JAL-1641 JSONFile format support for jalview alignment

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2e94782..bbd32be 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -47,7 +47,7 @@ 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, "HTML" }; // ,
+      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "HTML" }; // ,
                                                                               // "SimpleBLAST"
                                                                               // };
 
@@ -57,23 +57,23 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
           { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
-    "STH", PhylipFile.FILE_DESC };
+    "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-          { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-    "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT };
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_DESC, "jvp" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
   public static final String[] WRITABLE_FNAMES = new String[]
-          { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-    "STH", "Jalview", PhylipFile.FILE_DESC };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
 
   /**
    * List of readable format file extensions by application in order
@@ -81,7 +81,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
           { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT,
+      "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
  "html" }; // ".blast"
 
   /**
@@ -90,7 +90,8 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
           { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-      "Stockholm", "RNAML", PhylipFile.FILE_DESC, "HTML" };// ,
+      "Stockholm", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+      "HTML" };// ,
 
   // "SimpleBLAST"
   // };
@@ -126,6 +127,21 @@ public class AppletFormatAdapter
 
   public static String CLASSLOADER = "ClassLoader";
 
+  /**
+   * add jalview-derived non-secondary structure annotation from PDB structure
+   */
+  boolean annotFromStructure = false;
+
+  /**
+   * add secondary structure from PDB data with built-in algorithms
+   */
+  boolean localSecondaryStruct = false;
+
+  /**
+   * process PDB data with web services
+   */
+  boolean serviceSecondaryStruct = false;
+
   AlignFile afile = null;
 
   String inFile;
@@ -239,7 +255,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(true,true,inFile, type);
+        afile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
         // Uncomment to test Jmol data based PDB processing: JAL-1213
         // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
       }
@@ -255,10 +272,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(inFile, type);
       }
-      // else if (format.equals(HtmlFile.FILE_DESC))
-      // {
-      // afile = new HtmlFile(inFile, type);
-      // }
+       else if (format.equals(JSONFile.FILE_DESC))
+       {
+       afile = new JSONFile(inFile, type);
+       }
       else if (format.equals("RNAML"))
       {
         afile = new RnamlFile(inFile, type);
@@ -364,7 +381,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(true,true,source);
+        afile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {
@@ -382,10 +400,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(source);
       }
-      // else if (format.equals(HtmlFile.FILE_DESC))
-      // {
-      // afile = new HtmlFile(source);
-      // }
+       else if (format.equals(JSONFile.FILE_DESC))
+       {
+       afile = new JSONFile(source);
+       }
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -521,10 +539,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile();
       }
-      // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC))
-      // {
-      // afile = new HtmlFile();
-      // }
+       else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+       {
+       afile = new JSONFile();
+       }
       else if (format.equalsIgnoreCase("RNAML"))
       {
         afile = new RnamlFile();