From 212ef83be8ca4e967dc1d3e2b9e76750f9175e14 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 4 Feb 2016 10:28:29 +0000 Subject: [PATCH] JAL-2003 export features on alignment, not alignment dataset --- src/jalview/ext/ensembl/EnsemblOverlap.java | 122 --------------------------- src/jalview/gui/AnnotationExporter.java | 3 +- 2 files changed, 1 insertion(+), 124 deletions(-) delete mode 100644 src/jalview/ext/ensembl/EnsemblOverlap.java diff --git a/src/jalview/ext/ensembl/EnsemblOverlap.java b/src/jalview/ext/ensembl/EnsemblOverlap.java deleted file mode 100644 index 507b6f8..0000000 --- a/src/jalview/ext/ensembl/EnsemblOverlap.java +++ /dev/null @@ -1,122 +0,0 @@ -package jalview.ext.ensembl; - -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.io.FeaturesFile; -import jalview.io.FileParse; - -import java.io.IOException; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.List; - -/** - * A client for fetching and processing Ensembl overlap data in GFF feature - * format - * - * @author gmcarstairs - * @see http://rest.ensembl.org/documentation/info/overlap_id - */ -public class EnsemblOverlap extends EnsemblRestClient -{ - /* - * The default features to retrieve from Ensembl; can override in getSequenceRecords - */ - private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds, - EnsemblFeatureType.exon, EnsemblFeatureType.variation }; - - @Override - public String getDbName() - { - return "ENSEMBL (overlap)"; - } - - /** - * Makes a query to the REST overlap endpoint for the given sequence - * identifier. This returns an 'alignment' consisting of one 'dummy sequence' - * (the genomic sequence for which overlap features are returned by the - * service). This sequence will have on it sequence features which are the - * real information of interest, such as CDS regions or sequence variations. - */ - @Override - public AlignmentI getSequenceRecords(String query) throws IOException - { - // TODO: use a vararg String... for getSequenceRecords instead? - List queries = new ArrayList(); - queries.add(query); - FileParse fp = getSequenceReader(queries); - FeaturesFile fr = new FeaturesFile(fp); - return new Alignment(fr.getSeqsAsArray()); - } - - /** - * Returns a URL for the REST overlap endpoint - * - * @param ids - * @return - */ - @Override - protected URL getUrl(List ids) throws MalformedURLException - { - StringBuffer urlstring = new StringBuffer(128); - urlstring.append(ENSEMBL_REST).append("/overlap/id/") - .append(ids.get(0)); - - // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats - urlstring.append("?content-type=text/x-gff3"); - - /* - * specify features to retrieve - * @see http://rest.ensembl.org/documentation/info/overlap_id - * could make the list a configurable entry in jalview.properties - */ - for (EnsemblFeatureType feature : featuresWanted) - { - urlstring.append("&feature=").append(feature.name()); - } - - return new URL(urlstring.toString()); - } - - @Override - protected boolean useGetRequest() - { - return true; - } - - /** - * Returns the MIME type for GFF3. For GET requests the Content-type header - * describes the required encoding of the response. - */ - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return "text/x-gff3"; - } - - /** - * Returns the MIME type for GFF3. - */ - @Override - protected String getResponseMimeType() - { - return "text/x-gff3"; - } - - /** - * Overloaded method that allows a list of features to retrieve to be - * specified - * - * @param accId - * @param features - * @return - * @throws IOException - */ - protected AlignmentI getSequenceRecords(String accId, - EnsemblFeatureType[] features) throws IOException - { - featuresWanted = features; - return getSequenceRecords(accId); - } -} diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 136a38e..d688ddd 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -156,8 +156,7 @@ public class AnnotationExporter extends JPanel if (features) { FeaturesFile formatter = new FeaturesFile(); - SequenceI[] sequences = ap.av.getAlignment().getDataset() - .getSequencesArray(); + SequenceI[] sequences = ap.av.getAlignment().getSequencesArray(); Map featureColours = ap.getFeatureRenderer() .getDisplayedFeatureCols(); boolean includeNonPositional = ap.av.isShowNPFeats(); -- 1.7.10.2