Merge branch 'develop' into releases/Release_2_10_Branch

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 285a953..552f00e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,7 +26,9 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.structure.StructureViewSettings;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -87,7 +89,7 @@ public class AppletFormatAdapter
   public static final String[] READABLE_FORMATS = new String[] { "BLC",
       "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
       "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
-      IdentifyFile.GFF3File, "HTML", "mmCIF" };
+      IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
 
   /**
    * List of readable format file extensions by application in order
@@ -104,7 +106,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[] { "Fasta",
       "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
-      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
       "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
 
   /**
@@ -276,33 +278,12 @@ public class AppletFormatAdapter
         alignFile = new JPredFile(inFile, type);
         ((JPredFile) alignFile).removeNonSequences();
       }
-      else if (format.equals("PDB"))
+      else if (format.equals("PDB") || format.equalsIgnoreCase("mmCIF"))
       {
-        // TODO obtain config value from preference settings.
-        // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = false;
-        if (isParseWithJMOL)
-        {
-          StructureViewSettings.addSettings(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  type);
-        }
-        else
-        {
-          StructureViewSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  type);
-        }
-      }
-      else if (format.equals("mmCIF"))
-      {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        alignFile = new JmolParser(inFile, type);
+        ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("STH"))
       {
@@ -328,9 +309,9 @@ public class AppletFormatAdapter
       {
         alignFile = new RnamlFile(inFile, type);
       }
-      else if (format.equals(IdentifyFile.GFF3File))
+      else if (format.equals(IdentifyFile.FeaturesFile))
       {
-        alignFile = new Gff3File(inFile, type);
+        alignFile = new FeaturesFile(true, inFile, type);
       }
       return buildAlignmentFrom(alignFile);
     } catch (Exception e)
@@ -433,24 +414,24 @@ public class AppletFormatAdapter
         boolean isParseWithJMOL = false;
         if (isParseWithJMOL)
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, source);
+          alignFile = new JmolParser(source);
         }
         else
         {
-          StructureViewSettings.setShowSeqFeatures(true);
+          StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
+        ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
-      else if (format.equals("mmCIF"))
+      else if (format.equalsIgnoreCase("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, source);
+        alignFile = new JmolParser(source);
+        ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
       }
       else if (format.equals("STH"))
       {
@@ -468,9 +449,9 @@ public class AppletFormatAdapter
       {
         alignFile = new PhylipFile(source);
       }
-      else if (format.equals(IdentifyFile.GFF3File))
+      else if (format.equals(IdentifyFile.FeaturesFile))
       {
-        alignFile = new Gff3File(inFile, type);
+        alignFile = new FeaturesFile(inFile, type);
       }
       else if (format.equals(JSONFile.FILE_DESC))
       {
@@ -711,7 +692,7 @@ public class AppletFormatAdapter
           long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
           AlignmentI al = afa.readFile(args[i], FILE,
-                  new IdentifyFile().Identify(args[i], FILE));
+                  new IdentifyFile().identify(args[i], FILE));
           t1 += System.currentTimeMillis();
           System.gc();
           memf += r.totalMemory() - r.freeMemory();
@@ -877,7 +858,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        String idformat = new jalview.io.IdentifyFile().Identify(file,
+        String idformat = new jalview.io.IdentifyFile().identify(file,
                 protocol);
         if (idformat == null)
         {