From 6b8f46dd2ffc7f73948f0523c9b45336d2bd8128 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Wed, 15 Jun 2016 16:02:16 +0100 Subject: [PATCH] JAL-2002 disabled 'Best Uniport Coverage' filter. JAL-1990 i18n for status messages in the newly introduced progress indicator for Structure Chooser interface --- resources/lang/Messages.properties | 6 ++++++ src/jalview/gui/StructureChooser.java | 19 ++++++++++--------- .../structure/StructureSelectionManager.java | 6 ++++-- 3 files changed, 20 insertions(+), 11 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index cb9aa77..62e1a6e 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1302,3 +1302,9 @@ label.next_page_tooltip=Next Page label.prev_page_tooltip=Previous Page exception.bad_request=Bad request. There is a problem with your input. exception.service_not_available=Service not available. The server is being updated, try again later. +status.launching_3d_structure_viewer = Launching 3D Structure viewer... +status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries... +status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping +status.fetching_3d_structures_for = Fetching 3D Structure for {0} +status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS +status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 426f092..3d80f79 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -533,8 +533,6 @@ public class StructureChooser extends GStructureChooser implements { cmb_filterOption.addItem(new FilterOption("Best Quality", "overall_quality", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage", - "uniprot_coverage", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Best Resolution", "resolution", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Protein Chain", @@ -859,7 +857,8 @@ public class StructureChooser extends GStructureChooser implements final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { - ssm.setProgressBar("Launching PDB structure viewer.."); + ssm.setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer")); final StructureViewer sViewer = new StructureViewer(ssm); if (SiftsSettings.isMapWithSifts()) @@ -877,9 +876,9 @@ public class StructureChooser extends GStructureChooser implements { int y = seqsWithoutSourceDBRef.size(); ssm.setProgressBar(null); - ssm.setProgressBar("Fetching db refs for " + y - + " sequence" + (y > 1 ? "s" : "") - + " without valid db ref required for SIFTS mapping"); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y)); SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; int x = 0; for (SequenceI fSeq : seqsWithoutSourceDBRef) @@ -898,14 +897,16 @@ public class StructureChooser extends GStructureChooser implements } SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); ssm.setProgressBar(null); - ssm.setProgressBar("Fetching PDB Structures for selected entries.."); + ssm.setProgressBar(MessageManager + .getString("status.fetching_3d_structures_for_selected_entries")); sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); } else { ssm.setProgressBar(null); - ssm.setProgressBar("Fetching PDB Structure for " - + pdbEntriesToView[0].getId()); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId())); sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } } diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 33c566d..fb96b22 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -501,7 +501,8 @@ public class StructureSelectionManager if (isMapUsingSIFTs) { setProgressBar(null); - setProgressBar("Obtaining mapping with SIFTS"); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts")); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); if (targetChainId != null && !targetChainId.trim().isEmpty()) @@ -559,7 +560,8 @@ public class StructureSelectionManager else { setProgressBar(null); - setProgressBar("Obtaining mapping with NW alignment"); + setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment")); seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq)); } -- 1.7.10.2