/*
- * 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.
*
* 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, "HTML" }; // ,
- // "SimpleBLAST"
- // };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.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, JSONFile.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, JSONFile.FILE_DESC, "Jalview", "HTML" };
/**
* List of valid format strings for use by callers of the formatSequences
*/
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_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,
- "html" }; // ".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, "HTML" };// ,
-
- // "SimpleBLAST"
- // };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
public static String INVALID_CHARACTERS = "Contains invalid characters";
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);
}
{
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);
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
+ afile.addSeqGroups(al);
return al;
} catch (Exception e)
// Possible sequence is just residues with no label
afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
Alignment al = new Alignment(afile.getSeqsAsArray());
+
+ afile.addSeqGroups(al);
afile.addAnnotations(al);
return al;
}
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"))
{
{
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);
+ afile.addSeqGroups(al);
return al;
} catch (Exception e)
afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
+ afile.addSeqGroups(al);
return al;
} catch (Exception ex)
try
{
AlignFile afile = null;
-
if (format.equalsIgnoreCase("FASTA"))
{
afile = new FastaFile();
{
afile = new PhylipFile();
}
- // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC))
- // {
- // afile = new HtmlFile();
- // }
+ else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+ {
+ afile = new JSONFile();
+ // Add groups to AlignFile
+ afile.seqGroups = alignment.getGroups();
+
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
+ {
+ if (annot != null && !annot.autoCalculated)
+ {
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ afile.annotations.add(annot);
+ }
+ }
+ }
else if (format.equalsIgnoreCase("RNAML"))
{
afile = new RnamlFile();
afile.setSeqs(alignment.getSequencesArray());
+
String afileresp = afile.print();
if (afile.hasWarningMessage())
{
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