/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
-import com.stevesoft.pat.*;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.Format;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+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;
+
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.rna.RNA;
// import org.apache.log4j.*;
* into Jalview's local representation.
*
* @author bsb at sanger.ac.uk
+ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
+ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as
+ * stockholm)
+ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
* @version 0.3 + jalview mods
*
*/
public class StockholmFile extends AlignFile
{
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
- StringBuffer out;
+ protected ArrayList<RNA> result;
+
+ StringBuffer out; // output buffer
+
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
{
super(inFile, type);
}
/**
+ * Parse a file in Stockholm format into Jalview's data model using VARNA
+ *
+ * @throws IOException
+ * If there is an error with the input file
+ */
+ public void parse_with_VARNA(java.io.File inFile) throws IOException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ result = null;
+ try
+ {
+ result = RNAFactory.loadSecStrStockholm(r);
+ } catch (ExceptionUnmatchedClosingParentheses umcp)
+ {
+ errormessage = "Unmatched parentheses in annotation. Aborting ("
+ + umcp.getMessage() + ")";
+ throw new IOException(umcp);
+ }
+ // DEBUG System.out.println("this is the secondary scructure:"
+ // +result.size());
+ SequenceI[] seqs = new SequenceI[result.size()];
+ String id = null;
+ for (int i = 0; i < result.size(); i++)
+ {
+ // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
+ RNA current = result.get(i);
+
+ String seq = current.getSeq();
+ String rna = current.getStructDBN(true);
+ // DEBUG System.out.println(seq);
+ // DEBUG System.err.println(rna);
+ int begin = 0;
+ int end = seq.length() - 1;
+ id = safeName(getDataName());
+ seqs[i] = new Sequence(id, seq, begin, end);
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = rna.substring(j, j + 1);
+
+ }
+
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
+
+ }
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+ this.annotations.addElement(align);
+ }
+ this.setSeqs(seqs);
+
+ }
+
+ /**
* Parse a file in Stockholm format into Jalview's data model. The file has to
* be passed at construction time
*
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
Regex p, r, rend, s, x;
-
// Temporary line for processing RNA annotation
// String RNAannot = "";
// ------------------ Parsing File ----------------------
// First, we have to check that this file has STOCKHOLM format, i.e. the
// first line must match
+
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
throw new IOException(
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+ MessageManager
+ .getString("exception.stockholm_invalid_format"));
}
else
{
version = r.stringMatched(1);
+
// logger.debug("Stockholm version: " + version);
}
if (rend.search(line))
{
// End of the alignment, pass stuff back
-
this.noSeqs = seqs.size();
+
+ String seqdb, dbsource = null;
+ Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
+ Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+ if (getAlignmentProperty("AC") != null)
+ {
+ String dbType = getAlignmentProperty("AC").toString();
+ if (pf.search(dbType))
+ {
+ // PFAM Alignment - so references are typically from Uniprot
+ dbsource = "PFAM";
+ }
+ else if (rf.search(dbType))
+ {
+ dbsource = "RFAM";
+ }
+ }
// logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
+ for (Map.Entry<String, String> skey : seqs.entrySet())
{
- String acc = (String) accs.nextElement();
// logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.remove(acc);
+ String acc = skey.getKey();
+ String seq = skey.getValue();
if (maxLength < seq.length())
{
maxLength = seq.length();
String src = dbr.substring(0, dbr.indexOf(";"));
String acn = dbr.substring(dbr.indexOf(";") + 1);
jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
- // seqO.addDBRef(dbref);
}
- }
+ }
+
+ if (accAnnotations != null && accAnnotations.containsKey("AC"))
+ {
+ if (dbsource != null)
+ {
+ String dbr = (String) accAnnotations.get("AC");
+ if (dbr != null)
+ {
+ // we could get very clever here - but for now - just try to
+ // guess accession type from source of alignment plus structure
+ // of accession
+ guessDatabaseFor(seqO, dbr, dbsource);
+
+ }
+ }
+ // else - do what ? add the data anyway and prompt the user to
+ // specify what references these are ?
+ }
Hashtable features = null;
// We need to adjust the positions of all features to account for gaps
// TODO: map coding region to core jalview feature types
String type = i.nextElement().toString();
Hashtable content = (Hashtable) features.remove(type);
-
+
// add alignment annotation for this feature
String key = type2id(type);
- if (key != null)
+ if (key != null)
{
- if (accAnnotations != null && accAnnotations.containsKey(key))
+ if (accAnnotations != null
+ && accAnnotations.containsKey(key))
{
- Vector vv = (Vector) accAnnotations.get(key);
+ Vector vv = (Vector) accAnnotations.get(key);
for (int ii = 0; ii < vv.size(); ii++)
{
- AlignmentAnnotation an = (AlignmentAnnotation) vv.elementAt(ii);
- seqO.addAlignmentAnnotation(an);
- }
+ AlignmentAnnotation an = (AlignmentAnnotation) vv
+ .elementAt(ii);
+ seqO.addAlignmentAnnotation(an);
+ annotations.add(an);
+ }
}
}
-
+
Enumeration j = content.keys();
while (j.hasMoreElements())
{
if (!x.search(line))
{
// logger.error("Could not parse sequence line: " + line);
- throw new IOException("Could not parse sequence line: " + line);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.couldnt_parse_sequence_line", new String[]
+ { line }));
}
- String ns = (String) seqs.get(x.stringMatched(1));
+ String ns = seqs.get(x.stringMatched(1));
if (ns == null)
{
ns = "";
}
else
{
- throw new IOException("Error parsing " + line);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.error_parsing_line", new String[]
+ { line }));
}
}
else if (annType.equals("GC"))
}
ns += seq;
content.put(description, ns);
+
+ // if(type.equals("SS")){
Hashtable strucAnn;
if (seqAnn.containsKey(acc))
{
strucAnn = new Hashtable();
}
- Vector newStruc = new Vector();
+ Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
parseAnnotationRow(newStruc, type, ns);
+ for (AlignmentAnnotation alan : newStruc)
+ {
+ alan.visible = false;
+ }
+ // annotations.addAll(newStruc);
strucAnn.put(type, newStruc);
seqAnn.put(acc, strucAnn);
}
+ // }
else
{
System.err
}
else
{
- throw new IOException("Unknown annotation detected: " + annType
- + " " + annContent);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.unknown_annotation_detected", new String[]
+ { annType, annContent }));
}
}
}
}
}
+ /**
+ * Demangle an accession string and guess the originating sequence database
+ * for a given sequence
+ *
+ * @param seqO
+ * sequence to be annotated
+ * @param dbr
+ * Accession string for sequence
+ * @param dbsource
+ * source database for alignment (PFAM or RFAM)
+ */
+ private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
+ {
+ DBRefEntry dbrf = null;
+ List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ String seqdb = "Unknown", sdbac = "" + dbr;
+ int st = -1, en = -1, p;
+ if ((st = sdbac.indexOf("/")) > -1)
+ {
+ String num, range = sdbac.substring(st + 1);
+ sdbac = sdbac.substring(0, st);
+ if ((p = range.indexOf("-")) > -1)
+ {
+ p++;
+ if (p < range.length())
+ {
+ num = range.substring(p).trim();
+ try
+ {
+ en = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ en = -1;
+ }
+ }
+ }
+ else
+ {
+ p = range.length();
+ }
+ num = range.substring(0, p).trim();
+ try
+ {
+ st = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ st = -1;
+ }
+ }
+ if (dbsource.equals("PFAM"))
+ {
+ seqdb = "UNIPROT";
+ if (sdbac.indexOf(".") > -1)
+ {
+ // strip of last subdomain
+ sdbac = sdbac.substring(0, sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+ sdbac);
+ if (dbrf != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+ dbr);
+ if (dbr != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ else
+ {
+ seqdb = "EMBL"; // total guess - could be ENA, or something else these
+ // days
+ if (sdbac.indexOf(".") > -1)
+ {
+ // strip off last subdomain
+ sdbac = sdbac.substring(0, sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+ sdbac);
+ if (dbrf != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+ dbr);
+ if (dbrf != null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ if (st != -1 && en != -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.datamodel.Mapping mping = new Mapping(mp);
+ d.setMap(mping);
+ }
+ }
+ }
+
protected static AlignmentAnnotation parseAnnotationRow(
Vector annotation, String label, String annots)
{
convert2 = closeparen.replaceAll(convert1);
annots = convert2;
- String type = (label.indexOf("_cons") == label.length() - 5) ? label
- .substring(0, label.length() - 5) : label;
+ String type = label;
+ if (label.contains("_cons"))
+ {
+ 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"))
// be written out
if (ss)
{
- if (detectbrackets.search(pos))
- {
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getRNASecStrucState(pos).charAt(0);
- }
- else
+ //if (" .-_".indexOf(pos) == -1)
{
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getDssp3state(pos).charAt(0);
- }
+ if (detectbrackets.search(pos))
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getRNASecStrucState(pos).charAt(0);
+ }
+ else
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getDssp3state(pos).charAt(0);
+ }
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
- {
- ann.displayCharacter = ""; // null; // " ";
- }
- else
- {
- ann.displayCharacter = " " + ann.displayCharacter;
+ if (ann.secondaryStructure == pos.charAt(0))
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
}
+
}
els[i] = ann;
{
annot = (AlignmentAnnotation) e.nextElement();
if (annot.label.equals(type))
+ {
break;
+ }
annot = null;
}
if (annot == null)
public String print(SequenceI[] s)
{
- // find max length of id
- int max = 0;
- int maxid = 0;
- int in = 0;
- while ((in < s.length) && (s[in] != null))
- {
- String tmp = printId(s[in]);
- if (s[in].getSequence().length > max)
- {
- max = s[in].getSequence().length;
- }
-
- if (tmp.length() > maxid)
- {
- maxid = tmp.length();
- }
-
- in++;
- }
- maxid += 9;
- int i = 0;
-
- while (i < s.length && s[i] != null)
- {
- if (s[i].getDatasetSequence() != 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++)
- {
- if (ds.getSequenceFeatures() != null)
- {
- feature = ds.getSequenceFeatures()[0].type;
- }
- String key = type2id(feature);
-
- // output annotations
- if (key == null)
- continue;
-
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form("#=GR " + printId(s[i]) + " " + key + " "));
- ann = alAnot[j].annotations;
- String seq = "";
- for (int k = 0; k < ann.length; k++)
- {
- annot = ann[k];
- String ch = (annot == null) ? Character.toString(s[i].getCharAt(k)) : annot.displayCharacter;
- if (ch.length() == 0)
- {
- if (key.equals("SS")) {
- char ll = annot.secondaryStructure;
- seq = (Character.toString(ll).equals(" ")) ? seq + "C" : seq + ll;
- } else {
- seq += ".";
- }
- } else if (ch.length() == 1) {
- seq += ch;
- } else if (ch.length() > 1) {
- seq += ch.charAt(1) ;
- }
- }
- out.append(seq);
- out.append(newline);
- }
- }
- }
-
- out.append(new Format("%-" + maxid + "s").form(printId(s[i])+" "));
- out.append(s[i].getSequenceAsString());
- out.append(newline);
- i++;
- }
-
- // alignment annotation
- AlignmentAnnotation aa;
- if (al.getAlignmentAnnotation() != null)
- {
- for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
- {
- aa = al.getAlignmentAnnotation()[ia];
- if (aa.autoCalculated || !aa.visible)
- {
- continue;
- }
- String seq = "";
- String label = type2id(aa.label);
-
- if (label == null)
- label = aa.label;
-
- label += "_cons";
-
- out.append(new Format("%-" + maxid + "s").form("#=GC " + label+" "));
- for (int j = 0; j < aa.annotations.length; j++)
- {
- String ch = (aa.annotations[j] == null) ? "-" : aa.annotations[j].displayCharacter ;
- if (ch.length() == 0)
- {
- char ll = aa.annotations[j].secondaryStructure;
- if (Character.toString(ll).equals(" "))
- seq += "C";
- else
- seq += ll;
- } else if (ch.length() == 1) {
- seq += ch;
- } else if (ch.length() > 1) {
- seq += ch.charAt(1) ;
- }
- }
- out.append(seq);
- out.append(newline);
- }
- }
- return out.toString();
+ // 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;
+ }
+
+ if (tmp.length() > maxid)
+ {
+ maxid = tmp.length();
+ }
+ if (s[in].getDBRef() != null)
+ {
+ for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+ {
+ if (dataRef == null)
+ {
+ dataRef = new Hashtable();
+ }
+
+ String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+ + " ; "
+ + s[in].getDBRef()[idb].getAccessionId().toString();
+ dataRef.put(tmp, datAs1);
+ }
+ }
+ in++;
+ }
+ maxid += 9;
+ int i = 0;
+
+ // output database type
+ if (al.getProperties() != null)
+ {
+ if (!al.getProperties().isEmpty())
+ {
+ 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
+ if (dataRef != null)
+ {
+ Enumeration en = dataRef.keys();
+ while (en.hasMoreElements())
+ {
+ 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
+ {
+ out.append(" DR " + type + " ");
+ }
+ out.append(newline);
+ }
+ }
+
+ // output annotations
+ while (i < s.length && s[i] != null)
+ {
+ if (s[i].getDatasetSequence() != 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++)
+ {
+ if (ds.getSequenceFeatures() != null)
+ {
+ feature = ds.getSequenceFeatures()[0].type;
+ }
+ 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++)
+ {
+ seq += outputCharacter(key, k, isrna, ann, s[i]);
+ }
+ out.append(seq);
+ out.append(newline);
+ }
+ }
+ }
+
+ out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
+ out.append(s[i].getSequenceAsString());
+ out.append(newline);
+ i++;
+ }
+
+ // alignment annotation
+ AlignmentAnnotation aa;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
+ {
+ aa = al.getAlignmentAnnotation()[ia];
+ if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
+ {
+ continue;
+ }
+ String seq = "";
+ String label;
+ String key = "";
+ if (aa.label.equals("seq"))
+ {
+ label = "seq_cons";
+ }
+ else
+ {
+ key = type2id(aa.label.toLowerCase());
+ if (key == null)
+ {
+ label = aa.label;
+ }
+ else
+ {
+ 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();
+ for (int j = 0; j < aa.annotations.length; j++)
+ {
+ seq += outputCharacter(key, j, isrna, aa.annotations, null);
+ }
+ out.append(seq);
+ out.append(newline);
+ }
+ }
+ return out.toString();
+ }
+
+ /**
+ * add an annotation character 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)
+ {
+ char seq = ' ';
+ Annotation annot = ann[k];
+ 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);
+ }
+ else
+ {
+ // valid secondary structure AND no alternative label (e.g. ' B')
+ if (annot.secondaryStructure > ' ' && ch.length() < 2)
+ {
+ return annot.secondaryStructure;
+ }
+ }
+ }
+
+ if (ch.length() == 0)
+ {
+ seq = '.';
+ }
+ else if (ch.length() == 1)
+ {
+ seq = ch.charAt(0);
+ }
+ else if (ch.length() > 1)
+ {
+ seq = ch.charAt(1);
+ }
+ return seq;
}
public String print()
{
- out = new StringBuffer();
- out.append("# STOCKHOLM 1.0");
- out.append(newline);
+ out = new StringBuffer();
+ out.append("# STOCKHOLM 1.0");
+ out.append(newline);
print(getSeqsAsArray());
-
+
out.append("//");
- out.append(newline);
+ out.append(newline);
return out.toString();
}
+ 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)
+ String key = null;
+ Enumeration e = typeIds.keys();
+ while (e.hasMoreElements())
+ {
+ Object ll = e.nextElement();
+ if (typeIds.get(ll).toString().equals(type))
{
- return (String) key;
+ key = (String) ll;
+ break;
}
- System.err.println("Warning : Unknown Stockholm annotation type: "
+ }
+ if (key != null)
+ {
+ return key;
+ }
+ System.err.println("Warning : Unknown Stockholm annotation type: "
+ type);
return key;
}
+
/**
- * //ssline is complete secondary structure line private AlignmentAnnotation
- * addHelices(Vector annotation, String label, String ssline) {
- *
- * // decide on secondary structure or not. Annotation[] els = new
- * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
- * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
- * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
- *
- * ann.secondaryStructure =
- * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
- *
- * ann.displayCharacter = "x" + ann.displayCharacter;
- *
- * System.out.println(ann.displayCharacter);
- *
- * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
- * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
- * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
- * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
- * new AlignmentAnnotation(type, type, els);
- * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
- * Annotation[helicesAnnot.annotations.length + els.length];
- * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
- * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
- * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
- * anns; }
+ * make a friendly ID string.
*
- * helicesAnnot.features = Rna.GetBasePairs(ssline);
- * Rna.HelixMap(helicesAnnot.features);
- *
- *
- * return helicesAnnot; }
+ * @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