import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
import com.stevesoft.pat.Regex;
{
private static final String ANNOTATION = "annotation";
- private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ private static final char UNDERSCORE = '_';
- 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
- AlignmentI al;
+ 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()
{
}
/**
- * Creates a new StockholmFile object for output.
+ * Creates a new StockholmFile object for output
*/
public StockholmFile(AlignmentI al)
{
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()
{
// logger.debug("Stockholm version: " + version);
}
- // We define some Regexes here that will be used regularily later
+ // We define some Regexes here that will be used regularly later
rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
// id/from/to
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 = type2id(type);
+ String key = descriptionToType(type);
/*
* have we added annotation rows for this type ?
}
Hashtable content;
- if (features.containsKey(this.id2type(type)))
+ if (features.containsKey(StockholmFile.typeToDescription(type)))
{
// logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
+ content = (Hashtable) features
+ .get(StockholmFile.typeToDescription(type));
}
else
{
// logger.debug("Creating new content holder for " +
// this.id2type(type));
content = new Hashtable();
- features.put(this.id2type(type), content);
+ features.put(StockholmFile.typeToDescription(type), content);
}
String ns = (String) content.get(ANNOTATION);
Vector<AlignmentAnnotation> annotation, String label,
String annots)
{
- String convert1, convert2 = null;
-
- // convert1 = OPEN_PAREN.replaceAll(annots);
- // convert2 = CLOSE_PAREN.replaceAll(convert1);
+ // String convert1 = OPEN_PAREN.replaceAll(annots);
+ // String convert2 = CLOSE_PAREN.replaceAll(convert1);
// annots = convert2;
String type = label;
type = id2type(type);
boolean isrnass = false;
+
if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
for (int i = 0; i < annots.length(); i++)
{
String pos = annots.substring(i, i + 1);
+ if (UNDERSCORE == pos.charAt(0))
+ {
+ pos = " ";
+ }
Annotation ann;
ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
// be written out
}
@Override
- public String print(SequenceI[] s, boolean jvSuffix)
+ public String print(final SequenceI[] sequences, boolean jvSuffix)
{
- out = new StringBuffer();
+ StringBuilder out = new StringBuilder();
out.append("# STOCKHOLM 1.0");
out.append(newline);
- // find max length of id
- int max = 0;
- int maxid = 0;
- int in = 0;
- Hashtable dataRef = null;
- while ((in < s.length) && (s[in] != null))
+ int maxIdWidth = 0;
+ for (SequenceI seq : sequences)
{
- String tmp = printId(s[in], jvSuffix);
- max = Math.max(max, s[in].getLength());
-
- if (tmp.length() > maxid)
+ if (seq != null)
{
- maxid = tmp.length();
+ String formattedId = printId(seq, jvSuffix);
+ maxIdWidth = Math.max(maxIdWidth, formattedId.length());
}
- if (s[in].getDBRefs() != null)
- {
- 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++;
}
- maxid += 9;
- int i = 0;
+ maxIdWidth += 9;
- // output database type
- if (al.getProperties() != null)
+ /*
+ * generic alignment properties
+ */
+ Hashtable props = al.getProperties();
+ if (props != null)
{
- if (!al.getProperties().isEmpty())
+ for (Object key : props.keySet())
{
- Enumeration key = al.getProperties().keys();
- Enumeration val = al.getProperties().elements();
- while (key.hasMoreElements())
- {
- out.append("#=GF " + key.nextElement() + " " + val.nextElement());
- out.append(newline);
- }
+ out.append(String.format("#=GF %s %s", key.toString(),
+ props.get(key).toString()));
+ out.append(newline);
}
}
- // output database accessions
- if (dataRef != null)
+ /*
+ * 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)
{
- Enumeration en = dataRef.keys();
- while (en.hasMoreElements())
+ if (seq != 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"))
- {
-
- out.append(" AC " + type.substring(type.indexOf(";") + 1));
- }
- else
+ DBRefEntry[] dbRefs = seq.getDBRefs();
+ if (dbRefs != null)
{
- out.append(" DR " + type + " ");
+ String idField = formatter
+ .form("#=GS " + printId(seq, jvSuffix) + " ");
+ for (DBRefEntry dbRef : dbRefs)
+ {
+ out.append(idField);
+ printDbRef(out, dbRef);
+ }
}
- out.append(newline);
}
}
- // output annotations
- while (i < s.length && s[i] != null)
+ /*
+ * output annotations
+ */
+ for (SequenceI seq : sequences)
{
- AlignmentAnnotation[] alAnot = s[i].getAnnotation();
- if (alAnot != null)
+ if (seq != null)
{
- Annotation[] ann;
- for (int j = 0; j < alAnot.length; j++)
+ AlignmentAnnotation[] alAnot = seq.getAnnotation();
+ if (alAnot != null)
{
-
- String key = type2id(alAnot[j].label);
- boolean isrna = alAnot[j].isValidStruc();
-
- if (isrna)
+ for (int j = 0; j < alAnot.length; j++)
{
- // hardwire to secondary structure if there is RNA secondary
- // structure on the annotation
- key = "SS";
- }
- if (key == null)
- {
-
- continue;
- }
+ 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("#=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(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);
}
- 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++;
+ out.append(new Format("%-" + maxIdWidth + "s")
+ .form(printId(seq, jvSuffix) + " "));
+ out.append(seq.getSequenceAsString());
+ out.append(newline);
+ }
}
- // alignment annotation
- AlignmentAnnotation aa;
+ /*
+ * output alignment annotation (but not auto-calculated or sequence-related)
+ */
if (al.getAlignmentAnnotation() != null)
{
for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
{
- aa = al.getAlignmentAnnotation()[ia];
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[ia];
if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
{
continue;
}
- String seq = "";
- String label;
+ String label = aa.label;
String key = "";
if (aa.label.equals("seq"))
{
}
else
{
- key = type2id(aa.label.toLowerCase());
- if (key == null)
+ key = descriptionToType(aa.label);
+ if ("RF".equals(key))
{
- label = aa.label;
+ label = key;
}
- else
+ else if (key != null)
{
label = key + "_cons";
}
}
- if (label == null)
- {
- label = aa.label;
- }
label = label.replace(" ", "_");
out.append(
- new Format("%-" + maxid + "s").form("#=GC " + label + " "));
- boolean isrna = aa.isValidStruc();
+ new Format("%-" + maxIdWidth + "s")
+ .form("#=GC " + label + " "));
+ StringBuilder sb = new StringBuilder(aa.annotations.length);
for (int j = 0; j < aa.annotations.length; j++)
{
- seq += outputCharacter(key, j, isrna, aa.annotations, null);
+ sb.append(
+ getAnnotationCharacter(key, j, aa.annotations[j], null));
}
- out.append(seq);
+ out.append(sb.toString());
out.append(newline);
}
}
}
/**
- * add an annotation character to the output row
+ * 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
*
* @param seq
* @param key
* @param k
- * @param isrna
* @param ann
* @param sequenceI
*/
- private char outputCharacter(String key, int k, boolean isrna,
- Annotation[] ann, SequenceI sequenceI)
+ static char getAnnotationCharacter(String key, int k, Annotation annot,
+ 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)
{
- // sensible gap character
- ssannotchar = ' ';
- charset = true;
+ // TODO: TVA: Check against develop for correct behaviour!
+ // Stockholm format requires underscore, not space
+ return UNDERSCORE;
}
else
{
: seq;
}
- 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;
- }
-
/**
* make a friendly ID string.
*
git://source.jalview.org / jalview.git / blobdiff