/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* 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 };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+ PhylipFile.FILE_DESC, "Jalview" };
/**
* List of readable format file extensions by application in order
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;
}
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);
}
}
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"))
{