-package jalview.datamodel.xdb.embl;\r
-\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceFeature;\r
-import jalview.datamodel.SequenceI;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.Iterator;\r
-import java.util.Vector;\r
-\r
-public class EmblEntry {\r
- String accession;\r
- String version;\r
- String taxDivision;\r
- String desc;\r
- String rCreated;\r
- String rLastUpdated;\r
- String lastUpdated;\r
- Vector keywords;\r
- Vector refs;\r
- Vector dbRefs;\r
- Vector features;\r
- EmblSequence sequence;\r
- /**\r
- * @return the accession\r
- */\r
- public String getAccession() {\r
- return accession;\r
- }\r
- /**\r
- * @param accession the accession to set\r
- */\r
- public void setAccession(String accession) {\r
- this.accession = accession;\r
- }\r
- /**\r
- * @return the dbRefs\r
- */\r
- public Vector getDbRefs() {\r
- return dbRefs;\r
- }\r
- /**\r
- * @param dbRefs the dbRefs to set\r
- */\r
- public void setDbRefs(Vector dbRefs) {\r
- this.dbRefs = dbRefs;\r
- }\r
- /**\r
- * @return the desc\r
- */\r
- public String getDesc() {\r
- return desc;\r
- }\r
- /**\r
- * @param desc the desc to set\r
- */\r
- public void setDesc(String desc) {\r
- this.desc = desc;\r
- }\r
- /**\r
- * @return the features\r
- */\r
- public Vector getFeatures() {\r
- return features;\r
- }\r
- /**\r
- * @param features the features to set\r
- */\r
- public void setFeatures(Vector features) {\r
- this.features = features;\r
- }\r
- /**\r
- * @return the keywords\r
- */\r
- public Vector getKeywords() {\r
- return keywords;\r
- }\r
- /**\r
- * @param keywords the keywords to set\r
- */\r
- public void setKeywords(Vector keywords) {\r
- this.keywords = keywords;\r
- }\r
- /**\r
- * @return the lastUpdated\r
- */\r
- public String getLastUpdated() {\r
- return lastUpdated;\r
- }\r
- /**\r
- * @param lastUpdated the lastUpdated to set\r
- */\r
- public void setLastUpdated(String lastUpdated) {\r
- this.lastUpdated = lastUpdated;\r
- }\r
- /**\r
- * @return the refs\r
- */\r
- public Vector getRefs() {\r
- return refs;\r
- }\r
- /**\r
- * @param refs the refs to set\r
- */\r
- public void setRefs(Vector refs) {\r
- this.refs = refs;\r
- }\r
- /**\r
- * @return the releaseCreated\r
- */\r
- public String getRCreated() {\r
- return rCreated;\r
- }\r
- /**\r
- * @param releaseCreated the releaseCreated to set\r
- */\r
- public void setRcreated(String releaseCreated) {\r
- this.rCreated = releaseCreated;\r
- }\r
- /**\r
- * @return the releaseLastUpdated\r
- */\r
- public String getRLastUpdated() {\r
- return rLastUpdated;\r
- }\r
- /**\r
- * @param releaseLastUpdated the releaseLastUpdated to set\r
- */\r
- public void setRLastUpdated(String releaseLastUpdated) {\r
- this.rLastUpdated = releaseLastUpdated;\r
- }\r
- /**\r
- * @return the sequence\r
- */\r
- public EmblSequence getSequence() {\r
- return sequence;\r
- }\r
- /**\r
- * @param sequence the sequence to set\r
- */\r
- public void setSequence(EmblSequence sequence) {\r
- this.sequence = sequence;\r
- }\r
- /**\r
- * @return the taxDivision\r
- */\r
- public String getTaxDivision() {\r
- return taxDivision;\r
- }\r
- /**\r
- * @param taxDivision the taxDivision to set\r
- */\r
- public void setTaxDivision(String taxDivision) {\r
- this.taxDivision = taxDivision;\r
- }\r
- /**\r
- * @return the version\r
- */\r
- public String getVersion() {\r
- return version;\r
- }\r
- /**\r
- * @param version the version to set\r
- */\r
- public void setVersion(String version) {\r
- this.version = version;\r
- }\r
-/*\r
- * EMBL Feature support is limited. The text below is included for the benefit of\r
- * any developer working on improving EMBL feature import in Jalview.\r
- * Extract from EMBL feature specification\r
- * see http://www.embl-ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html\r
-3.5 Location\r
-3.5.1 Purpose\r
-\r
-The location indicates the region of the presented sequence which corresponds \r
-to a feature. \r
-\r
-3.5.2 Format and conventions\r
-The location contains at least one sequence location descriptor and may \r
-contain one or more operators with one or more sequence location descriptors. \r
-Base numbers refer to the numbering in the entry. This numbering designates \r
-the first base (5' end) of the presented sequence as base 1. \r
-Base locations beyond the range of the presented sequence may not be used in \r
-location descriptors, the only exception being location in a remote entry (see \r
-3.5.2.1, e). \r
-\r
-Location operators and descriptors are discussed in more detail below. \r
-\r
-3.5.2.1 Location descriptors\r
-\r
-The location descriptor can be one of the following: \r
-(a) a single base number\r
-(b) a site between two indicated adjoining bases\r
-(c) a single base chosen from within a specified range of bases (not allowed for new\r
- entries)\r
-(d) the base numbers delimiting a sequence span\r
-(e) a remote entry identifier followed by a local location descriptor\r
- (i.e., a-d)\r
-\r
-A site between two adjoining nucleotides, such as endonucleolytic cleavage \r
-site, is indicated by listing the two points separated by a carat (^). The \r
-permitted formats for this descriptor are n^n+1 (for example 55^56), or, for \r
-circular molecules, n^1, where "n" is the full length of the molecule, ie \r
-1000^1 for circular molecule with length 1000.\r
-\r
-A single base chosen from a range of bases is indicated by the first base\r
-number and the last base number of the range separated by a single period\r
-(e.g., '12.21' indicates a single base taken from between the indicated\r
-points). From October 2006 the usage of this descriptor is restricted :\r
-it is illegal to use "a single base from a range" (c) either on its own or\r
-in combination with the "sequence span" (d) descriptor for newly created entries.\r
-The existing entries where such descriptors exist are going to be retrofitted.\r
-\r
-Sequence spans are indicated by the starting base number and the ending base \r
-number separated by two periods (e.g., '34..456'). The '<' and '>' symbols may \r
-be used with the starting and ending base numbers to indicate that an end \r
-point is beyond the specified base number. The starting and ending base \r
-positions can be represented as distinct base numbers ('34..456') or a site \r
-between two indicated adjoining bases. \r
-\r
-A location in a remote entry (not the entry to which the feature table \r
-belongs) can be specified by giving the accession-number and sequence version \r
-of the remote entry, followed by a colon ":", followed by a location \r
-descriptor which applies to that entry's sequence (i.e. J12345.1:1..15, see \r
-also examples below) \r
-\r
-3.5.2.2 Operators\r
-\r
-The location operator is a prefix that specifies what must be done to the \r
-indicated sequence to find or construct the location corresponding to the \r
-feature. A list of operators is given below with their definitions and most \r
-common format. \r
-\r
-complement(location) \r
-Find the complement of the presented sequence in the span specified by "\r
-location" (i.e., read the complement of the presented strand in its 5'-to-3' \r
-direction) \r
-\r
-join(location,location, ... location) \r
-The indicated elements should be joined (placed end-to-end) to form one \r
-contiguous sequence \r
-\r
-order(location,location, ... location) \r
-The elements can be found in the \r
-specified order (5' to 3' direction), but nothing is implied about the \r
-reasonableness about joining them \r
-\r
-Note : location operator "complement" can be used in combination with either "\r
-join" or "order" within the same location; combinations of "join" and "order" \r
-within the same location (nested operators) are illegal.\r
-\r
-\r
-\r
-3.5.3 Location examples \r
-\r
-The following is a list of common location descriptors with their meanings: \r
-\r
-Location Description \r
-\r
-467 Points to a single base in the presented sequence \r
-\r
-340..565 Points to a continuous range of bases bounded by and\r
- including the starting and ending bases\r
-\r
-<345..500 Indicates that the exact lower boundary point of a feature\r
- is unknown. The location begins at some base previous to\r
- the first base specified (which need not be contained in \r
- the presented sequence) and continues to and includes the \r
- ending base \r
-\r
-<1..888 The feature starts before the first sequenced base and \r
- continues to and includes base 888\r
-\r
-1..>888 The feature starts at the first sequenced base and \r
- continues beyond base 888\r
-\r
-102.110 Indicates that the exact location is unknown but that it is \r
- one of the bases between bases 102 and 110, inclusive\r
-\r
-123^124 Points to a site between bases 123 and 124\r
-\r
-join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form \r
- one contiguous sequence\r
-\r
-\r
-complement(34..126) Start at the base complementary to 126 and finish at the \r
- base complementary to base 34 (the feature is on the strand \r
- complementary to the presented strand)\r
-\r
-\r
-complement(join(2691..4571,4918..5163))\r
- Joins regions 2691 to 4571 and 4918 to 5163, then \r
- complements the joined segments (the feature is on the \r
- strand complementary to the presented strand) \r
-\r
-join(complement(4918..5163),complement(2691..4571))\r
- Complements regions 4918 to 5163 and 2691 to 4571, then \r
- joins the complemented segments (the feature is on the \r
- strand complementary to the presented strand)\r
- \r
-J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in \r
- this database) with primary accession number 'J00194'\r
- \r
-join(1..100,J00194.1:100..202)\r
- Joins region 1..100 of the existing entry with the region\r
- 100..202 of remote entry J00194\r
-\r
- */\r
- /**\r
- * Recover annotated sequences from EMBL file\r
- * @param noNa don't return nucleic acid sequences \r
- * @param sourceDb TODO\r
- * @param noProtein don't return any translated protein sequences marked in features\r
- * @return dataset sequences with DBRefs and features - DNA always comes first\r
- */\r
- public jalview.datamodel.SequenceI[] getSequences(boolean noNa, boolean noPeptide, String sourceDb) {\r
- Vector seqs=new Vector();\r
- Sequence dna=null;\r
- if (!noNa) {\r
- dna = new Sequence(sourceDb+"|"+accession, sequence.getSequence());\r
- dna.setDescription(desc);\r
- dna.addDBRef(new DBRefEntry(sourceDb, version, accession));\r
- // TODO: add mapping for parentAccession attribute\r
- // TODO: transform EMBL Database refs to canonical form\r
- if (dbRefs!=null)\r
- for (Iterator i=dbRefs.iterator(); i.hasNext(); dna.addDBRef((DBRefEntry)i.next()));\r
- }\r
- for (Iterator i=features.iterator(); i.hasNext(); ) {\r
- EmblFeature feature = (EmblFeature) i.next();\r
- if (!noNa) {\r
- if (feature.dbRefs!=null && feature.dbRefs.size()>0) {\r
- for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); dna.addDBRef((DBRefEntry)dbr.next()) )\r
- ;\r
- }\r
- }\r
- if (feature.getName().equalsIgnoreCase("CDS")) {\r
- // extract coding region(s)\r
- jalview.datamodel.Mapping map = null;\r
- int[] exon=null;\r
- if (feature.locations!=null && feature.locations.size()>0) {\r
- for (Iterator locs=feature.locations.iterator();\r
- locs.hasNext(); ) {\r
- EmblFeatureLocations loc = (EmblFeatureLocations) locs.next();\r
- int[] se = loc.getElementRanges();\r
- if (exon==null) {\r
- exon=se;\r
- } else {\r
- int[] t=new int[exon.length+se.length];\r
- System.arraycopy(exon, 0, t, 0, exon.length);\r
- System.arraycopy(se, 0, t, exon.length,se.length);\r
- exon=t;\r
- }\r
- }\r
- }\r
- String prseq=null;\r
- String prname=new String();\r
- String prid=null;\r
- Hashtable vals=new Hashtable();\r
- int prstart=1;\r
- // get qualifiers\r
- if (feature.getQualifiers()!=null && feature.getQualifiers().size()>0) {\r
- for (Iterator quals=feature.getQualifiers().iterator(); quals.hasNext(); ) {\r
- Qualifier q = (Qualifier) quals.next();\r
- if (q.getName().equals("translation")) \r
- {\r
- prseq=q.getValue();\r
- } \r
- else\r
- if (q.getName().equals("protein_id")) \r
- {\r
- prid=q.getValue();\r
- }\r
- else\r
- if (q.getName().equals("codon_start"))\r
- {\r
- prstart = Integer.parseInt(q.getValue());\r
- }\r
- else \r
- if (q.getName().equals("product")){\r
- prname = q.getValue();\r
- } else {\r
- // throw anything else into the additional properties hash\r
- vals.put(q.getName(), q.getValue());\r
- }\r
- }\r
- }\r
- Sequence product=null;\r
- if (prseq!=null && prname!=null && prid!=null) {\r
- // extract proteins.\r
- if (!noPeptide) {\r
- product = new Sequence(sourceDb+"|"+"EMBLCDS|"+prid+"|"+prname, prseq, prstart, prstart+prseq.length()-1);\r
- product.setDescription("Protein Product from "+sourceDb);\r
- seqs.add(product);\r
- }\r
- // we have everything - create the mapping and perhaps the protein sequence\r
- map = new jalview.datamodel.Mapping(product, exon, new int[] { prstart, prstart+prseq.length()-1}, 3, 1);\r
- // add cds feature to dna seq - this may include the stop codon\r
- for (int xint=0;xint<exon.length; xint+=2) {\r
- SequenceFeature sf = new SequenceFeature();\r
- sf.setBegin(exon[xint]);\r
- sf.setEnd(exon[xint+1]);\r
- sf.setType(feature.getName());\r
- sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL);\r
- sf.setDescription("Exon "+(1+xint)+" for protein '"+prname+"' EMBLCDS:"+prid);\r
- if (vals!=null && vals.size()>0) {\r
- Enumeration kv = vals.elements();\r
- while (kv.hasMoreElements()) {\r
- Object key=kv.nextElement();\r
- if (key!=null)\r
- sf.setValue(key.toString(), vals.get(key));\r
- }\r
- }\r
- dna.addSequenceFeature(sf);\r
- }\r
- }\r
- // add dbRefs to sequence\r
- if (feature.dbRefs!=null && feature.dbRefs.size()>0) \r
- {\r
- for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); ) \r
- {\r
- DBRefEntry ref = (DBRefEntry)dbr.next();\r
- ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref.getSource()));\r
- if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT)) \r
- {\r
- ref.setMap(map);\r
- }\r
- if (product!=null) {\r
- DBRefEntry pref = new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId());\r
- pref.setMap(null); // reference is direct\r
- }\r
- dna.addDBRef(ref);\r
- }\r
- }\r
- \r
- } else {\r
- // General feature type.\r
- if (!noNa) {\r
- if (feature.dbRefs!=null && feature.dbRefs.size()>0) {\r
- for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); dna.addDBRef((DBRefEntry)dbr.next()) )\r
- ;\r
- }\r
- }\r
- }\r
-\r
- }\r
- if (!noNa) {\r
- seqs.add(dna);\r
- }\r
- SequenceI[] sqs = new SequenceI[seqs.size()];\r
- for (int i=0,j=seqs.size();i<j; i++) {\r
- sqs[i] = (SequenceI) seqs.elementAt(i);\r
- seqs.set(i, null);\r
- }\r
- return sqs;\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel.xdb.embl;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+
+public class EmblEntry
+{
+ String accession;
+
+ String version;
+
+ String taxDivision;
+
+ String desc;
+
+ String rCreated;
+
+ String rLastUpdated;
+
+ String lastUpdated;
+
+ Vector keywords;
+
+ Vector refs;
+
+ Vector dbRefs;
+
+ Vector features;
+
+ EmblSequence sequence;
+
+ /**
+ * @return the accession
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * @param accession
+ * the accession to set
+ */
+ public void setAccession(String accession)
+ {
+ this.accession = accession;
+ }
+
+ /**
+ * @return the dbRefs
+ */
+ public Vector getDbRefs()
+ {
+ return dbRefs;
+ }
+
+ /**
+ * @param dbRefs
+ * the dbRefs to set
+ */
+ public void setDbRefs(Vector dbRefs)
+ {
+ this.dbRefs = dbRefs;
+ }
+
+ /**
+ * @return the desc
+ */
+ public String getDesc()
+ {
+ return desc;
+ }
+
+ /**
+ * @param desc
+ * the desc to set
+ */
+ public void setDesc(String desc)
+ {
+ this.desc = desc;
+ }
+
+ /**
+ * @return the features
+ */
+ public Vector getFeatures()
+ {
+ return features;
+ }
+
+ /**
+ * @param features
+ * the features to set
+ */
+ public void setFeatures(Vector features)
+ {
+ this.features = features;
+ }
+
+ /**
+ * @return the keywords
+ */
+ public Vector getKeywords()
+ {
+ return keywords;
+ }
+
+ /**
+ * @param keywords
+ * the keywords to set
+ */
+ public void setKeywords(Vector keywords)
+ {
+ this.keywords = keywords;
+ }
+
+ /**
+ * @return the lastUpdated
+ */
+ public String getLastUpdated()
+ {
+ return lastUpdated;
+ }
+
+ /**
+ * @param lastUpdated
+ * the lastUpdated to set
+ */
+ public void setLastUpdated(String lastUpdated)
+ {
+ this.lastUpdated = lastUpdated;
+ }
+
+ /**
+ * @return the refs
+ */
+ public Vector getRefs()
+ {
+ return refs;
+ }
+
+ /**
+ * @param refs
+ * the refs to set
+ */
+ public void setRefs(Vector refs)
+ {
+ this.refs = refs;
+ }
+
+ /**
+ * @return the releaseCreated
+ */
+ public String getRCreated()
+ {
+ return rCreated;
+ }
+
+ /**
+ * @param releaseCreated
+ * the releaseCreated to set
+ */
+ public void setRcreated(String releaseCreated)
+ {
+ this.rCreated = releaseCreated;
+ }
+
+ /**
+ * @return the releaseLastUpdated
+ */
+ public String getRLastUpdated()
+ {
+ return rLastUpdated;
+ }
+
+ /**
+ * @param releaseLastUpdated
+ * the releaseLastUpdated to set
+ */
+ public void setRLastUpdated(String releaseLastUpdated)
+ {
+ this.rLastUpdated = releaseLastUpdated;
+ }
+
+ /**
+ * @return the sequence
+ */
+ public EmblSequence getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * @param sequence
+ * the sequence to set
+ */
+ public void setSequence(EmblSequence sequence)
+ {
+ this.sequence = sequence;
+ }
+
+ /**
+ * @return the taxDivision
+ */
+ public String getTaxDivision()
+ {
+ return taxDivision;
+ }
+
+ /**
+ * @param taxDivision
+ * the taxDivision to set
+ */
+ public void setTaxDivision(String taxDivision)
+ {
+ this.taxDivision = taxDivision;
+ }
+
+ /**
+ * @return the version
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ */
+ public void setVersion(String version)
+ {
+ this.version = version;
+ }
+
+ /*
+ * EMBL Feature support is limited. The text below is included for the benefit
+ * of any developer working on improving EMBL feature import in Jalview.
+ * Extract from EMBL feature specification see
+ * http://www.embl-ebi.ac.uk/embl/Documentation
+ * /FT_definitions/feature_table.html 3.5 Location 3.5.1 Purpose
+ *
+ * The location indicates the region of the presented sequence which
+ * corresponds to a feature.
+ *
+ * 3.5.2 Format and conventions The location contains at least one sequence
+ * location descriptor and may contain one or more operators with one or more
+ * sequence location descriptors. Base numbers refer to the numbering in the
+ * entry. This numbering designates the first base (5' end) of the presented
+ * sequence as base 1. Base locations beyond the range of the presented
+ * sequence may not be used in location descriptors, the only exception being
+ * location in a remote entry (see 3.5.2.1, e).
+ *
+ * Location operators and descriptors are discussed in more detail below.
+ *
+ * 3.5.2.1 Location descriptors
+ *
+ * The location descriptor can be one of the following: (a) a single base
+ * number (b) a site between two indicated adjoining bases (c) a single base
+ * chosen from within a specified range of bases (not allowed for new entries)
+ * (d) the base numbers delimiting a sequence span (e) a remote entry
+ * identifier followed by a local location descriptor (i.e., a-d)
+ *
+ * A site between two adjoining nucleotides, such as endonucleolytic cleavage
+ * site, is indicated by listing the two points separated by a carat (^). The
+ * permitted formats for this descriptor are n^n+1 (for example 55^56), or,
+ * for circular molecules, n^1, where "n" is the full length of the molecule,
+ * ie 1000^1 for circular molecule with length 1000.
+ *
+ * A single base chosen from a range of bases is indicated by the first base
+ * number and the last base number of the range separated by a single period
+ * (e.g., '12.21' indicates a single base taken from between the indicated
+ * points). From October 2006 the usage of this descriptor is restricted : it
+ * is illegal to use "a single base from a range" (c) either on its own or in
+ * combination with the "sequence span" (d) descriptor for newly created
+ * entries. The existing entries where such descriptors exist are going to be
+ * retrofitted.
+ *
+ * Sequence spans are indicated by the starting base number and the ending
+ * base number separated by two periods (e.g., '34..456'). The '<' and '>'
+ * symbols may be used with the starting and ending base numbers to indicate
+ * that an end point is beyond the specified base number. The starting and
+ * ending base positions can be represented as distinct base numbers
+ * ('34..456') or a site between two indicated adjoining bases.
+ *
+ * A location in a remote entry (not the entry to which the feature table
+ * belongs) can be specified by giving the accession-number and sequence
+ * version of the remote entry, followed by a colon ":", followed by a
+ * location descriptor which applies to that entry's sequence (i.e.
+ * J12345.1:1..15, see also examples below)
+ *
+ * 3.5.2.2 Operators
+ *
+ * The location operator is a prefix that specifies what must be done to the
+ * indicated sequence to find or construct the location corresponding to the
+ * feature. A list of operators is given below with their definitions and most
+ * common format.
+ *
+ * complement(location) Find the complement of the presented sequence in the
+ * span specified by " location" (i.e., read the complement of the presented
+ * strand in its 5'-to-3' direction)
+ *
+ * join(location,location, ... location) The indicated elements should be
+ * joined (placed end-to-end) to form one contiguous sequence
+ *
+ * order(location,location, ... location) The elements can be found in the
+ * specified order (5' to 3' direction), but nothing is implied about the
+ * reasonableness about joining them
+ *
+ * Note : location operator "complement" can be used in combination with
+ * either " join" or "order" within the same location; combinations of "join"
+ * and "order" within the same location (nested operators) are illegal.
+ *
+ *
+ *
+ * 3.5.3 Location examples
+ *
+ * The following is a list of common location descriptors with their meanings:
+ *
+ * Location Description
+ *
+ * 467 Points to a single base in the presented sequence
+ *
+ * 340..565 Points to a continuous range of bases bounded by and including the
+ * starting and ending bases
+ *
+ * <345..500 Indicates that the exact lower boundary point of a feature is
+ * unknown. The location begins at some base previous to the first base
+ * specified (which need not be contained in the presented sequence) and
+ * continues to and includes the ending base
+ *
+ * <1..888 The feature starts before the first sequenced base and continues to
+ * and includes base 888
+ *
+ * 1..>888 The feature starts at the first sequenced base and continues beyond
+ * base 888
+ *
+ * 102.110 Indicates that the exact location is unknown but that it is one of
+ * the bases between bases 102 and 110, inclusive
+ *
+ * 123^124 Points to a site between bases 123 and 124
+ *
+ * join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
+ * form one contiguous sequence
+ *
+ *
+ * complement(34..126) Start at the base complementary to 126 and finish at
+ * the base complementary to base 34 (the feature is on the strand
+ * complementary to the presented strand)
+ *
+ *
+ * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
+ * to 5163, then complements the joined segments (the feature is on the strand
+ * complementary to the presented strand)
+ *
+ * join(complement(4918..5163),complement(2691..4571)) Complements regions
+ * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
+ * feature is on the strand complementary to the presented strand)
+ *
+ * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
+ * this database) with primary accession number 'J00194'
+ *
+ * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
+ * with the region 100..202 of remote entry J00194
+ */
+ /**
+ * Recover annotated sequences from EMBL file
+ *
+ * @param noNa
+ * don't return nucleic acid sequences
+ * @param sourceDb
+ * TODO
+ * @param noProtein
+ * don't return any translated protein sequences marked in features
+ * @return dataset sequences with DBRefs and features - DNA always comes first
+ */
+ public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
+ boolean noPeptide, String sourceDb)
+ { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
+ // cases of noNa and noPeptide
+ Vector seqs = new Vector();
+ Sequence dna = null;
+ if (!noNa)
+ {
+ // In theory we still need to create this if noNa is set to avoid a null
+ // pointer exception
+ dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
+ dna.setDescription(desc);
+ DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+ dna.addDBRef(retrievedref);
+ // add map to indicate the sequence is a valid coordinate frame for the
+ // dbref
+ retrievedref.setMap(new Mapping(null, new int[]
+ { 1, dna.getLength() }, new int[]
+ { 1, dna.getLength() }, 1, 1));
+ // TODO: transform EMBL Database refs to canonical form
+ if (dbRefs != null)
+ for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
+ .addDBRef((DBRefEntry) i.next()))
+ ;
+ }
+ try
+ {
+ for (Iterator i = features.iterator(); i.hasNext();)
+ {
+ EmblFeature feature = (EmblFeature) i.next();
+ if (!noNa)
+ {
+ if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ {
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
+ .addDBRef((DBRefEntry) dbr.next()))
+ ;
+ }
+ }
+ if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
+ {
+ parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
+ }
+ else
+ {
+ // General feature type.
+ if (!noNa)
+ {
+ if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ {
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
+ .addDBRef((DBRefEntry) dbr.next()))
+ ;
+ }
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println("EMBL Record Features parsing error!");
+ System.err
+ .println("Please report the following to help@jalview.org :");
+ System.err.println("EMBL Record " + accession);
+ System.err.println("Resulted in exception: " + e.getMessage());
+ e.printStackTrace(System.err);
+ }
+ if (!noNa && dna != null)
+ {
+ seqs.add(dna);
+ }
+ SequenceI[] sqs = new SequenceI[seqs.size()];
+ for (int i = 0, j = seqs.size(); i < j; i++)
+ {
+ sqs[i] = (SequenceI) seqs.elementAt(i);
+ seqs.set(i, null);
+ }
+ return sqs;
+ }
+
+ /**
+ * attempt to extract coding region and product from a feature and properly
+ * decorate it with annotations.
+ *
+ * @param feature
+ * coding feature
+ * @param sourceDb
+ * source database for the EMBLXML
+ * @param seqs
+ * place where sequences go
+ * @param dna
+ * parent dna sequence for this record
+ * @param noPeptide
+ * flag for generation of Peptide sequence objects
+ */
+ private void parseCodingFeature(EmblFeature feature, String sourceDb,
+ Vector seqs, Sequence dna, boolean noPeptide)
+ {
+ boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
+ // extract coding region(s)
+ jalview.datamodel.Mapping map = null;
+ int[] exon = null;
+ if (feature.locations != null && feature.locations.size() > 0)
+ {
+ for (Enumeration locs = feature.locations.elements(); locs
+ .hasMoreElements();)
+ {
+ EmblFeatureLocations loc = (EmblFeatureLocations) locs
+ .nextElement();
+ int[] se = loc.getElementRanges(accession);
+ if (exon == null)
+ {
+ exon = se;
+ }
+ else
+ {
+ int[] t = new int[exon.length + se.length];
+ System.arraycopy(exon, 0, t, 0, exon.length);
+ System.arraycopy(se, 0, t, exon.length, se.length);
+ exon = t;
+ }
+ }
+ }
+ String prseq = null;
+ String prname = new String();
+ String prid = null;
+ Hashtable vals = new Hashtable();
+ int prstart = 1;
+ // get qualifiers
+ if (feature.getQualifiers() != null
+ && feature.getQualifiers().size() > 0)
+ {
+ for (Iterator quals = feature.getQualifiers().iterator(); quals
+ .hasNext();)
+ {
+ Qualifier q = (Qualifier) quals.next();
+ if (q.getName().equals("translation"))
+ {
+ StringBuffer prsq = new StringBuffer(q.getValues()[0]);
+ int p = prsq.indexOf(" ");
+ while (p > -1)
+ {
+ prsq.deleteCharAt(p);
+ p = prsq.indexOf(" ", p);
+ }
+ prseq = prsq.toString();
+ prsq = null;
+
+ }
+ else if (q.getName().equals("protein_id"))
+ {
+ prid = q.getValues()[0];
+ }
+ else if (q.getName().equals("codon_start"))
+ {
+ prstart = Integer.parseInt(q.getValues()[0]);
+ }
+ else if (q.getName().equals("product"))
+ {
+ prname = q.getValues()[0];
+ }
+ else
+ {
+ // throw anything else into the additional properties hash
+ String[] s = q.getValues();
+ StringBuffer sb = new StringBuffer();
+ if (s != null)
+ {
+ for (int i = 0; i < s.length; i++)
+ {
+ sb.append(s[i]);
+ sb.append("\n");
+ }
+ }
+ vals.put(q.getName(), sb.toString());
+ }
+ }
+ }
+ Sequence product = null;
+ exon = adjustForPrStart(prstart, exon);
+
+ if (prseq != null && prname != null && prid != null)
+ {
+ // extract proteins.
+ product = new Sequence(prid, prseq, 1, prseq.length());
+ product.setDescription(((prname.length() == 0) ? "Protein Product from "
+ + sourceDb
+ : prname));
+ if (!noPeptide)
+ {
+ // Protein is also added to vector of sequences returned
+ seqs.add(product);
+ }
+ // we have everything - create the mapping and perhaps the protein
+ // sequence
+ if (exon == null || exon.length == 0)
+ {
+ System.err
+ .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ + sourceDb + ":" + getAccession() + ")");
+ if (prseq.length() * 3 == (1 - prstart + dna.getSequence().length))
+ {
+ System.err
+ .println("Not allowing for additional stop codon at end of cDNA fragment... !");
+ // this might occur for CDS sequences where no features are
+ // marked.
+ exon = new int[]
+ { dna.getStart() + (prstart - 1), dna.getEnd() };
+ map = new jalview.datamodel.Mapping(product, exon, new int[]
+ { 1, prseq.length() }, 3, 1);
+ }
+ if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
+ {
+ System.err
+ .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
+ exon = new int[]
+ { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
+ map = new jalview.datamodel.Mapping(product, exon, new int[]
+ { 1, prseq.length() }, 3, 1);
+ }
+ }
+ else
+ {
+ // Trim the exon mapping if necessary - the given product may only be a
+ // fragment of a larger protein. (EMBL:AY043181 is an example)
+
+ if (isEmblCdna)
+ {
+ // TODO: Add a DbRef back to the parent EMBL sequence with the exon
+ // map
+ // if given a dataset reference, search dataset for parent EMBL
+ // sequence if it exists and set its map
+ // make a new feature annotating the coding contig
+ }
+ else
+ {
+ // final product length trunctation check
+
+ map = new jalview.datamodel.Mapping(product,
+ adjustForProteinLength(prseq.length(), exon), new int[]
+ { 1, prseq.length() }, 3, 1);
+ // reconstruct the EMBLCDS entry
+ // TODO: this is only necessary when there codon annotation is
+ // complete (I think JBPNote)
+ DBRefEntry pcdnaref = new DBRefEntry();
+ pcdnaref.setAccessionId(prid);
+ pcdnaref.setSource(DBRefSource.EMBLCDS);
+ pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
+ jalview.util.MapList mp = new jalview.util.MapList(new int[]
+ { 1, prseq.length() }, new int[]
+ { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
+ // { 1 + (prstart - 1) * 3,
+ // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
+ // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
+ pcdnaref.setMap(new Mapping(mp));
+ if (product != null)
+ product.addDBRef(pcdnaref);
+
+ }
+ }
+ // add cds feature to dna seq - this may include the stop codon
+ for (int xint = 0; exon != null && xint < exon.length; xint += 2)
+ {
+ SequenceFeature sf = new SequenceFeature();
+ sf.setBegin(exon[xint]);
+ sf.setEnd(exon[xint + 1]);
+ sf.setType(feature.getName());
+ sf.setFeatureGroup(sourceDb);
+ sf.setDescription("Exon " + (1 + (int) (xint / 2))
+ + " for protein '" + prname + "' EMBLCDS:" + prid);
+ sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
+ sf.setValue(FeatureProperties.EXONPRODUCT, prname);
+ if (vals != null && vals.size() > 0)
+ {
+ Enumeration kv = vals.elements();
+ while (kv.hasMoreElements())
+ {
+ Object key = kv.nextElement();
+ if (key != null)
+ sf.setValue(key.toString(), vals.get(key));
+ }
+ }
+ dna.addSequenceFeature(sf);
+ }
+ }
+ // add dbRefs to sequence
+ if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ {
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ {
+ DBRefEntry ref = (DBRefEntry) dbr.next();
+ ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
+ .getSource()));
+ // Hard code the kind of protein product accessions that EMBL cite
+ if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
+ {
+ ref.setMap(map);
+ if (map != null && map.getTo() != null)
+ {
+ map.getTo().addDBRef(
+ new DBRefEntry(ref.getSource(), ref.getVersion(), ref
+ .getAccessionId())); // don't copy map over.
+ if (map.getTo().getName().indexOf(prid) == 0)
+ {
+ map.getTo().setName(
+ jalview.datamodel.DBRefSource.UNIPROT + "|"
+ + ref.getAccessionId());
+ }
+ }
+ }
+ if (product != null)
+ {
+ DBRefEntry pref = new DBRefEntry(ref.getSource(),
+ ref.getVersion(), ref.getAccessionId());
+ pref.setMap(null); // reference is direct
+ product.addDBRef(pref);
+ // Add converse mapping reference
+ if (map != null)
+ {
+ Mapping pmap = new Mapping(dna, map.getMap().getInverse());
+ pref = new DBRefEntry(sourceDb, getVersion(),
+ this.getAccession());
+ pref.setMap(pmap);
+ if (map.getTo() != null)
+ {
+ map.getTo().addDBRef(pref);
+ }
+ }
+ }
+ dna.addDBRef(ref);
+ }
+ }
+ }
+
+ private int[] adjustForPrStart(int prstart, int[] exon)
+ {
+
+ int origxon[], sxpos = -1;
+ int sxstart, sxstop; // unnecessary variables used for debugging
+ // first adjust range for codon start attribute
+ if (prstart > 1)
+ {
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length && sxpos == -1; x += 2)
+ {
+ cdspos += exon[x + 1] - exon[x] + 1;
+ if (prstart <= cdspos)
+ {
+ sxpos = x;
+ sxstart = exon[x];
+ sxstop = exon[x + 1];
+ // and adjust start boundary of first exon.
+ exon[x] = exon[x + 1] - cdspos + prstart;
+ break;
+ }
+ }
+
+ if (sxpos > 0)
+ {
+ int[] nxon = new int[exon.length - sxpos];
+ System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
+ exon = nxon;
+ }
+ }
+ return exon;
+ }
+
+ /**
+ * truncate the last exon interval to the prlength'th codon
+ *
+ * @param prlength
+ * @param exon
+ * @return new exon
+ */
+ private int[] adjustForProteinLength(int prlength, int[] exon)
+ {
+
+ int origxon[], sxpos = -1, endxon = 0, cdslength = prlength * 3;
+ int sxstart, sxstop; // unnecessary variables used for debugging
+ // first adjust range for codon start attribute
+ if (prlength >= 1 && exon != null)
+ {
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length && sxpos == -1; x += 2)
+ {
+ cdspos += exon[x + 1] - exon[x] + 1;
+ if (cdslength <= cdspos)
+ {
+ // advanced beyond last codon.
+ sxpos = x;
+ sxstart = exon[x];
+ sxstop = exon[x + 1];
+ if (cdslength != cdspos)
+ {
+ System.err
+ .println("Truncating final exon interval on region by "
+ + (cdspos - cdslength));
+ }
+ // locate the new end boundary of final exon as endxon
+ endxon = exon[x + 1] - cdspos + cdslength;
+ break;
+ }
+ }
+
+ if (sxpos != -1)
+ {
+ // and trim the exon interval set if necessary
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
+ exon = nxon;
+ }
+ }
+ return exon;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff