X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=f5b517728c85ce77ad785c9030e7b7e475ed2046;hb=75b4e1bacc2df850c7f1ae022d92c7d39e803357;hp=c2f3683a491126fb8250edcd50d5bbf626415d89;hpb=f05332c8cc2a3a1d00a8dae38b8920ae799fb840;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index c2f3683..f5b5177 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -74,6 +74,8 @@ import fr.orsay.lri.varna.models.rna.RNA; */ public class StockholmFile extends AlignFile { + private static final String ANNOTATION = "annotation"; + private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "("); private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")"); @@ -163,8 +165,8 @@ public class StockholmFile extends AlignFile for (int k = 0; k < rna.length(); k++) { - ann[k] = new Annotation(annot[k], "", Rna.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.", @@ -207,9 +209,8 @@ 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 { @@ -392,7 +393,7 @@ public class StockholmFile extends AlignFile while (j.hasMoreElements()) { String desc = j.nextElement().toString(); - if ("annotations".equals(desc) && annotsAdded) + if (ANNOTATION.equals(desc) && annotsAdded) { // don't add features if we already added an annotation row continue; @@ -412,7 +413,7 @@ 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); } @@ -439,8 +440,8 @@ 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) @@ -635,7 +636,7 @@ public class StockholmFile extends AlignFile content = new Hashtable(); features.put(this.id2type(type), content); } - String ns = (String) content.get("annotation"); + String ns = (String) content.get(ANNOTATION); if (ns == null) { @@ -643,7 +644,7 @@ public class StockholmFile extends AlignFile } // finally, append the annotation line ns += seq; - content.put("annotation", ns); + content.put(ANNOTATION, ns); // // end of wrapped annotation block. // // Now a new row is created with the current set of data @@ -671,8 +672,8 @@ public class StockholmFile extends AlignFile // } else { - System.err - .println("Warning - couldn't parse sequence annotation row line:\n" + System.err.println( + "Warning - couldn't parse sequence annotation row line:\n" + line); // throw new IOException("Error parsing " + line); } @@ -680,8 +681,8 @@ 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 })); } } } @@ -794,8 +795,10 @@ 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); } @@ -815,8 +818,9 @@ public class StockholmFile extends AlignFile String type = label; if (label.contains("_cons")) { - type = (label.indexOf("_cons") == label.length() - 5) ? label - .substring(0, label.length() - 5) : label; + type = (label.indexOf("_cons") == label.length() - 5) + ? label.substring(0, label.length() - 5) + : label; } boolean ss = false, posterior = false; type = id2type(type); @@ -850,14 +854,14 @@ public class StockholmFile extends AlignFile ann.secondaryStructure = ResidueProperties.getDssp3state(pos) .charAt(0); - if (ann.secondaryStructure == pos.charAt(0)) - { - ann.displayCharacter = ""; // null; // " "; - } - else - { - ann.displayCharacter = " " + ann.displayCharacter; - } + if (ann.secondaryStructure == pos.charAt(0)) + { + ann.displayCharacter = ""; // null; // " "; + } + else + { + ann.displayCharacter = " " + ann.displayCharacter; + } } } @@ -928,10 +932,7 @@ public class StockholmFile extends AlignFile while ((in < s.length) && (s[in] != null)) { String tmp = printId(s[in], jvSuffix); - if (s[in].getSequence().length > max) - { - max = s[in].getSequence().length; - } + max = Math.max(max, s[in].getLength()); if (tmp.length() > maxid) { @@ -980,8 +981,8 @@ public class StockholmFile extends AlignFile { Object idd = en.nextElement(); String type = (String) dataRef.remove(idd); - out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS " - + idd.toString() + " ")); + out.append(new Format("%-" + (maxid - 2) + "s") + .form("#=GS " + idd.toString() + " ")); if (type.contains("PFAM") || type.contains("RFAM")) { @@ -1021,8 +1022,8 @@ public class StockholmFile extends AlignFile } // out.append("#=GR "); - out.append(new Format("%-" + maxid + "s").form("#=GR " - + printId(s[i], jvSuffix) + " " + key + " ")); + 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++) @@ -1077,8 +1078,8 @@ public class StockholmFile extends AlignFile } label = label.replace(" ", "_"); - out.append(new Format("%-" + maxid + "s").form("#=GC " + label - + " ")); + out.append( + new Format("%-" + maxid + "s").form("#=GC " + label + " ")); boolean isrna = aa.isValidStruc(); for (int j = 0; j < aa.annotations.length; j++) { @@ -1110,8 +1111,10 @@ public class StockholmFile extends AlignFile { char seq = ' '; Annotation annot = ann[k]; - String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character - .toString(sequenceI.getCharAt(k))) : annot.displayCharacter; + String ch = (annot == null) + ? ((sequenceI == null) ? "-" + : Character.toString(sequenceI.getCharAt(k))) + : annot.displayCharacter; if (key != null && key.equals("SS")) { if (annot == null) @@ -1188,8 +1191,8 @@ public class StockholmFile extends AlignFile { return (String) typeIds.get(id); } - System.err.println("Warning : Unknown Stockholm annotation type code " - + id); + System.err.println( + "Warning : Unknown Stockholm annotation type code " + id); return id; } @@ -1210,8 +1213,8 @@ public class StockholmFile extends AlignFile { return key; } - System.err.println("Warning : Unknown Stockholm annotation type: " - + type); + System.err.println( + "Warning : Unknown Stockholm annotation type: " + type); return key; }