X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=c69a0c7cc339cff67ede323081546b2e42fb19b3;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=d43e7c150ecbdb8107f71e1dcf581749670087bd;hpb=77abb3fac2965a8966410cd77cd749c7c1dc6453;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d43e7c1..c69a0c7 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  *
  * This file is part of Jalview.
  *
@@ -25,6 +25,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
+import jalview.util.MessageManager;
 
 import java.io.File;
 import java.io.InputStream;
@@ -45,8 +46,24 @@ public class AppletFormatAdapter
    * List of valid format strings used in the isValidFormat method
    */
   public static final String[] READABLE_FORMATS = new String[]
-          { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-    "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC }; // , "SimpleBLAST" };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" };
+
+  /**
+   * List of readable format file extensions by application in order
+   * corresponding to READABLE_FNAMES
+   */
+  public static final String[] READABLE_EXTENSIONS = new String[]
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, "jar,jvp", "html" };
+
+  /**
+   * List of readable formats by application in order corresponding to
+   * READABLE_EXTENSIONS
+   */
+  public static final String[] READABLE_FNAMES = new String[]
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
+      "RNAML", PhylipFile.FILE_DESC, "Jalview", "HTML" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -61,35 +78,16 @@ public class AppletFormatAdapter
    * 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, "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 };
-
-  /**
-   * List of readable format file extensions by application in order
-   * corresponding to READABLE_FNAMES
-   */
-  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 }; // ".blast"
-
-  /**
-   * List of readable formats by application in order corresponding to
-   * READABLE_EXTENSIONS
-   */
-  public static final String[] READABLE_FNAMES = new String[]
-          { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
-    "Stockholm", "RNAML", PhylipFile.FILE_DESC };// ,
-
-  // "SimpleBLAST"
-  // };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+      PhylipFile.FILE_DESC, "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -108,7 +106,7 @@ public class AppletFormatAdapter
     for (int i = 0, iSize = els.length - 1; i < iSize; i++)
     {
       list.append(els[i]);
-      list.append(",");
+      list.append(", ");
     }
     list.append(" and " + els[els.length - 1] + ".");
     return list.toString();
@@ -122,6 +120,21 @@ 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;
@@ -235,7 +248,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(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);
       }
@@ -251,6 +265,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(inFile, type);
       }
+      // else if (format.equals(HtmlFile.FILE_DESC))
+      // {
+      // afile = new HtmlFile(inFile, type);
+      // }
       else if (format.equals("RNAML"))
       {
         afile = new RnamlFile(inFile, type);
@@ -356,7 +374,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(source);
+        afile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {
@@ -374,6 +393,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile(source);
       }
+      // else if (format.equals(HtmlFile.FILE_DESC))
+      // {
+      // afile = new HtmlFile(source);
+      // }
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -509,6 +532,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile();
       }
+      // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC))
+      // {
+      // afile = new HtmlFile();
+      // }
       else if (format.equalsIgnoreCase("RNAML"))
       {
         afile = new RnamlFile();
@@ -516,8 +543,7 @@ public class AppletFormatAdapter
 
       else
       {
-        throw new Exception(
-                "Implementation error: Unknown file format string");
+        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);