X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=d7ba24ddbc12e33e90a3bf82eaa988fc3b0a22ad;hb=7f8ddabd82dcf91860e0a8dc972cfd1ab6c59fc5;hp=a778ab148ff667ba470b9cea00b843c93066699c;hpb=6add24465322b49396087a1ae6f55e427d197d7b;p=jalview.git diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java index a778ab1..d7ba24d 100644 --- a/src/jalview/ws/DasSequenceFeatureFetcher.java +++ b/src/jalview/ws/DasSequenceFeatureFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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. * @@ -181,7 +181,7 @@ public class DasSequenceFeatureFetcher int refCount = 0; for (int i = 0; i < sequences.length; i++) { - DBRefEntry[] dbref = sequences[i].getDBRef(); + DBRefEntry[] dbref = sequences[i].getDBRefs(); if (dbref != null) { for (int j = 0; j < dbref.length; j++) @@ -205,8 +205,10 @@ public class DasSequenceFeatureFetcher reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"), - MessageManager.getString("label.find_uniprot_accession_ids"), + MessageManager + .getString("info.you_want_jalview_to_find_uniprot_accessions"), + MessageManager + .getString("label.find_uniprot_accession_ids"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); } @@ -236,6 +238,7 @@ public class DasSequenceFeatureFetcher class FetchSeqFeatures implements Runnable { + @Override public void run() { startFetching(); @@ -245,10 +248,15 @@ public class DasSequenceFeatureFetcher class FetchDBRefs implements Runnable { + @Override public void run() { running = true; - new DBRefFetcher(sequences, af).fetchDBRefs(true); + boolean isNuclueotide = af.getViewport().getAlignment() + .isNucleotide(); + new jalview.ws.DBRefFetcher(sequences, af, null, af.featureSettings, + isNuclueotide).fetchDBRefs(true); + startFetching(); setGuiFetchComplete(); } @@ -264,7 +272,9 @@ public class DasSequenceFeatureFetcher startTime = System.currentTimeMillis(); if (af != null) { - af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime); + af.setProgressBar(MessageManager + .getString("status.fetching_das_sequence_features"), + startTime); } if (sourceRegistry == null) { @@ -378,8 +388,7 @@ public class DasSequenceFeatureFetcher source)); for (String id : idl) { - List qid = Arrays.asList(new String[] - { id }); + List qid = Arrays.asList(new String[] { id }); try { DasGFFAdapter dga = featuresc.fetchData(source, qid); @@ -537,7 +546,9 @@ public class DasSequenceFeatureFetcher if (af != null) { - af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime); + af.setProgressBar( + MessageManager.getString("status.no_das_sources_active"), + startTime); } if (getFeatSettings() != null) { @@ -567,7 +578,9 @@ public class DasSequenceFeatureFetcher { if (af != null) { - af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime); + af.setProgressBar(MessageManager + .getString("status.das_feature_fetching_cancelled"), + startTime); } cancelled = true; } @@ -582,12 +595,13 @@ public class DasSequenceFeatureFetcher if (!cancelled && af != null) { // only update the progress bar if we've completed the fetch normally - af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime); + af.setProgressBar(MessageManager + .getString("status.das_feature_fetching_complete"), startTime); } if (af != null && af.featureSettings != null) { - af.featureSettings.setTableData(); + af.featureSettings.discoverAllFeatureData(); } if (getFeatSettings() != null) @@ -630,8 +644,7 @@ public class DasSequenceFeatureFetcher return null; } DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs( - seq.getDBRef(), new String[] - { + seq.getDBRefs(), new String[] { // jalview.datamodel.DBRefSource.PDB, jalview.datamodel.DBRefSource.UNIPROT, // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord @@ -710,8 +723,7 @@ public class DasSequenceFeatureFetcher } } - return new Object[] - { ids, qstring }; + return new Object[] { ids, qstring }; } /**