X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=9b5a5cdb56420af978d70feebb27cd53faea721f;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=62fec79db681ebcd0daa92a04657fcd61c4d04b7;hpb=91f6f98109a5c9ffda2ed8da3875773e3469f2f2;p=jalview.git
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 62fec79..9b5a5cd 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,6 +1,6 @@
/*
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,6 +14,7 @@
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
@@ -44,21 +45,22 @@ import jalview.util.Format;
public class StockholmFile extends AlignFile
{
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
- StringBuffer out;
+ 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);
@@ -143,8 +145,24 @@ public class StockholmFile extends AlignFile
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())
@@ -187,6 +205,7 @@ public class StockholmFile extends AlignFile
String desc = (String) accAnnotations.get("DE");
seqO.setDescription((desc == null) ? "" : desc);
}
+
// Add DB References (if any)
if (accAnnotations != null && accAnnotations.containsKey("DR"))
{
@@ -196,9 +215,23 @@ public class StockholmFile extends AlignFile
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
@@ -224,22 +257,24 @@ public class StockholmFile extends AlignFile
// 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);
+ }
}
}
-
+
Enumeration j = content.keys();
while (j.hasMoreElements())
{
@@ -533,6 +568,95 @@ public class StockholmFile extends AlignFile
}
}
+ /**
+ * 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 dbrs=new ArrayList();
+ 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-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)
{
@@ -549,8 +673,12 @@ public class StockholmFile extends AlignFile
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"))
@@ -619,138 +747,208 @@ public class StockholmFile extends AlignFile
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;
+ 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;
+
+ if (aa.label.equals("seq"))
+ label = "seq_cons";
+ else
+ label = type2id(aa.label.toLowerCase()) + "_cons";
+
+ if (label == null)
+ label = aa.label;
+
+ 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();
}
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();
}
@@ -789,25 +987,25 @@ public class StockholmFile extends AlignFile
+ 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 (String) key;
+ }
+ System.err.println("Warning : Unknown Stockholm annotation type: "
+ type);
return key;
}