private static final String ANNOTATION = "annotation";
private static final char UNDERSCORE = '_';
+
+ private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+
+ private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- /*
- * lookup table of Stockholm 'feature' (annotation) types
- * see http://sonnhammer.sbc.su.se/Stockholm.html
- */
- private static Map<String, String> featureTypes = null;
-
// WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
StringBuffer out; // output buffer
- static
- {
- featureTypes = new HashMap<>();
- featureTypes.put("SS", "Secondary Structure");
- featureTypes.put("SA", "Surface Accessibility");
- featureTypes.put("TM", "transmembrane");
- featureTypes.put("PP", "Posterior Probability");
- featureTypes.put("LI", "ligand binding");
- featureTypes.put("AS", "active site");
- featureTypes.put("IN", "intron");
- featureTypes.put("IR", "interacting residue");
- featureTypes.put("AC", "accession");
- featureTypes.put("OS", "organism");
- featureTypes.put("CL", "class");
- featureTypes.put("DE", "description");
- featureTypes.put("DR", "reference");
- featureTypes.put("LO", "look");
- featureTypes.put("RF", "Reference Positions");
- }
-
private AlignmentI al;
public StockholmFile()
super(source);
}
- /**
- * Answers the readable description for a (case-sensitive) annotation type
- * code, for example "Reference Positions" for "RF". Returns the type code if
- * no description is found.
- *
- * @param id
- * @return
- */
- public static String typeToDescription(String id)
- {
- if (featureTypes.containsKey(id))
- {
- return featureTypes.get(id);
- }
- System.err.println(
- "Warning : Unknown Stockholm annotation type code " + id);
- return id;
- }
-
- /**
- * Answers the annotation type code for a (non-case-sensitive) readable
- * description, for example "RF" for "Reference Positions" (or null if not
- * found)
- *
- * @param description
- * @return
- */
- public static String descriptionToType(String description)
- {
- for (Entry<String, String> entry : featureTypes.entrySet())
- {
- if (entry.getValue().equalsIgnoreCase(description))
- {
- return entry.getKey();
- }
- }
- System.err.println(
- "Warning : Unknown Stockholm annotation type: " + description);
- return null;
- }
-
@Override
public void initData()
{
Regex closeparen = new Regex("(>|\\])", ")");
// Detect if file is RNA by looking for bracket types
- // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
Hashtable content = (Hashtable) features.remove(type);
// add alignment annotation for this feature
- String key = descriptionToType(type);
+ String key = type2id(type);
/*
* have we added annotation rows for this type ?
}
Hashtable content;
- if (features.containsKey(StockholmFile.typeToDescription(type)))
+ if (features.containsKey(this.id2type(type)))
{
// logger.debug("Found content for " + this.id2type(type));
content = (Hashtable) features
- .get(StockholmFile.typeToDescription(type));
+ .get(this.id2type(type));
}
else
{
// logger.debug("Creating new content holder for " +
// this.id2type(type));
content = new Hashtable();
- features.put(StockholmFile.typeToDescription(type), content);
+ features.put(id2type(type), content);
}
String ns = (String) content.get(ANNOTATION);
Vector<AlignmentAnnotation> annotation, String label,
String annots)
{
+ String convert1, convert2 = null;
// String convert1 = OPEN_PAREN.replaceAll(annots);
// String convert2 = CLOSE_PAREN.replaceAll(convert1);
// annots = convert2;
}
@Override
- public String print(final SequenceI[] sequences, boolean jvSuffix)
+ public String print(SequenceI[] s, boolean jvSuffix)
{
- StringBuilder out = new StringBuilder();
+ out = new StringBuffer();
out.append("# STOCKHOLM 1.0");
out.append(newline);
- int maxIdWidth = 0;
- for (SequenceI seq : sequences)
+ // find max length of id
+ int max = 0;
+ int maxid = 0;
+ int in = 0;
+ Hashtable dataRef = null;
+ while ((in < s.length) && (s[in] != null))
{
- if (seq != null)
+ String tmp = printId(s[in], jvSuffix);
+ max = Math.max(max, s[in].getLength());
+
+ if (tmp.length() > maxid)
+ {
+ maxid = tmp.length();
+ }
+ if (s[in].getDBRefs() != null)
{
- String formattedId = printId(seq, jvSuffix);
- maxIdWidth = Math.max(maxIdWidth, formattedId.length());
+ for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
+ {
+ if (dataRef == null)
+ {
+ dataRef = new Hashtable();
+ }
+
+ String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
+ + " ; "
+ + s[in].getDBRefs()[idb].getAccessionId().toString();
+ dataRef.put(tmp, datAs1);
+ }
}
+ in++;
}
- maxIdWidth += 9;
+ maxid += 9;
+ int i = 0;
- /*
- * generic alignment properties
- */
- Hashtable props = al.getProperties();
- if (props != null)
+ // output database type
+ if (al.getProperties() != null)
{
- for (Object key : props.keySet())
+ if (!al.getProperties().isEmpty())
{
- out.append(String.format("#=GF %s %s", key.toString(),
- props.get(key).toString()));
- out.append(newline);
+ Enumeration key = al.getProperties().keys();
+ Enumeration val = al.getProperties().elements();
+ while (key.hasMoreElements())
+ {
+ out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+ out.append(newline);
+ }
}
}
- /*
- * output database accessions as #=GS (per sequence annotation)
- * PFAM or RFAM are output as AC <accession number>
- * others are output as DR <dbname> ; <accession>
- */
- Format formatter = new Format("%-" + (maxIdWidth - 2) + "s");
- for (SequenceI seq : sequences)
+ // output database accessions
+ if (dataRef != null)
{
- if (seq != null)
+ Enumeration en = dataRef.keys();
+ while (en.hasMoreElements())
{
- DBRefEntry[] dbRefs = seq.getDBRefs();
- if (dbRefs != null)
+ Object idd = en.nextElement();
+ String type = (String) dataRef.remove(idd);
+ out.append(new Format("%-" + (maxid - 2) + "s")
+ .form("#=GS " + idd.toString() + " "));
+ if (type.contains("PFAM") || type.contains("RFAM"))
{
- String idField = formatter
- .form("#=GS " + printId(seq, jvSuffix) + " ");
- for (DBRefEntry dbRef : dbRefs)
- {
- out.append(idField);
- printDbRef(out, dbRef);
- }
+
+ out.append(" AC " + type.substring(type.indexOf(";") + 1));
}
+ else
+ {
+ out.append(" DR " + type + " ");
+ }
+ out.append(newline);
}
}
- /*
- * output annotations
- */
- for (SequenceI seq : sequences)
+ // output annotations
+ while (i < s.length && s[i] != null)
{
- if (seq != null)
+ AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+ if (alAnot != null)
{
- AlignmentAnnotation[] alAnot = seq.getAnnotation();
- if (alAnot != null)
+ Annotation[] ann;
+ for (int j = 0; j < alAnot.length; j++)
{
- for (int j = 0; j < alAnot.length; j++)
+
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
+
+ if (isrna)
+ {
+ // hardwire to secondary structure if there is RNA secondary
+ // structure on the annotation
+ key = "SS";
+ }
+ if (key == null)
{
- AlignmentAnnotation ann = alAnot[j];
- String key = descriptionToType(ann.label);
- boolean isrna = ann.isValidStruc();
- if (isrna)
- {
- /*
- * output as secondary structure if there is
- * RNA secondary structure on the annotation
- */
- key = "SS";
- }
- if (key == null)
- {
- continue;
- }
- out.append(new Format("%-" + maxIdWidth + "s").form(
- "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
- Annotation[] anns = ann.annotations;
- StringBuilder seqString = new StringBuilder();
- for (int k = 0; k < anns.length; k++)
- {
- seqString
- .append(getAnnotationCharacter(key, k, anns[k], seq));
- }
- out.append(seqString.toString());
- out.append(newline);
+ continue;
}
- }
- out.append(new Format("%-" + maxIdWidth + "s")
- .form(printId(seq, jvSuffix) + " "));
- out.append(seq.getSequenceAsString());
- out.append(newline);
+ // out.append("#=GR ");
+ 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++)
+ {
+ seq += outputCharacter(key, k, isrna, ann, s[i]);
+ }
+ out.append(seq);
+ out.append(newline);
+ }
}
+
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[i], jvSuffix) + " "));
+ out.append(s[i].getSequenceAsString());
+ out.append(newline);
+ i++;
}
- /*
- * output alignment annotation (but not auto-calculated or sequence-related)
- */
+ // alignment annotation
+ AlignmentAnnotation aa;
if (al.getAlignmentAnnotation() != null)
{
for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
{
- AlignmentAnnotation aa = al.getAlignmentAnnotation()[ia];
+ aa = al.getAlignmentAnnotation()[ia];
if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
{
continue;
}
- String label = aa.label;
+ String seq = "";
+ String label;
String key = "";
if (aa.label.equals("seq"))
{
}
else
{
- key = descriptionToType(aa.label);
- if ("RF".equals(key))
+ key = type2id(aa.label.toLowerCase());
+ if (key == null)
{
- label = key;
+ label = aa.label;
}
- else if (key != null)
+ else
{
label = key + "_cons";
}
}
+ if (label == null)
+ {
+ label = aa.label;
+ }
label = label.replace(" ", "_");
out.append(
- new Format("%-" + maxIdWidth + "s")
- .form("#=GC " + label + " "));
- StringBuilder sb = new StringBuilder(aa.annotations.length);
+ new Format("%-" + maxid + "s").form("#=GC " + label + " "));
+ boolean isrna = aa.isValidStruc();
for (int j = 0; j < aa.annotations.length; j++)
{
- sb.append(
- getAnnotationCharacter(key, j, aa.annotations[j], null));
+ seq += outputCharacter(key, j, isrna, aa.annotations, null);
}
- out.append(sb.toString());
+ out.append(seq);
out.append(newline);
}
}
return out.toString();
}
- /**
- * A helper method that appends a formatted dbref to the output buffer
- *
- * @param out
- * @param dbRef
- */
- protected void printDbRef(StringBuilder out, DBRefEntry dbRef)
- {
- String db = dbRef.getSource();
- String acc = dbRef.getAccessionId();
- if (DBRefSource.PFAM.equalsIgnoreCase(db)
- || DBRefSource.RFAM.equalsIgnoreCase(db))
- {
- out.append(" AC " + acc);
- }
- else
- {
- out.append(" DR " + db + " ; " + acc);
- }
- out.append(newline);
- }
/**
- * Returns an annotation character to add to the output row
+ * add an annotation character to the output row
*
* @param seq
* @param key
* @param k
+ * @param isrna
* @param ann
* @param sequenceI
*/
- static char getAnnotationCharacter(String key, int k, Annotation annot,
- SequenceI sequenceI)
+ private char outputCharacter(String key, int k, boolean isrna,
+ Annotation[] ann, SequenceI sequenceI)
{
char seq = ' ';
+ Annotation annot = ann[k];
String ch = (annot == null)
? ((sequenceI == null) ? "-"
: Character.toString(sequenceI.getCharAt(k)))
boolean charset = false;
if (annot == null)
{
- // TODO: TVA: Check against develop for correct behaviour!
- // Stockholm format requires underscore, not space
- return UNDERSCORE;
+ // sensible gap character
+ ssannotchar = ' ';
+ charset = true;
}
else
{
dataName = dataName.substring(1, e).trim();
return dataName;
}
+
+
+ public String print()
+ {
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
+ print(getSeqsAsArray(), false);
+
+ out.append("//");
+ out.append(newline);
+ return out.toString();
+ }
+
+ private static Hashtable typeIds = null;
+
+ static
+ {
+ if (typeIds == null)
+ {
+ typeIds = new Hashtable();
+ typeIds.put("SS", "Secondary Structure");
+ typeIds.put("SA", "Surface Accessibility");
+ typeIds.put("TM", "transmembrane");
+ typeIds.put("PP", "Posterior Probability");
+ typeIds.put("LI", "ligand binding");
+ typeIds.put("AS", "active site");
+ typeIds.put("IN", "intron");
+ typeIds.put("IR", "interacting residue");
+ typeIds.put("AC", "accession");
+ typeIds.put("OS", "organism");
+ typeIds.put("CL", "class");
+ typeIds.put("DE", "description");
+ typeIds.put("DR", "reference");
+ typeIds.put("LO", "look");
+ typeIds.put("RF", "Reference Positions");
+
+ }
+ }
+
+ protected static String id2type(String id)
+ {
+ if (typeIds.containsKey(id))
+ {
+ return (String) typeIds.get(id);
+ }
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type code " + id);
+ return id;
+ }
+
+ 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().equalsIgnoreCase(type))
+ {
+ key = (String) ll;
+ break;
+ }
+ }
+ if (key != null)
+ {
+ return key;
+ }
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type: " + type);
+ return key;
+ }
}
git://source.jalview.org / jalview.git / commitdiff