JAL-2344 override to ignore (obsolete?) JalviewFileView

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 426f092..3581cf9 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -32,6 +32,7 @@ import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
 import jalview.jbgui.GStructureChooser;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -45,6 +46,7 @@ import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Objects;
+import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBox;
@@ -249,7 +251,7 @@ public class StructureChooser extends GStructureChooser implements
     boolean isPDBRefsFound = false;
     boolean isUniProtRefsFound = false;
     StringBuilder queryBuilder = new StringBuilder();
-    HashSet<String> seqRefs = new LinkedHashSet<String>();
+    Set<String> seqRefs = new LinkedHashSet<String>();
 
     if (seq.getAllPDBEntries() != null)
     {
@@ -257,9 +259,8 @@ public class StructureChooser extends GStructureChooser implements
       {
         if (isValidSeqName(entry.getId()))
         {
-          queryBuilder.append("pdb_id")
-                  .append(":")
-.append(entry.getId().toLowerCase())
+          queryBuilder.append("pdb_id:")
+                  .append(entry.getId().toLowerCase())
                   .append(" OR ");
           isPDBRefsFound = true;
           // seqRefs.add(entry.getId());
@@ -275,21 +276,18 @@ public class StructureChooser extends GStructureChooser implements
         {
           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
           {
-            queryBuilder
-.append("uniprot_accession").append(":")
+            queryBuilder.append("uniprot_accession:")
                     .append(getDBRefId(dbRef))
                     .append(" OR ");
-            queryBuilder
-.append("uniprot_id")
-                    .append(":")
-                    .append(getDBRefId(dbRef)).append(" OR ");
+            queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+                    .append(" OR ");
             isUniProtRefsFound = true;
           }
           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
           {
 
-            queryBuilder.append("pdb_id")
-                    .append(":").append(getDBRefId(dbRef).toLowerCase())
+            queryBuilder.append("pdb_id:")
+                    .append(getDBRefId(dbRef).toLowerCase())
                     .append(" OR ");
             isPDBRefsFound = true;
           }
@@ -338,7 +336,7 @@ 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*\\]", "")
@@ -460,7 +458,7 @@ public class StructureChooser extends GStructureChooser implements
                   lastPdbRequest, reorderedStructuresSet));
 
           FTSRestResponse.configureTableColumn(getResultTable(),
-                  wantedFields);
+                  wantedFields, tempUserPrefs);
           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
@@ -533,8 +531,6 @@ 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",
@@ -808,9 +804,13 @@ 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);
       }
@@ -829,13 +829,13 @@ public class StructureChooser extends GStructureChooser implements
       }
       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
               .associatePdbWithSeq(selectedPdbFileName,
-                      jalview.io.AppletFormatAdapter.FILE,
+                          DataSourceType.FILE,
                       selectedSequence, true, Desktop.instance);
 
           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
                   new SequenceI[] { selectedSequence });
     }
-    mainFrame.dispose();
+        closeAction();
       }
     }).start();
   }
@@ -859,7 +859,8 @@ 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 +878,9 @@ 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 +899,16 @@ 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);
     }
   }