X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=32e6ff7772befcbe99565e002ff0420ff8856f48;hb=4340010fc364a8f9a6fcab4f8c416393f5bda21d;hp=ab80ffa8f3bf15678a792de78abac19567b50861;hpb=8008331e9deca3898688a8f862a968a1d74135e9;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index ab80ffa..32e6ff7 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 @@ -91,7 +97,8 @@ 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); } @@ -119,7 +126,7 @@ public class StockholmFile extends AlignFile fr = new FileReader(inFile); BufferedReader r = new BufferedReader(fr); - result = null; + List result = null; try { result = RNAFactory.loadSecStrStockholm(r); @@ -156,9 +163,8 @@ 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.", @@ -789,20 +795,14 @@ 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")) @@ -828,15 +828,14 @@ 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); } else { - ann.secondaryStructure = jalview.schemes.ResidueProperties - .getDssp3state(pos).charAt(0); + ann.secondaryStructure = ResidueProperties.getDssp3state(pos) + .charAt(0); } if (ann.secondaryStructure == pos.charAt(0)) @@ -854,10 +853,10 @@ public class StockholmFile extends AlignFile 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; @@ -882,8 +881,13 @@ 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; @@ -891,7 +895,7 @@ 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; @@ -962,47 +966,44 @@ 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++; @@ -1055,6 +1056,10 @@ public class StockholmFile extends AlignFile out.append(newline); } } + + out.append("//"); + out.append(newline); + return out.toString(); } @@ -1107,13 +1112,12 @@ public class StockholmFile extends AlignFile return seq; } - @Override public String print() { out = new StringBuffer(); out.append("# STOCKHOLM 1.0"); out.append(newline); - print(getSeqsAsArray()); + print(getSeqsAsArray(), false); out.append("//"); out.append(newline); @@ -1121,6 +1125,7 @@ public class StockholmFile extends AlignFile } private static Hashtable typeIds = null; + static { if (typeIds == null)