X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=e34093dc836fcf6e2b7de7dbb14bb7f21b982411;hb=9b3219d225131af5a165553f206ebf8da304ee23;hp=7dc263bdf6261ec8e148bacf7bba6000c82b66ca;hpb=e58c9b0c6d453c75810eb08cb2651769fccf7f8a;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 7dc263b..e34093d 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -83,52 +83,51 @@ 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, JSONFile.FILE_DESC, IdentifyFile.GFF3File, - "HTML" }; + 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.FeaturesFile, "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", + 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, - ".gff2,gff3", - "jar,jvp", HtmlFile.FILE_EXT }; + ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT }; /** * 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, IdentifyFile.GFF3File, "Jalview", - HtmlFile.FILE_DESC }; + public static final String[] READABLE_FNAMES = new String[] { "Fasta", + "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML", + PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile, + "Jalview", HtmlFile.FILE_DESC }; /** * List of valid format strings for use by callers of the formatSequences * method */ - public static final String[] WRITEABLE_FORMATS = new String[] - { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", - "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC }; + public static final String[] WRITEABLE_FORMATS = new String[] { "BLC", + "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "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", + public static final String[] WRITABLE_EXTENSIONS = new String[] { + "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", "STH", + public static final String[] WRITABLE_FNAMES = new String[] { "Fasta", + "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -170,7 +169,6 @@ public class AppletFormatAdapter return list.toString(); } - public void setNewlineString(String nl) { newline = nl; @@ -308,9 +306,9 @@ 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) @@ -428,9 +426,10 @@ public class AppletFormatAdapter { alignFile = new PhylipFile(source); } - else if (format.equals(IdentifyFile.GFF3File)) + else if (format.equals(IdentifyFile.FeaturesFile)) { - alignFile = new Gff3File(inFile, type); + // enforce 'parseImmediately' here: + alignFile = new FeaturesFile(true, inFile, type); } else if (format.equals(JSONFile.FILE_DESC)) { @@ -480,7 +479,6 @@ public class AppletFormatAdapter } } - /** * boilerplate method to handle data from an AlignFile and construct a new * alignment or import to an existing alignment @@ -504,6 +502,7 @@ public class AppletFormatAdapter /** * create an alignment flatfile from a Jalview alignment view + * * @param format * @param jvsuffix * @param av @@ -592,10 +591,10 @@ public class AppletFormatAdapter { afile = new PhylipFile(); } - else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) - { + else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) + { afile = new JSONFile(); - } + } else if (format.equalsIgnoreCase("RNAML")) { afile = new RnamlFile(); @@ -603,7 +602,9 @@ public class AppletFormatAdapter else { - throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string")); + throw new Exception( + MessageManager + .getString("error.implementation_error_unknown_file_format_string")); } afile.setNewlineString(newline); @@ -669,7 +670,7 @@ 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(); @@ -684,7 +685,7 @@ public class AppletFormatAdapter } catch (Exception e) { System.err - .println("Couln't format the alignment for output as a FASTA file."); + .println("Couln't format the alignment for output as a FASTA file."); e.printStackTrace(System.err); } } @@ -694,8 +695,8 @@ public class AppletFormatAdapter } System.out.println("Read took " + (t1 / 1000.0) + " seconds."); System.out - .println("Difference between free memory now and before is " - + (memf / (1024.0 * 1024.0) * 1.0) + " MB"); + .println("Difference between free memory now and before is " + + (memf / (1024.0 * 1024.0) * 1.0) + " MB"); } catch (Exception e) { System.err.println("Exception when dealing with " + i @@ -761,7 +762,7 @@ public class AppletFormatAdapter } catch (Exception ex) { System.err - .println("Exception checking resources: " + file + " " + ex); + .println("Exception checking resources: " + file + " " + ex); } if (file.indexOf("://") > -1) @@ -835,7 +836,7 @@ public class AppletFormatAdapter { try { - String idformat = new jalview.io.IdentifyFile().Identify(file, + String idformat = new jalview.io.IdentifyFile().identify(file, protocol); if (idformat == null) { @@ -863,7 +864,7 @@ public class AppletFormatAdapter if (debug) { System.out - .println("File deemed not accessible via " + protocol); + .println("File deemed not accessible via " + protocol); } fp.close(); return null;