X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=11fe95e36330a721254024d17bde26b939ecdb4d;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=a125ce42f83cfb32589500afa6f5a87b78067a9b;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index a125ce4..11fe95e 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,20 +20,22 @@ */ package jalview.ws.dbsources; +import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; +import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; +import jalview.io.PDBFeatureSettings; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; import jalview.ws.ebi.EBIFetchClient; -import jalview.ws.seqfetcher.DbSourceProxy; import java.util.ArrayList; import java.util.List; -import java.util.Vector; import com.stevesoft.pat.Regex; @@ -41,12 +43,17 @@ import com.stevesoft.pat.Regex; * @author JimP * */ -public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy +public class Pdb extends EbiFileRetrievedProxy { + private static final String SEPARATOR = "|"; + + private static final String COLON = ":"; + + private static final int PDB_ID_LENGTH = 4; + public Pdb() { super(); - addDbSourceProperty(DBRefSource.PROTSEQDB); } /* @@ -54,9 +61,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy * * @see jalview.ws.DbSourceProxy#getAccessionSeparator() */ + @Override public String getAccessionSeparator() { - // TODO Auto-generated method stub return null; } @@ -65,6 +72,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy * * @see jalview.ws.DbSourceProxy#getAccessionValidator() */ + @Override public Regex getAccessionValidator() { return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)"); @@ -75,6 +83,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy * * @see jalview.ws.DbSourceProxy#getDbSource() */ + @Override public String getDbSource() { return DBRefSource.PDB; @@ -85,6 +94,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy * * @see jalview.ws.DbSourceProxy#getDbVersion() */ + @Override public String getDbVersion() { return "0"; @@ -95,34 +105,45 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy * * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[]) */ + @Override public AlignmentI getSequenceRecords(String queries) throws Exception { - AlignmentI pdbfile = null; - Vector result = new Vector(); + AlignmentI pdbAlignment = null; String chain = null; String id = null; - if (queries.indexOf(":") > -1) + if (queries.indexOf(COLON) > -1) { - chain = queries.substring(queries.indexOf(":") + 1); - id = queries.substring(0, queries.indexOf(":")); + chain = queries.substring(queries.indexOf(COLON) + 1); + id = queries.substring(0, queries.indexOf(COLON)); } else { id = queries; } - if (queries.length() > 4 && chain == null) + + /* + * extract chain code if it is appended to the id and we + * don't already have one + */ + if (queries.length() > PDB_ID_LENGTH && chain == null) { - chain = queries.substring(4, 5); - id = queries.substring(0, 4); + chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1); + id = queries.substring(0, PDB_ID_LENGTH); } + if (!isValidReference(id)) { System.err.println("Ignoring invalid pdb query: '" + id + "'"); stopQuery(); return null; } + String ext = StructureImportSettings.getDefaultStructureFileFormat() + .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml"; EBIFetchClient ebi = new EBIFetchClient(); - file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath(); + file = ebi.fetchDataAsFile( + "pdb:" + id, + StructureImportSettings.getDefaultStructureFileFormat() + .toLowerCase(), ext).getAbsolutePath(); stopQuery(); if (file == null) { @@ -131,12 +152,13 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy try { - pdbfile = new FormatAdapter().readFile(file, - jalview.io.AppletFormatAdapter.FILE, "PDB"); - if (pdbfile != null) + pdbAlignment = new FormatAdapter().readFile(file, + jalview.io.AppletFormatAdapter.FILE, + StructureImportSettings.getDefaultStructureFileFormat()); + if (pdbAlignment != null) { List toremove = new ArrayList(); - for (SequenceI pdbcs : pdbfile.getSequences()) + for (SequenceI pdbcs : pdbAlignment.getSequences()) { String chid = null; // Mapping map=null; @@ -147,16 +169,16 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy chid = pid.getChainCode(); } - ; - } if (chain == null || (chid != null && (chid.equals(chain) || chid.trim().equals(chain.trim()) || (chain .trim().length() == 0 && chid.equals("_"))))) { - pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id - + "|" + pdbcs.getName()); + // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant. + // TODO: suggest simplify naming to 1qip|A as default name defined + pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + + id + SEPARATOR + pdbcs.getName()); // Might need to add more metadata to the PDBEntry object // like below /* @@ -188,18 +210,18 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy // now remove marked sequences for (SequenceI pdbcs : toremove) { - pdbfile.deleteSequence(pdbcs); + pdbAlignment.deleteSequence(pdbcs); if (pdbcs.getAnnotation() != null) { for (AlignmentAnnotation aa : pdbcs.getAnnotation()) { - pdbfile.deleteAnnotation(aa); + pdbAlignment.deleteAnnotation(aa); } } } } - if (pdbfile == null || pdbfile.getHeight() < 1) + if (pdbAlignment == null || pdbAlignment.getHeight() < 1) { throw new Exception(MessageManager.formatMessage( "exception.no_pdb_records_for_chain", new String[] { id, @@ -211,7 +233,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy stopQuery(); throw (ex); } - return pdbfile; + return pdbAlignment; } /* @@ -219,6 +241,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy * * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) */ + @Override public boolean isValidReference(String accession) { Regex r = getAccessionValidator(); @@ -226,13 +249,15 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy } /** - * obtain human glyoxalase chain A sequence + * human glyoxalase */ + @Override public String getTestQuery() { - return "1QIPA"; + return "1QIP"; } + @Override public String getDbName() { return "PDB"; // getDbSource(); @@ -243,4 +268,19 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy { return 0; } + + /** + * Returns a descriptor for suitable feature display settings with + * + */ + @Override + public FeatureSettingsModelI getFeatureColourScheme() + { + return new PDBFeatureSettings(); + } }