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 jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MessageManager;
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.StringTokenizer;
+import java.util.Map.Entry;
import java.util.Vector;
import com.stevesoft.pat.Regex;
*/
public class StockholmFile extends AlignFile
{
- private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ private static final String ANNOTATION = "annotation";
- private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+ private static final char UNDERSCORE = '_';
- private static final Regex DETECT_BRACKETS = new Regex(
- "(<|>|\\[|\\]|\\(|\\))");
+ // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
- StringBuffer out; // output buffer
+ public static final Regex DETECT_BRACKETS = new Regex(
+ "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- AlignmentI al;
+ /*
+ * lookup table of Stockholm 'feature' (annotation) types
+ * see http://sonnhammer.sbc.su.se/Stockholm.html
+ */
+ private static Map<String, String> featureTypes = null;
+
+ 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)
{
this.al = al;
}
- public StockholmFile(String inFile, String type) throws IOException
+ public StockholmFile(String inFile, DataSourceType type)
+ throws IOException
{
super(inFile, type);
}
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()
{
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.",
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
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
{
// 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 ?
+ */
+ boolean annotsAdded = false;
if (key != null)
{
if (accAnnotations != null
Vector vv = (Vector) accAnnotations.get(key);
for (int ii = 0; ii < vv.size(); ii++)
{
+ annotsAdded = true;
AlignmentAnnotation an = (AlignmentAnnotation) vv
.elementAt(ii);
seqO.addAlignmentAnnotation(an);
while (j.hasMoreElements())
{
String desc = j.nextElement().toString();
+ if (ANNOTATION.equals(desc) && annotsAdded)
+ {
+ // don't add features if we already added an annotation row
+ continue;
+ }
String ns = content.get(desc).toString();
char[] byChar = ns.toCharArray();
for (int k = 0; k < byChar.length; k++)
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)
{
String acc = s.stringMatched(1);
String type = s.stringMatched(2);
- String seq = new String(s.stringMatched(3));
- String description = null;
- // Check for additional information about the current annotation
- // We use a simple string tokenizer here for speed
- StringTokenizer sep = new StringTokenizer(seq, " \t");
- description = sep.nextToken();
- if (sep.hasMoreTokens())
- {
- seq = sep.nextToken();
- }
- else
- {
- seq = description;
- description = new String();
- }
- // sequence id with from-to fields
+ String oseq = s.stringMatched(3);
+ /*
+ * copy of annotation field that may be processed into whitespace chunks
+ */
+ String seq = new String(oseq);
Hashtable ann;
// Get an object with all the annotations for this sequence
ann = new Hashtable();
seqAnn.put(acc, ann);
}
+
+ // // start of block for appending annotation lines for wrapped
+ // stokchholm file
// TODO test structure, call parseAnnotationRow with vector from
// hashtable for specific sequence
+
Hashtable features;
// Get an object with all the content for an annotation
if (ann.containsKey("features"))
}
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(description);
+ String ns = (String) content.get(ANNOTATION);
+
if (ns == null)
{
ns = "";
}
+ // finally, append the annotation line
ns += seq;
- content.put(description, ns);
+ content.put(ANNOTATION, ns);
+ // // end of wrapped annotation block.
+ // // Now a new row is created with the current set of data
- // if(type.equals("SS")){
Hashtable strucAnn;
if (seqAnn.containsKey(acc))
{
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
alan.visible = false;
}
- // annotations.addAll(newStruc);
+ // new annotation overwrites any existing annotation...
+
strucAnn.put(type, newStruc);
seqAnn.put(acc, strucAnn);
}
// }
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 }));
}
}
}
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
{
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);
}
Vector<AlignmentAnnotation> annotation, String label,
String annots)
{
- String convert1, convert2 = null;
-
- convert1 = OPEN_PAREN.replaceAll(annots);
- convert2 = CLOSE_PAREN.replaceAll(convert1);
- annots = convert2;
+ // String convert1 = OPEN_PAREN.replaceAll(annots);
+ // String convert2 = CLOSE_PAREN.replaceAll(convert1);
+ // annots = convert2;
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;
- type = id2type(type);
- if (type.equals("secondary structure"))
+ boolean ss = false, posterior = false;
+ type = typeToDescription(type);
+ 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++)
{
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
{
if (DETECT_BRACKETS.search(pos))
{
- ann.secondaryStructure = Rna.getRNASecStrucState(
- pos).charAt(0);
+ ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
+ ann.displayCharacter = "" + pos.charAt(0);
}
else
{
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;
return annot;
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(final SequenceI[] sequences, boolean jvSuffix)
{
- // find max length of id
- int max = 0;
- int maxid = 0;
- int in = 0;
- Hashtable dataRef = null;
- while ((in < s.length) && (s[in] != null))
- {
- String tmp = printId(s[in]);
- if (s[in].getSequence().length > max)
- {
- max = s[in].getSequence().length;
- }
+ StringBuilder out = new StringBuilder();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
- if (tmp.length() > maxid)
+ int maxIdWidth = 0;
+ for (SequenceI seq : sequences)
+ {
+ 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)
{
- if (s[i].getDatasetSequence() != null)
+ if (seq != null)
{
- SequenceI ds = s[i].getDatasetSequence();
- AlignmentAnnotation[] alAnot;
- Annotation[] ann;
- Annotation annot;
- alAnot = s[i].getAnnotation();
- String feature = "";
+ AlignmentAnnotation[] alAnot = seq.getAnnotation();
if (alAnot != null)
{
for (int j = 0; j < alAnot.length; j++)
{
- if (ds.getSequenceFeatures() != null)
+ AlignmentAnnotation ann = alAnot[j];
+ String key = descriptionToType(ann.label);
+ boolean isrna = ann.isValidStruc();
+ if (isrna)
{
- feature = ds.getSequenceFeatures()[0].type;
+ /*
+ * output as secondary structure if there is
+ * RNA secondary structure on the annotation
+ */
+ key = "SS";
}
- // ?bug - feature may still have previous loop value
- String key = type2id(feature);
-
if (key == null)
{
continue;
}
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form("#=GR "
- + printId(s[i]) + " " + key + " "));
- ann = alAnot[j].annotations;
- boolean isrna = alAnot[j].isValidStruc();
- String seq = "";
- for (int k = 0; k < ann.length; k++)
+ 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++)
{
- seq += outputCharacter(key, k, isrna, ann, s[i]);
+ seqString
+ .append(getAnnotationCharacter(key, k, anns[k], seq));
}
- out.append(seq);
+ out.append(seqString.toString());
out.append(newline);
}
}
- }
- out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
- 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();
+ out.append(
+ 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);
}
}
+
+ out.append("//");
+ out.append(newline);
+
return out.toString();
}
/**
- * 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))) : annot.displayCharacter;
+ String ch = (annot == null)
+ ? ((sequenceI == null) ? "-"
+ : Character.toString(sequenceI.getCharAt(k)))
+ : annot.displayCharacter;
if (key != null && key.equals("SS"))
{
if (annot == null)
{
- // sensible gap character if one is available or make one up
- return sequenceI == null ? '-' : sequenceI.getCharAt(k);
+ // Stockholm format requires underscore, not space
+ return UNDERSCORE;
}
else
{
return seq;
}
- @Override
- public String print()
- {
- out = new StringBuffer();
- out.append("# STOCKHOLM 1.0");
- out.append(newline);
- print(getSeqsAsArray());
-
- 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().equals(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