\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.Annotation;\r
import jalview.datamodel.DBRefEntry;\r
import jalview.datamodel.Mapping;\r
* into Jalview's local representation.\r
* \r
* @author bsb at sanger.ac.uk\r
+ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)\r
+ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)\r
+ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)\r
* @version 0.3 + jalview mods\r
* \r
*/\r
{\r
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
protected ArrayList<RNA> result;\r
- \r
- StringBuffer out; // output buffer\r
-\r
- AlignmentI al;\r
+ StringBuffer out; // output buffer
+
+ AlignmentI al;
\r
public StockholmFile()\r
{\r
{\r
super.initData();\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(java.io.File inFile) 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
+ \r
/**\r
* Parse a file in Stockholm format into Jalview's data model. The file has to\r
* be passed at construction time\r
// --------------- Variable Definitions -------------------\r
String line;\r
String version;\r
- // String id;
+ // String id;\r
Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
Hashtable seqs = new Hashtable();\r
Regex p, r, rend, s, x;\r
if (rend.search(line))\r
{\r
// End of the alignment, pass stuff back\r
- this.noSeqs = seqs.size();
+ this.noSeqs = seqs.size();\r
\r
- String seqdb,dbsource = null;
- Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
- Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
- if (getAlignmentProperty("AC") != null)
- {
- String dbType = getAlignmentProperty("AC").toString();
- if (pf.search(dbType))
- {
- // PFAM Alignment - so references are typically from Uniprot
- dbsource = "PFAM";
- }
- else if (rf.search(dbType))
- {
- dbsource = "RFAM";
- }
- }
+ String seqdb,dbsource = null;\r
+ Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam\r
+ Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam\r
+ if (getAlignmentProperty("AC") != null)\r
+ {\r
+ String dbType = getAlignmentProperty("AC").toString();\r
+ if (pf.search(dbType))\r
+ {\r
+ // PFAM Alignment - so references are typically from Uniprot\r
+ dbsource = "PFAM";\r
+ }\r
+ else if (rf.search(dbType))\r
+ {\r
+ dbsource = "RFAM";\r
+ }\r
+ }\r
// logger.debug("Number of sequences: " + this.noSeqs);\r
Enumeration accs = seqs.keys();\r
while (accs.hasMoreElements())\r
int end = -1;\r
String sid = acc;\r
/*\r
- * Retrieve hash of annotations for this accession Associate
- * Annotation with accession
+ * Retrieve hash of annotations for this accession Associate\r
+ * Annotation with accession\r
*/\r
Hashtable accAnnotations = null;\r
\r
jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
}\r
} \r
-
- if (accAnnotations != null && accAnnotations.containsKey("AC"))
- {
- if (dbsource != null)
- {
- String dbr = (String) accAnnotations.get("AC");
- if (dbr != null)
+\r
+ if (accAnnotations != null && accAnnotations.containsKey("AC"))\r
+ {\r
+ if (dbsource != null)\r
+ {\r
+ String dbr = (String) accAnnotations.get("AC");\r
+ if (dbr != null)\r
{\r
- // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession
- guessDatabaseFor(seqO, dbr, dbsource);
+ // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession\r
+ guessDatabaseFor(seqO, dbr, dbsource);\r
\r
}\r
}\r
- // else - do what ? add the data anyway and prompt the user to specify what references these are ?
- }
+ // else - do what ? add the data anyway and prompt the user to specify what references these are ?\r
+ }\r
\r
Hashtable features = null;\r
// We need to adjust the positions of all features to account for gaps\r
// TODO: map coding region to core jalview feature types\r
String type = i.nextElement().toString();\r
Hashtable content = (Hashtable) features.remove(type);\r
-
- // add alignment annotation for this feature
- String key = type2id(type);
- if (key != null)
- {
- if (accAnnotations != null
- && accAnnotations.containsKey(key))
- {
- Vector vv = (Vector) accAnnotations.get(key);
- for (int ii = 0; ii < vv.size(); ii++)
- {
- AlignmentAnnotation an = (AlignmentAnnotation) vv
- .elementAt(ii);
- seqO.addAlignmentAnnotation(an);
- }
- }
- }
-
+\r
+ // add alignment annotation for this feature\r
+ String key = type2id(type);\r
+ if (key != null)\r
+ {\r
+ if (accAnnotations != null\r
+ && accAnnotations.containsKey(key))\r
+ {\r
+ Vector vv = (Vector) accAnnotations.get(key);\r
+ for (int ii = 0; ii < vv.size(); ii++)\r
+ {\r
+ AlignmentAnnotation an = (AlignmentAnnotation) vv\r
+ .elementAt(ii);\r
+ seqO.addAlignmentAnnotation(an);\r
+ }\r
+ }\r
+ }\r
+\r
Enumeration j = content.keys();\r
while (j.hasMoreElements())\r
{\r
ann = new Hashtable();\r
seqAnn.put(acc, ann);\r
}\r
- // TODO test structure, call parseAnnotationRow with vector from
- // hashtable for specific sequence
+ // TODO test structure, call parseAnnotationRow with vector from\r
+ // hashtable for specific sequence\r
Hashtable features;\r
// Get an object with all the content for an annotation\r
if (ann.containsKey("features"))\r
}\r
ns += seq;\r
content.put(description, ns);\r
-
+ \r
// if(type.equals("SS")){\r
Hashtable strucAnn;\r
if (seqAnn.containsKey(acc))\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
+ id);\r
return id;\r
}\r
-
- protected static String type2id(String type)
- {
- String key = null;
- Enumeration e = typeIds.keys();
- while (e.hasMoreElements())
- {
- Object ll = e.nextElement();
- if (typeIds.get(ll).toString().equals(type))
- {
- key = (String) ll;
- break;
- }
- }
- if (key != null)
- {
- return (String) key;
- }
- System.err.println("Warning : Unknown Stockholm annotation type: "
- + type);
- return key;
+\r
+ protected static String type2id(String type)\r
+ {\r
+ String key = null;\r
+ Enumeration e = typeIds.keys();\r
+ while (e.hasMoreElements())\r
+ {\r
+ Object ll = e.nextElement();\r
+ if (typeIds.get(ll).toString().equals(type))\r
+ {\r
+ key = (String) ll;\r
+ break;\r
+ }\r
+ }\r
+ if (key != null)\r
+ {\r
+ return (String) key;\r
+ }\r
+ System.err.println("Warning : Unknown Stockholm annotation type: "\r
+ + type);\r
+ return key;\r
}
/**\r
* make a friendly ID string.\r
git://source.jalview.org / jalview.git / blobdiff