*/
package jalview.io;
+import jalview.analysis.Rna;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
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.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.StringTokenizer;
import java.util.Vector;
import com.stevesoft.pat.Regex;
*/
public class StockholmFile extends AlignFile
{
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
- protected ArrayList<RNA> result;
+ 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(
+ "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
+
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+ public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+
+ // use the following regex to decide an annotations (whole) line is NOT an RNA
+ // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
+ private static final Regex NOT_RNASS = new Regex(
+ "^[^<>[\\](){}A-DF-Za-df-z]*$");
StringBuffer out; // output buffer
- AlignmentI al;
+ 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, DataSourceType sourceType)
+ public StockholmFile(String inFile, DataSourceType type)
throws IOException
{
- super(inFile, sourceType);
+ super(inFile, type);
}
public StockholmFile(FileParse source) throws IOException
fr = new FileReader(inFile);
BufferedReader r = new BufferedReader(fr);
- result = null;
+ List<RNA> result = null;
try
{
result = RNAFactory.loadSecStrStockholm(r);
for (int k = 0; k < rna.length(); k++)
{
ann[k] = new Annotation(annot[k], "",
- jalview.schemes.ResidueProperties.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
+ 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
// add alignment annotation for this feature
String key = type2id(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)
}
else
{
- // throw new IOException(MessageManager.formatMessage(
- // "exception.error_parsing_line", new String[] { line }));
+ // throw new IOException("Error parsing " + line);
System.err.println(">> missing annotation: " + line);
}
}
{
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"))
if (features.containsKey(this.id2type(type)))
{
// logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
+ content = (Hashtable) features
+ .get(this.id2type(type));
}
else
{
// logger.debug("Creating new content holder for " +
// this.id2type(type));
content = new Hashtable();
- features.put(this.id2type(type), content);
+ features.put(id2type(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);
}
}
protected static AlignmentAnnotation parseAnnotationRow(
- Vector annotation, String label, String annots)
+ Vector<AlignmentAnnotation> annotation, String label,
+ String annots)
{
- String convert1, convert2 = null;
-
- // Convert all bracket types to parentheses
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
-
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
-
- convert1 = openparen.replaceAll(annots);
- convert2 = closeparen.replaceAll(convert1);
- annots = convert2;
+ String convert1, convert2 = null;
+ // 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;
+ boolean ss = false, posterior = false;
type = id2type(type);
- if (type.equals("secondary structure"))
+
+ boolean isrnass = false;
+
+ if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
+ isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+ // here (it's easier for dealing with
+ // other non-alpha-non-brace chars)
+ }
+ 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 (" .-_".indexOf(pos) == -1)
{
- if (detectbrackets.search(pos))
+ if (isrnass && RNASS_BRACKETS.indexOf(pos) >= 0)
{
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getRNASecStrucState(pos).charAt(0);
+ ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
+ ann.displayCharacter = "" + pos.charAt(0);
}
else
{
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getDssp3state(pos).charAt(0);
- }
+ 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;
}
AlignmentAnnotation annot = null;
- Enumeration e = annotation.elements();
+ Enumeration<AlignmentAnnotation> e = annotation.elements();
while (e.hasMoreElements())
{
- annot = (AlignmentAnnotation) e.nextElement();
+ annot = e.nextElement();
if (annot.label.equals(type))
{
break;
return annot;
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvSuffix)
{
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
+
// find max length of id
int max = 0;
int maxid = 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;
- }
+ String tmp = printId(s[in], jvSuffix);
+ 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"))
{
// output annotations
while (i < s.length && s[i] != null)
{
- if (s[i].getDatasetSequence() != null)
+ AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+ if (alAnot != null)
{
- SequenceI ds = s[i].getDatasetSequence();
- AlignmentAnnotation[] alAnot;
Annotation[] ann;
- Annotation annot;
- alAnot = s[i].getAnnotation();
- String feature = "";
- if (alAnot != null)
+
+ for (int j = 0; j < alAnot.length; j++)
{
- for (int j = 0; j < alAnot.length; j++)
+ if (alAnot[j].annotations != null)
{
- if (ds.getSequenceFeatures() != null)
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
+
+ if (isrna)
{
- feature = ds.getSequenceFeatures()[0].type;
+ // hardwire to 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 + " "));
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
ann = alAnot[j].annotations;
- boolean isrna = alAnot[j].isValidStruc();
String seq = "";
for (int k = 0; k < ann.length; k++)
{
out.append(newline);
}
}
+
}
- out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[i], jvSuffix) + " "));
out.append(s[i].getSequenceAsString());
out.append(newline);
i++;
}
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++)
{
out.append(newline);
}
}
+
+ out.append("//");
+ out.append(newline);
+
return out.toString();
}
+
/**
* add an annotation character to the output row
*
{
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 == null
+ ? String.valueOf(annot.secondaryStructure)
+ : annot.displayCharacter);
+ if (ch == null)
+ {
+ ch = " ";
+ }
if (key != null && key.equals("SS"))
{
+ char ssannotchar = ' ';
+ boolean charset = false;
if (annot == null)
{
- // sensible gap character if one is available or make one up
- return sequenceI == null ? '-' : sequenceI.getCharAt(k);
+ // sensible gap character
+ ssannotchar = ' ';
+ charset = true;
}
else
{
// valid secondary structure AND no alternative label (e.g. ' B')
if (annot.secondaryStructure > ' ' && ch.length() < 2)
{
- return annot.secondaryStructure;
+ ssannotchar = annot.secondaryStructure;
+ charset = true;
}
}
+ if (charset)
+ {
+ return (ssannotchar == ' ' && isrna) ? '.' : ssannotchar;
+ }
}
if (ch.length() == 0)
{
seq = ch.charAt(1);
}
- return seq;
+
+ return (seq == ' ' && key != null && key.equals("SS") && isrna) ? '.'
+ : seq;
}
- @Override
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
+
+
public String print()
{
out = new StringBuffer();
out.append("# STOCKHOLM 1.0");
out.append(newline);
- print(getSeqsAsArray());
+ print(getSeqsAsArray(), false);
out.append("//");
out.append(newline);
}
private static Hashtable typeIds = null;
+
static
{
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");
}
}
-
+
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);
+ 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;
}
-
- /**
- * make a friendly ID string.
- *
- * @param dataName
- * @return truncated dataName to after last '/'
- */
- private String safeName(String dataName)
- {
- int b = 0;
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
- {
- dataName = dataName.substring(b + 1).trim();
-
- }
- int e = (dataName.length() - dataName.indexOf(".")) + 1;
- dataName = dataName.substring(1, e).trim();
- return dataName;
- }
}
git://source.jalview.org / jalview.git / blobdiff