Merge branch 'apifix/JAL-1926_JAL-2106' into develop

JAL-1919 JAL-2148 regularise use of jalview.datamodel.PDBEntry.Type for PDB/mmCIF file type
JAL-1919 JAL-2148 use new enum jalview.structure.StructureImportSettings.StructureParser

diff --cc src/jalview/bin/Cache.java
index 23277a4,8493dff..6f16a6e
--- 1/src/jalview/bin/Cache.java
--- 2/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@@ -20,6 -20,6 +20,7 @@@
   */
  package jalview.bin;
  
++import jalview.datamodel.PDBEntry;
  import jalview.structure.StructureImportSettings;
  import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
@@@ -226,10 -226,11 +227,15 @@@ public class Cach
    private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
  
    private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
--
-   private final static String DEFAULT_STRUCTURE_FORMAT = StructureImportSettings.MMCIF;
 +  
-   private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.JMOL_PARSER;
+   /**
+    * Allowed values are PDB or mmCIF
+    */
 -  private final static String DEFAULT_STRUCTURE_FORMAT = "PDB";
++  private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
++          .toString();
++
++  private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
++          .toString();
  
    /**
     * Initialises the Jalview Application Log

diff --cc src/jalview/ext/jmol/JmolParser.java
Simple merge

diff --cc src/jalview/io/AppletFormatAdapter.java
index fca7263,fb414f4..2243a5c
--- 1/src/jalview/io/AppletFormatAdapter.java
--- 2/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@@ -26,6 -26,6 +26,7 @@@ import jalview.datamodel.Alignment
  import jalview.datamodel.AlignmentAnnotation;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.AlignmentView;
++import jalview.datamodel.PDBEntry.Type;
  import jalview.structure.StructureImportSettings;
  import jalview.util.MessageManager;
  
@@@ -280,9 -280,8 +281,9 @@@ public class AppletFormatAdapte
        {
          // TODO obtain config value from preference settings.
          // Set value to 'true' to test PDB processing with Jmol: JAL-1213
 -        boolean isParseWithJMOL = !StructureImportSettings
 -                .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
 +        boolean isParseWithJMOL = StructureImportSettings
-                 .getDefaultPDBFileParser().equalsIgnoreCase(
-                         StructureImportSettings.JMOL_PARSER);
++                .getDefaultPDBFileParser()
++                .equals(StructureImportSettings.StructureParser.JMOL_PARSER);
          if (isParseWithJMOL)
          {
            StructureImportSettings.addSettings(annotFromStructure,
@@@ -450,8 -447,6 +451,7 @@@
            alignFile = new MCview.PDBfile(annotFromStructure,
                    localSecondaryStruct, serviceSecondaryStruct, source);
          }
-         ((StructureFile) alignFile)
-                 .setDbRefType(StructureImportSettings.PDB);
++        ((StructureFile) alignFile).setDbRefType(Type.PDB);
        }
        else if (format.equals("mmCIF"))
        {
@@@ -459,8 -454,6 +459,7 @@@
                  localSecondaryStruct, serviceSecondaryStruct);
          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                  localSecondaryStruct, serviceSecondaryStruct, source);
-         ((StructureFile) alignFile)
-                 .setDbRefType(StructureImportSettings.MMCIF);
++        ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
        }
        else if (format.equals("STH"))
        {

diff --cc src/jalview/io/StructureFile.java
index 97e11eb,b2e5b23..fc0e207
--- 1/src/jalview/io/StructureFile.java
--- 2/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@@ -8,6 -8,6 +8,7 @@@ import jalview.datamodel.AlignmentI
  import jalview.datamodel.DBRefEntry;
  import jalview.datamodel.DBRefSource;
  import jalview.datamodel.PDBEntry;
++import jalview.datamodel.PDBEntry.Type;
  import jalview.datamodel.SequenceI;
  import jalview.structure.StructureImportSettings;
  
@@@ -25,7 -25,7 +26,7 @@@ public abstract class StructureFile ext
  
    private String id;
  
--  private String dbRefType;
++  private PDBEntry.Type dbRefType;
  
    /**
     * set to true to add derived sequence annotations (temp factor read from
@@@ -401,13 -399,13 +400,18 @@@
      this.chains = chains;
    }
  
--  public String getDbRefType()
++  public Type getDbRefType()
    {
      return dbRefType;
    }
  
    public void setDbRefType(String dbRefType)
    {
++    this.dbRefType = Type.valueOf(dbRefType);
++  }
++
++  public void setDbRefType(Type dbRefType)
++  {
      this.dbRefType = dbRefType;
    }
  

diff --cc src/jalview/structure/StructureImportSettings.java
index 4c06e0f,ed53425..388ccbd
--- 1/src/jalview/structure/StructureImportSettings.java
--- 2/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@@ -1,7 -1,6 +1,14 @@@
  package jalview.structure;
  
- import jalview.datamodel.DBRefSource;
--
++import jalview.datamodel.PDBEntry;
++import jalview.datamodel.PDBEntry.Type;
++
++/**
++ * bean holding settings for structure IO. TODO: tests for validation of values
++ * 
++ * @author tcofoegbu
++ *
++ */
  public class StructureImportSettings
  {
    /**
@@@ -26,30 -25,18 +33,28 @@@
  
    private static boolean processHETATMs = false;
  
-   public static final String JMOL_PARSER = "JMolParser";
- 
-   public static final String JALVIEW_PARSER = "JalViewParser";
- 
-   public static final String MMCIF = "mmCIF";
 -  public enum StructureFormat
++  public enum StructureParser
+   {
 -    PDB, MMCIF
 -  };
++    JMOL_PARSER, JALVIEW_PARSER
++  }
  
-   public static final String PDB = "PDB";
 -  private static StructureFormat currentDefaultFormat = StructureFormat.PDB;
  
 +  /**
 +   * Determines the default file format for structure files to be downloaded
 +   * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
 +   */
-   private static String defaultStructureFileFormat = DBRefSource.PDB;
++  private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
 +
 +  /**
 +   * Determines the parser used for parsing PDB format file. Possible options
 +   * are : JMolParser|JalveiwParser
 +   */
-   private static String defaultPDBFileParser = JMOL_PARSER;
++  private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
    public static void addSettings(boolean addAlignmentAnnotations,
-           boolean predictSecStr, boolean externalSecStr)
+           boolean processSecStr, boolean externalSecStr)
    {
      StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
-     StructureImportSettings.predictSecStr = predictSecStr;
+     StructureImportSettings.processSecStr = processSecStr;
      StructureImportSettings.externalSecondaryStructure = externalSecStr;
      StructureImportSettings.showSeqFeatures = true;
    }
@@@ -97,15 -84,15 +102,16 @@@
      StructureImportSettings.showSeqFeatures = showSeqFeatures;
    }
  
 -  public static String getCurrentDefaultFormat()
 +  public static String getDefaultStructureFileFormat()
    {
-     return defaultStructureFileFormat;
 -    return currentDefaultFormat.toString();
++    return defaultStructureFileFormat.toString();
    }
  
 -  public static void setCurrentDefaultFormat(String currentDefaultFormat)
 +  public static void setDefaultStructureFileFormat(
 +          String defaultStructureFileFormat)
    {
-     StructureImportSettings.defaultStructureFileFormat = defaultStructureFileFormat;
 -    StructureImportSettings.currentDefaultFormat = StructureFormat
 -            .valueOf(currentDefaultFormat);
++    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
++            .valueOf(defaultStructureFileFormat);
    }
  
    public static boolean isProcessHETATMs()
@@@ -118,14 -105,4 +124,21 @@@
      StructureImportSettings.processHETATMs = processHETATMs;
    }
  
 +  public static String getDefaultPDBFileParser()
 +  {
-     return defaultPDBFileParser;
++    return defaultPDBFileParser.toString();
 +  }
 +
-   public static void setDefaultPDBFileParser(String defaultPDBFileParser)
++  public static void setDefaultPDBFileParser(
++          StructureParser defaultPDBFileParser)
 +  {
 +    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
 +  }
 +
++  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
++  {
++    StructureImportSettings.defaultPDBFileParser = StructureParser
++            .valueOf(defaultPDBFileParser);
++  }
++
  }

diff --cc src/jalview/ws/dbsources/Pdb.java
index 1a58466,a06f0c8..fc636c6
--- 1/src/jalview/ws/dbsources/Pdb.java
--- 2/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@@ -27,6 -27,6 +27,7 @@@ import jalview.datamodel.AlignmentI
  import jalview.datamodel.DBRefEntry;
  import jalview.datamodel.DBRefSource;
  import jalview.datamodel.PDBEntry;
++import jalview.datamodel.PDBEntry.Type;
  import jalview.datamodel.SequenceI;
  import jalview.io.FormatAdapter;
  import jalview.io.PDBFeatureSettings;
@@@ -132,12 -133,11 +133,11 @@@ public class Pdb extends EbiFileRetriev
        stopQuery();
        return null;
      }
 -    String ext = StructureImportSettings.getCurrentDefaultFormat().equals(
 -            StructureFormat.MMCIF) ? ".cif" : ".xml";
 +    String ext = StructureImportSettings.getDefaultStructureFileFormat()
-             .equalsIgnoreCase("mmcif") ? ".cif"
-             : ".xml";
++            .equals(Type.MMCIF) ? ".cif" : ".xml";
      EBIFetchClient ebi = new EBIFetchClient();
      file = ebi.fetchDataAsFile("pdb:" + id,
 -            StructureImportSettings.getCurrentDefaultFormat().toLowerCase(),
 +            StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
              ext)
              .getAbsolutePath();
      stopQuery();

diff --cc test/jalview/ext/jmol/JmolParserTest.java
index 0010321,0627a4a..2ea0b80
--- 1/test/jalview/ext/jmol/JmolParserTest.java
--- 2/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@@ -31,6 -31,6 +31,7 @@@ import jalview.gui.AlignFrame
  import jalview.io.AppletFormatAdapter;
  import jalview.io.FileLoader;
  import jalview.structure.StructureImportSettings;
++import jalview.structure.StructureImportSettings.StructureParser;
  
  import java.util.Vector;
  
@@@ -89,9 -89,6 +90,9 @@@ public class JmolParserTes
              Boolean.TRUE.toString());
      Cache.applicationProperties.setProperty("ADD_SS_ANN",
              Boolean.TRUE.toString());
 +    StructureImportSettings.setDefaultStructureFileFormat("PDB");
 +    StructureImportSettings
-             .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
++            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
    }
  
    @Test(groups = { "Functional" })

diff --cc test/jalview/io/AnnotatedPDBFileInputTest.java
index 5368d41,3524a88..e6019aa
--- 1/test/jalview/io/AnnotatedPDBFileInputTest.java
--- 2/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@@ -32,6 -32,6 +32,7 @@@ import jalview.datamodel.SequenceFeatur
  import jalview.datamodel.SequenceI;
  import jalview.gui.AlignFrame;
  import jalview.structure.StructureImportSettings;
++import jalview.structure.StructureImportSettings.StructureParser;
  
  import java.io.File;
  
@@@ -66,9 -66,7 +67,9 @@@ public class AnnotatedPDBFileInputTes
      al = af.getViewport().getAlignment();
      pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
              .get(0).getId();
 -    StructureImportSettings.setCurrentDefaultFormat("PDB");
 +    StructureImportSettings.setDefaultStructureFileFormat("PDB");
 +    StructureImportSettings
-             .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
++            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
    }
  
    @Test(groups = { "Functional" })

diff --cc test/jalview/ws/PDBSequenceFetcherTest.java
index d082785,0c810a3..fda0198
--- 1/test/jalview/ws/PDBSequenceFetcherTest.java
--- 2/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@@ -26,6 -26,6 +26,7 @@@ import jalview.bin.Cache
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.SequenceI;
  import jalview.structure.StructureImportSettings;
++import jalview.structure.StructureImportSettings.StructureParser;
  import jalview.ws.seqfetcher.DbSourceProxy;
  
  import java.util.List;
@@@ -86,9 -86,7 +87,9 @@@ public class PDBSequenceFetcherTes
    {
      Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
              Boolean.TRUE.toString());
 -    StructureImportSettings.setCurrentDefaultFormat("PDB");
 +    StructureImportSettings.setDefaultStructureFileFormat("PDB");
 +    StructureImportSettings
-             .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
++            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
  
      testRetrieveProteinSeqFromPDB();
    }