import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MessageManager;
*/
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("(>|\\])", ")");
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.",
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
{
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;
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);
}
{
// 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)
content = new Hashtable();
features.put(this.id2type(type), content);
}
- String ns = (String) content.get("annotation");
+ String ns = (String) content.get(ANNOTATION);
if (ns == null)
{
}
// 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
// }
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);
}
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.unknown_annotation_detected", new String[] {
- annType, annContent }));
+ "exception.unknown_annotation_detected", new String[]
+ { annType, annContent }));
}
}
}
{
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);
}
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;
+ boolean ss = false, posterior = false;
type = id2type(type);
- if (type.equals("secondary structure"))
+ if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
}
+ if (type.equalsIgnoreCase("posterior probability"))
+ {
+ posterior = true;
+ }
// decide on secondary structure or not.
Annotation[] els = new Annotation[annots.length()];
for (int i = 0; i < annots.length(); i++)
ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
.charAt(0);
- if (ann.secondaryStructure == pos.charAt(0))
- {
- ann.displayCharacter = ""; // null; // " ";
+ if (ann.secondaryStructure == pos.charAt(0))
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
}
- else
+ }
+
+ }
+ if (posterior && !ann.isWhitespace()
+ && !Comparison.isGap(pos.charAt(0)))
+ {
+ float val = 0;
+ // symbol encodes values - 0..*==0..10
+ if (pos.charAt(0) == '*')
+ {
+ val = 10;
+ }
+ else
+ {
+ val = pos.charAt(0) - '0';
+ if (val > 9)
{
- ann.displayCharacter = " " + ann.displayCharacter;
- }
+ val = 10;
}
}
-
+ ann.value = val;
}
els[i] = ann;
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)
{
{
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"))
{
}
// 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++)
}
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++)
{
{
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)
if (typeIds == null)
{
typeIds = new Hashtable();
- typeIds.put("SS", "secondary structure");
- typeIds.put("SA", "surface accessibility");
+ typeIds.put("SS", "Secondary Structure");
+ typeIds.put("SA", "Surface Accessibility");
typeIds.put("TM", "transmembrane");
- typeIds.put("PP", "posterior probability");
+ typeIds.put("PP", "Posterior Probability");
typeIds.put("LI", "ligand binding");
typeIds.put("AS", "active site");
typeIds.put("IN", "intron");
typeIds.put("DE", "description");
typeIds.put("DR", "reference");
typeIds.put("LO", "look");
- typeIds.put("RF", "reference positions");
+ typeIds.put("RF", "Reference Positions");
}
}
{
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;
}
while (e.hasMoreElements())
{
Object ll = e.nextElement();
- if (typeIds.get(ll).toString().equals(type))
+ if (typeIds.get(ll).toString().equalsIgnoreCase(type))
{
key = (String) ll;
break;
{
return key;
}
- System.err.println("Warning : Unknown Stockholm annotation type: "
- + type);
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type: " + type);
return key;
}
git://source.jalview.org / jalview.git / blobdiff