From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 15 Jun 2016 15:02:16 +0000 (+0100)
Subject: JAL-2002 disabled 'Best Uniport Coverage' filter. JAL-1990 i18n for status messages... 
X-Git-Tag: Release_2_10_0~178
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6b8f46dd2ffc7f73948f0523c9b45336d2bd8128;hp=85246904e92e140d75830e191e7eb3e4467dac06;p=jalview.git

JAL-2002 disabled 'Best Uniport Coverage' filter. JAL-1990 i18n for status messages in the newly introduced progress indicator for Structure Chooser interface
---

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));
       }