOCKHOLM 1.0"); out.append(newline); - print(getSeqsAsArray()); + print(getSeqsAsArray(), false); out.append("//"); out.append(newline); @@ -1119,15 +1159,16 @@ public class StockholmFile extends AlignFile } private static Hashtable typeIds = null; + static { if (typeIds == null) { typeIds = new Hashtable(); - typeIds.put("SS", "secondary structure"); - typeIds.put("SA", "surface accessibility"); + typeIds.put("SS", "Secondary Structure"); + typeIds.put("SA", "Surface Accessibility"); typeIds.put("TM", "transmembrane"); - typeIds.put("PP", "posterior probability"); + typeIds.put("PP", "Posterior Probability"); typeIds.put("LI", "ligand binding"); typeIds.put("AS", "active site"); typeIds.put("IN", "intron"); @@ -1138,7 +1179,7 @@ public class StockholmFile extends AlignFile typeIds.put("DE", "description"); typeIds.put("DR", "reference"); typeIds.put("LO", "look"); - typeIds.put("RF", "reference positions"); + typeIds.put("RF", "Reference Positions"); } } @@ -1161,7 +1202,7 @@ public class StockholmFile extends AlignFile while (e.hasMoreElements()) { Object ll = e.nextElement(); - if (typeIds.get(ll).toString().equals(type)) + if (typeIds.get(ll).toString().equalsIgnoreCase(type)) { key = (String) ll; break;