\r
/**\r
* This class is supposed to parse a Stockholm format file into Jalview\r
- * \r
+ * There are TODOs in this class: we do not know what the database source and\r
+ * version is for the file when parsing the #GS= AC tag which associates accessions\r
+ * with sequences. \r
+ * Database references are also not parsed correctly: a separate reference string\r
+ * parser must be added to parse the database reference form into Jalview's local\r
+ * representation.\r
* @author bsb at sanger.ac.uk\r
- * @version 0.3\r
+ * @version 0.3 + jalview mods\r
+ * \r
*/\r
public class StockholmFile extends AlignFile\r
{\r
{\r
super(inFile, type);\r
}\r
-\r
+ public StockholmFile(FileParse source) throws IOException\r
+ {\r
+ super(source);\r
+ }\r
public void initData()\r
{\r
super.initData();\r
rend = new Regex("\\/\\/"); // Find the end of an alignment\r
p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
// id/from/to\r
- s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype\r
+ s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
\r
{\r
String acc = (String) accs.nextElement();\r
// logger.debug("Processing sequence " + acc);\r
- String seq = (String) seqs.get(acc);\r
+ String seq = (String) seqs.remove(acc);\r
if (maxLength < seq.length())\r
{\r
maxLength = seq.length();\r
\r
if (seqAnn != null && seqAnn.containsKey(acc))\r
{\r
- accAnnotations = (Hashtable) seqAnn.get(acc);\r
+ accAnnotations = (Hashtable) seqAnn.remove(acc);\r
}\r
\r
// Split accession in id and from/to\r
{\r
String src = dbr.substring(0, dbr.indexOf(";"));\r
String acn = dbr.substring(dbr.indexOf(";") + 1);\r
- DBRefEntry dbref = new DBRefEntry(jalview.util.DBRefUtils\r
- .getCanonicalName(src), acn, "");\r
- seqO.addDBRef(dbref);\r
+ jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
+ //seqO.addDBRef(dbref);\r
}\r
}\r
Hashtable features = null;\r
// We need to adjust the positions of all features to account for gaps\r
try\r
{\r
- features = (Hashtable) accAnnotations.get("features");\r
+ features = (Hashtable) accAnnotations.remove("features");\r
} catch (java.lang.NullPointerException e)\r
{\r
// loggerwarn("Getting Features for " + acc + ": " +\r
// if we have features\r
if (features != null)\r
{\r
+ int posmap[] = seqO.findPositionMap();\r
Enumeration i = features.keys();\r
while (i.hasMoreElements())\r
{\r
// TODO: parse out scores as annotation row\r
// TODO: map coding region to core jalview feature types\r
String type = i.nextElement().toString();\r
- Hashtable content = (Hashtable) features.get(type);\r
-\r
+ Hashtable content = (Hashtable) features.remove(type);\r
Enumeration j = content.keys();\r
while (j.hasMoreElements())\r
{\r
for (int k = 0; k < byChar.length; k++)\r
{\r
char c = byChar[k];\r
- if (!(c == ' ' || c == '_' || c == '-'))\r
+ if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM uses '.' for feature background\r
{\r
- int new_pos = seqO.findPosition(k);\r
+ int new_pos = posmap[k]; // look up nearest seqeunce position to this column\r
SequenceFeature feat = new SequenceFeature(type, desc,\r
new_pos, new_pos, 0f, null);\r
\r
}\r
\r
}\r
-\r
+ \r
}\r
+ // garbage collect\r
+ \r
// logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
// + ": " + seq);\r
this.seqs.addElement(seqO);\r
}\r
+ return; // finished parsing this segment of source\r
}\r
else if (!r.search(line))\r
{\r
{\r
String acc = s.stringMatched(1);\r
String type = s.stringMatched(2);\r
- String seq = s.stringMatched(3);\r
- String description = new String();\r
-\r
+ String seq = new String(s.stringMatched(3));\r
+ String description = null;\r
// Check for additional information about the current annotation\r
- if (x.search(seq))\r
+ // We use a simple string tokenizer here for speed\r
+ StringTokenizer sep = new StringTokenizer(seq," \t");\r
+ description = sep.nextToken();\r
+ if (sep.hasMoreTokens())\r
{\r
- description = x.stringMatched(1);\r
- seq = x.stringMatched(2);\r
+ seq = sep.nextToken();\r
+ } else {\r
+ seq = description;\r
+ description = new String();\r
}\r
// sequence id with from-to fields\r
\r
}\r
else\r
{\r
- throw new IOException("Error parsing " + line);\r
+ System.err.println("Warning - couldn't parse sequence annotation row line:\n"+line);\r
+ // throw new IOException("Error parsing " + line);\r
}\r
}\r
else\r
{\r
String pos = annots.substring(i, i + 1);\r
Annotation ann;\r
- ann = new Annotation(pos, "", ' ', Float.NaN);\r
+ ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not be written out \r
if (ss)\r
{\r
ann.secondaryStructure = jalview.schemes.ResidueProperties\r
.getDssp3state(pos).charAt(0);\r
if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
{\r
- ann.displayCharacter = "";\r
+ ann.displayCharacter = ""; // null; // " ";\r
}\r
else\r
{\r
- ann.displayCharacter += " ";\r
+ ann.displayCharacter = " "+ann.displayCharacter;\r
}\r
}\r
\r
if (annot == null)\r
{\r
annot = new AlignmentAnnotation(type, type, els);\r
- annotation.add(annot);\r
+ annotation.addElement(annot);\r
}\r
else\r
{\r
git://source.jalview.org / jalview.git / blobdiff