*/
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.Format;
import jalview.util.MessageManager;
*/
public class StockholmFile extends AlignFile
{
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
- protected ArrayList<RNA> result;
+ private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+
+ private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+
+ private static final Regex DETECT_BRACKETS = new Regex(
+ "(<|>|\\[|\\]|\\(|\\))");
StringBuffer out; // output buffer
this.al = al;
}
- public StockholmFile(String inFile, String type) throws IOException
+ public StockholmFile(String inFile, DataSourceType type)
+ throws IOException
{
super(inFile, type);
}
super(source);
}
+ @Override
public void initData()
{
super.initData();
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);
+ ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
}
AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
* @throws IOException
* If there is an error with the input file
*/
+ @Override
public void parse() throws IOException
{
StringBuffer treeString = new StringBuffer();
{
// 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);
}
}
else if (annType.equals("GC"))
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);
}
}
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);
+ convert1 = OPEN_PAREN.replaceAll(annots);
+ convert2 = CLOSE_PAREN.replaceAll(convert1);
annots = convert2;
String type = label;
// be written out
if (ss)
{
- //if (" .-_".indexOf(pos) == -1)
+ // if (" .-_".indexOf(pos) == -1)
{
- if (detectbrackets.search(pos))
+ if (DETECT_BRACKETS.search(pos))
{
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getRNASecStrucState(pos).charAt(0);
+ ann.secondaryStructure = Rna.getRNASecStrucState(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 = " " + ann.displayCharacter;
}
}
-
+
}
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]);
+ String tmp = printId(s[in], jvSuffix);
if (s[in].getSequence().length > max)
{
max = s[in].getSequence().length;
{
maxid = tmp.length();
}
- if (s[in].getDBRef() != null)
+ if (s[in].getDBRefs() != null)
{
- for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+ for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
{
if (dataRef == null)
{
dataRef = new Hashtable();
}
- String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+ String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
+ " ; "
- + s[in].getDBRef()[idb].getAccessionId().toString();
+ + s[in].getDBRefs()[idb].getAccessionId().toString();
dataRef.put(tmp, datAs1);
}
}
{
feature = ds.getSequenceFeatures()[0].type;
}
+ // ?bug - feature may still have previous loop value
String key = type2id(feature);
if (key == null)
// out.append("#=GR ");
out.append(new Format("%-" + maxid + "s").form("#=GR "
- + printId(s[i]) + " " + key + " "));
+ + printId(s[i], jvSuffix) + " " + key + " "));
ann = alAnot[j].annotations;
boolean isrna = alAnot[j].isValidStruc();
String seq = "";
}
}
- 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++;
out.append(newline);
}
}
+
+ out.append("//");
+ out.append(newline);
+
return out.toString();
}
* @param ann
* @param sequenceI
*/
- private char outputCharacter(String key, int k,
- boolean isrna, Annotation[] ann, 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)))
- : annot.displayCharacter;
+ .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);
+ return sequenceI == null ? '-' : sequenceI.getCharAt(k);
}
else
{
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)
git://source.jalview.org / jalview.git / blobdiff