Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2972c69..c83f264 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -148,8 +148,8 @@ public class StructureChooser extends GStructureChooser implements
   {
     long startTime = System.currentTimeMillis();
     pdbRestCleint = PDBFTSRestClient.getInstance();
-    Collection<FTSDataColumnI> wantedFields = pdbRestCleint
-            .getAllDefaulDisplayedDataColumns();
+    Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+            .getStructureSummaryFields();
 
     discoveredStructuresSet = new LinkedHashSet<FTSData>();
     HashSet<String> errors = new HashSet<String>();
@@ -186,7 +186,8 @@ public class StructureChooser extends GStructureChooser implements
     if (discoveredStructuresSet != null
             && !discoveredStructuresSet.isEmpty())
     {
-      tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
+      getResultTable().setModel(
+              FTSRestResponse.getTableModel(lastPdbRequest,
               discoveredStructuresSet));
       structuresDiscovered = true;
       noOfStructuresFound = discoveredStructuresSet.size();
@@ -337,7 +338,7 @@ public class StructureChooser extends GStructureChooser implements
    * @param seqName
    * @return
    */
-  private static String sanitizeSeqName(String seqName)
+  static String sanitizeSeqName(String seqName)
   {
     Objects.requireNonNull(seqName);
     return seqName.replaceAll("\\[\\d*\\]", "")
@@ -397,8 +398,8 @@ public class StructureChooser extends GStructureChooser implements
         long startTime = System.currentTimeMillis();
         pdbRestCleint = PDBFTSRestClient.getInstance();
         lbl_loading.setVisible(true);
-        Collection<FTSDataColumnI> wantedFields = pdbRestCleint
-                .getAllDefaulDisplayedDataColumns();
+        Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+                .getStructureSummaryFields();
         Collection<FTSData> filteredResponse = new HashSet<FTSData>();
         HashSet<String> errors = new HashSet<String>();
 
@@ -454,15 +455,18 @@ public class StructureChooser extends GStructureChooser implements
           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
           reorderedStructuresSet.addAll(filteredResponse);
           reorderedStructuresSet.addAll(discoveredStructuresSet);
-          tbl_summary.setModel(FTSRestResponse.getTableModel(
+          getResultTable().setModel(
+                  FTSRestResponse.getTableModel(
                   lastPdbRequest, reorderedStructuresSet));
 
-          FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
-          tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
-          tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
-          tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
+          FTSRestResponse.configureTableColumn(getResultTable(),
+                  wantedFields);
+          getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
+          getResultTable().getColumn("Ref Sequence").setMinWidth(100);
+          getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
           // Update table selection model here
-          tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+          getResultTable().addRowSelectionInterval(0,
+                  filterResponseCount - 1);
           mainFrame.setTitle(MessageManager.formatMessage(
                   "label.structure_chooser_filter_time", totalTime));
         }
@@ -529,8 +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",
@@ -591,7 +593,7 @@ public class StructureChooser extends GStructureChooser implements
     String currentView = selectedFilterOpt.getView();
     if (currentView == VIEWS_FILTER)
     {
-      if (tbl_summary.getSelectedRows().length > 0)
+      if (getResultTable().getSelectedRows().length > 0)
       {
         btn_view.setEnabled(true);
       }
@@ -729,19 +731,21 @@ public class StructureChooser extends GStructureChooser implements
     String currentView = selectedFilterOpt.getView();
     if (currentView == VIEWS_FILTER)
     {
-          int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+          int pdbIdColIndex = getResultTable().getColumn("PDB Id")
                   .getModelIndex();
-          int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+          int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
               .getModelIndex();
-          int[] selectedRows = tbl_summary.getSelectedRows();
+          int[] selectedRows = getResultTable().getSelectedRows();
       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
       int count = 0;
       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
       for (int row : selectedRows)
       {
-            String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
+            String pdbIdStr = getResultTable().getValueAt(row,
+                    pdbIdColIndex)
                 .toString();
-            SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+            SequenceI selectedSeq = (SequenceI) getResultTable()
+                    .getValueAt(row,
                 refSeqColIndex);
         selectedSeqsToView.add(selectedSeq);
             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
@@ -802,9 +806,13 @@ public class StructureChooser extends GStructureChooser implements
         pdbEntry = new PDBEntry();
             if (pdbIdStr.split(":").length > 1)
             {
-              pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
+              pdbEntry.setId(pdbIdStr.split(":")[0]);
+              pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+            }
+            else
+            {
+              pdbEntry.setId(pdbIdStr);
             }
-        pdbEntry.setId(pdbIdStr);
         pdbEntry.setType(PDBEntry.Type.PDB);
         selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
       }
@@ -853,7 +861,8 @@ 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())
@@ -871,9 +880,9 @@ 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)
@@ -892,14 +901,16 @@ 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);
     }
   }
@@ -962,7 +973,7 @@ public class StructureChooser extends GStructureChooser implements
         {
           String searchTerm = txt_search.getText().toLowerCase();
           searchTerm = searchTerm.split(":")[0];
-          System.out.println(">>>>> search term : " + searchTerm);
+          // System.out.println(">>>>> search term : " + searchTerm);
           List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
           FTSRestRequest pdbRequest = new FTSRestRequest();
           pdbRequest.setAllowEmptySeq(false);