- Hashtable features;\r
- // Get an object with all the content for an annotation\r
- if (ann.containsKey("features"))\r
- {\r
- // logger.debug("Found features for " + acc);\r
- features = (Hashtable) ann.get("features");\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new features holder for " + acc);\r
- features = new Hashtable();\r
- ann.put("features", features);\r
- }\r
- \r
- Hashtable content;\r
- if (features.containsKey(this.id2type(type)))\r
- {\r
- // logger.debug("Found content for " + this.id2type(type));\r
- content = (Hashtable) features.get(this.id2type(type));\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new content holder for " +\r
- // this.id2type(type));\r
- content = new Hashtable();\r
- features.put(this.id2type(type), content);\r
- }\r
- String ns = (String) content.get(description);\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += seq;\r
- content.put(description, ns);\r
-
-// if(type.equals("SS")){\r
- Hashtable strucAnn;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- strucAnn = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- strucAnn = new Hashtable();\r
- }\r
- \r
- Vector newStruc=new Vector();\r
- parseAnnotationRow(newStruc, type,ns);\r
- \r
- strucAnn.put(type, newStruc);\r
- seqAnn.put(acc, strucAnn);\r
- }\r
-// }\r
- else\r
- {\r
- System.err\r
- .println("Warning - couldn't parse sequence annotation row line:\n"\r
- + line);\r
- // throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else\r
- {\r
- throw new IOException("Unknown annotation detected: " + annType\r
- + " " + annContent);\r
- }\r
- }\r
- }\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (1 + getTreeCount());\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- }\r
-\r
-/**\r
- * Demangle an accession string and guess the originating sequence database for a given sequence\r
- * @param seqO sequence to be annotated\r
- * @param dbr Accession string for sequence\r
- * @param dbsource source database for alignment (PFAM or RFAM)\r
- */\r
- private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)\r
- {\r
- DBRefEntry dbrf=null;\r
- List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();\r
- String seqdb="Unknown",sdbac=""+dbr;\r
- int st=-1,en=-1,p;\r
- if ((st=sdbac.indexOf("/"))>-1)\r
- {\r
- String num,range=sdbac.substring(st+1);\r
- sdbac = sdbac.substring(0,st);\r
- if ((p=range.indexOf("-"))>-1)\r
- {\r
- p++;\r
- if (p<range.length())\r
- {\r
- num = range.substring(p).trim();\r
- try {\r
- en = Integer.parseInt(num);\r
- } catch (NumberFormatException x)\r
- {\r
- // could warn here that index is invalid\r
- en = -1;\r
- }\r
- }\r
- } else {\r
- p=range.length();\r
- }\r
- num=range.substring(0,p).trim();\r
- try {\r
- st = Integer.parseInt(num);\r
- } catch (NumberFormatException x)\r
- {\r
- // could warn here that index is invalid\r
- st = -1;\r
- }\r
- }\r
- if (dbsource.equals("PFAM")) {\r
- seqdb = "UNIPROT";\r
- if (sdbac.indexOf(".")>-1)\r
- {\r
- // strip of last subdomain\r
- sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
- if (dbr!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- } else {\r
- seqdb = "EMBL"; // total guess - could be ENA, or something else these days\r
- if (sdbac.indexOf(".")>-1)\r
- {\r
- // strip off last subdomain\r
- sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- \r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- if (st!=-1 && en!=-1)\r
- {\r
- for (DBRefEntry d:dbrs)\r
- {\r
- jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);\r
- jalview.datamodel.Mapping mping = new Mapping(mp);\r
- d.setMap(mping);\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * Parse a file in Stockholm format into Jalview's data model using VARNA\r
- * \r
- * @throws IOException\r
- * If there is an error with the input file\r
- */\r
- public void parse_with_VARNA() throws IOException\r
- {\r
- FileReader fr = null;\r
- fr = new FileReader(inFile);\r
-\r
- BufferedReader r = new BufferedReader(fr);\r
- result = null;\r
- try\r
- {\r
- result = RNAFactory.loadSecStrStockholm(r);\r
- } catch (ExceptionUnmatchedClosingParentheses umcp)\r
- {\r
- errormessage = "Unmatched parentheses in annotation. Aborting ("\r
- + umcp.getMessage() + ")";\r
- throw new IOException(umcp);\r
- }\r
- // DEBUG System.out.println("this is the secondary scructure:"\r
- // +result.size());\r
- SequenceI[] seqs = new SequenceI[result.size()];\r
- String id=null;\r
- for (int i = 0; i < result.size(); i++)\r
- {\r
- // DEBUG System.err.println("Processing i'th sequence in Stockholm file")\r
- RNA current = result.get(i);\r
-\r
- String seq = current.getSeq();\r
- String rna = current.getStructDBN(true);\r
- // DEBUG System.out.println(seq);\r
- // DEBUG System.err.println(rna);\r
- int begin = 0;\r
- int end = seq.length() - 1;\r
- id = safeName(getDataName());\r
- seqs[i] = new Sequence(id, seq, begin, end);\r
- String[] annot = new String[rna.length()];\r
- Annotation[] ann = new Annotation[rna.length()];\r
- for (int j = 0; j < rna.length(); j++)\r
- {\r
- annot[j] = rna.substring(j, j + 1);\r
-\r
- }\r
-\r
- for (int k = 0; k < rna.length(); k++)\r
- {\r
- ann[k] = new Annotation(annot[k], "",\r
- jalview.schemes.ResidueProperties.getRNASecStrucState(\r
- annot[k]).charAt(0), 0f);\r
-\r
- }\r
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",\r
- current.getID(), ann);\r
-\r
- seqs[i].addAlignmentAnnotation(align);\r
- seqs[i].setRNA(result.get(i));\r
- this.annotations.addElement(align);\r
- }\r
- this.setSeqs(seqs);\r
-\r
- }\r
-\r
- protected static AlignmentAnnotation parseAnnotationRow(\r
- Vector annotation, String label, String annots)\r
- {\r
- String convert1, convert2 = null;\r
-\r
- // Convert all bracket types to parentheses\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
-\r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
-\r
- convert1 = openparen.replaceAll(annots);\r
- convert2 = closeparen.replaceAll(convert1);\r
- annots = convert2;\r
-\r
- String type = label;\r
- if (label.contains("_cons"))\r
- {\r
- type = (label.indexOf("_cons") == label.length() - 5) ? label\r
- .substring(0, label.length() - 5) : label;\r
- }\r
- boolean ss = false;\r
- type = id2type(type);\r
- if (type.equals("secondary structure"))\r
- {\r
- ss = true;\r
- }\r
- // decide on secondary structure or not.\r
- Annotation[] els = new Annotation[annots.length()];\r
- for (int i = 0; i < annots.length(); i++)\r
- {\r
- String pos = annots.substring(i, i + 1);\r
- Annotation ann;\r
- ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
- // be written out\r
- if (ss)\r
- {\r
- if (detectbrackets.search(pos))\r
- {\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getRNASecStrucState(pos).charAt(0);\r
- }\r
- else\r
- {\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getDssp3state(pos).charAt(0);\r
- }\r
-\r
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
- {\r
- ann.displayCharacter = ""; // null; // " ";\r
- }\r
- else\r
- {\r
- ann.displayCharacter = " " + ann.displayCharacter;\r
- }\r
- }\r
-\r
- els[i] = ann;\r
- }\r
- AlignmentAnnotation annot = null;\r
- Enumeration e = annotation.elements();\r
- while (e.hasMoreElements())\r
- {\r
- annot = (AlignmentAnnotation) e.nextElement();\r
- if (annot.label.equals(type))\r
- break;\r
- annot = null;\r
- }\r
- if (annot == null)\r
- {\r
- annot = new AlignmentAnnotation(type, type, els);\r
- annotation.addElement(annot);\r
- }\r
- else\r
- {\r
- Annotation[] anns = new Annotation[annot.annotations.length\r
- + els.length];\r
- System.arraycopy(annot.annotations, 0, anns, 0,\r
- annot.annotations.length);\r
- System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
- annot.annotations = anns;\r
- // System.out.println("else: ");\r
- }\r
- return annot;\r
- }\r
-\r
- public String print(SequenceI[] s)
+
+ Hashtable features;
+ // Get an object with all the content for an annotation
+ if (ann.containsKey("features"))
+ {
+ // logger.debug("Found features for " + acc);
+ features = (Hashtable) ann.get("features");
+ }
+ else
+ {
+ // logger.debug("Creating new features holder for " + acc);
+ features = new Hashtable();
+ ann.put("features", features);
+ }
+
+ Hashtable content;
+ if (features.containsKey(this.id2type(type)))
+ {
+ // logger.debug("Found content for " + this.id2type(type));
+ content = (Hashtable) features.get(this.id2type(type));
+ }
+ else
+ {
+ // logger.debug("Creating new content holder for " +
+ // this.id2type(type));
+ content = new Hashtable();
+ features.put(this.id2type(type), content);
+ }
+ String ns = (String) content.get(ANNOTATION);
+
+ if (ns == null)
+ {
+ ns = "";
+ }
+ // finally, append the annotation line
+ ns += seq;
+ content.put(ANNOTATION, ns);
+ // // end of wrapped annotation block.
+ // // Now a new row is created with the current set of data
+
+ Hashtable strucAnn;
+ if (seqAnn.containsKey(acc))
+ {
+ strucAnn = (Hashtable) seqAnn.get(acc);
+ }
+ else
+ {
+ strucAnn = new Hashtable();
+ }
+
+ Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ parseAnnotationRow(newStruc, type, ns);
+ for (AlignmentAnnotation alan : newStruc)
+ {
+ alan.visible = false;
+ }
+ // new annotation overwrites any existing annotation...
+
+ strucAnn.put(type, newStruc);
+ seqAnn.put(acc, strucAnn);
+ }
+ // }
+ else
+ {
+ System.err.println(
+ "Warning - couldn't parse sequence annotation row line:\n"
+ + line);
+ // throw new IOException("Error parsing " + line);
+ }
+ }
+ else
+ {
+ throw new IOException(MessageManager.formatMessage(
+ "exception.unknown_annotation_detected", new String[]
+ { annType, annContent }));
+ }
+ }
+ }
+ if (treeString.length() > 0)
+ {
+ if (treeName == null)
+ {
+ treeName = "Tree " + (1 + getTreeCount());
+ }
+ addNewickTree(treeName, treeString.toString());
+ }
+ }
+
+ /**
+ * Demangle an accession string and guess the originating sequence database
+ * for a given sequence
+ *
+ * @param seqO
+ * sequence to be annotated
+ * @param dbr
+ * Accession string for sequence
+ * @param dbsource
+ * source database for alignment (PFAM or RFAM)
+ */
+ private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)