X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=27be358ec23e7fc901a0cd1b0753137f31906cab;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=6490d28ab1c28329b28314c350be798632002e81;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 6490d28..27be358 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 +32,7 @@ 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; @@ -72,8 +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 @@ -101,6 +107,7 @@ public class StockholmFile extends AlignFile super(source); } + @Override public void initData() { super.initData(); @@ -118,7 +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); @@ -155,9 +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.", @@ -178,6 +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(); @@ -420,8 +427,8 @@ public class StockholmFile extends AlignFile { // logger.error("Could not parse sequence line: " + line); throw new IOException(MessageManager.formatMessage( - "exception.couldnt_parse_sequence_line", new String[] - { line })); + "exception.couldnt_parse_sequence_line", + new String[] { line })); } String ns = seqs.get(x.stringMatched(1)); if (ns == null) @@ -533,9 +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")) @@ -665,8 +671,8 @@ public class StockholmFile extends AlignFile else { throw new IOException(MessageManager.formatMessage( - "exception.unknown_annotation_detected", new String[] - { annType, annContent })); + "exception.unknown_annotation_detected", new String[] { + annType, annContent })); } } } @@ -779,9 +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); } @@ -789,19 +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; @@ -826,17 +825,16 @@ public class StockholmFile extends AlignFile // be written out if (ss) { - //if (" .-_".indexOf(pos) == -1) + // 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); } else { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getDssp3state(pos).charAt(0); + ann.secondaryStructure = ResidueProperties.getDssp3state(pos) + .charAt(0); } if (ann.secondaryStructure == pos.charAt(0)) @@ -848,16 +846,16 @@ public class StockholmFile extends AlignFile 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; @@ -901,18 +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); } } @@ -1068,21 +1066,19 @@ public class StockholmFile extends AlignFile * @param ann * @param sequenceI */ - private char outputCharacter(String key, int k, - boolean isrna, Annotation[] ann, SequenceI 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; + .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); + return sequenceI == null ? '-' : sequenceI.getCharAt(k); } else { @@ -1109,6 +1105,7 @@ public class StockholmFile extends AlignFile return seq; } + @Override public String print() { out = new StringBuffer(); @@ -1122,6 +1119,7 @@ public class StockholmFile extends AlignFile } private static Hashtable typeIds = null; + static { if (typeIds == null)