X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=c908b1586521d24a68e3cd0ea0f9f7cdd6fcc7d6;hb=4231d40261fef32ce4570a6bbad0d35df44e8baf;hp=e4c4f3deb8dea3d14329fe10f82e0014a5153991;hpb=c07eb2c5794833bd0241000d6844d783fe10cb82;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index e4c4f3d..c908b15 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -32,6 +32,11 @@ import java.io.File; import java.io.InputStream; import java.util.List; +import javajs.J2SIgnoreImport; + +import jalview.jsdev.Constants; +import jalview.jsdev.GenericFileAdapter; + /** * A low level class for alignment and feature IO with alignment formatting * methods used by both applet and application for generating flat alignment @@ -41,6 +46,7 @@ import java.util.List; * @author $author$ * @version $Revision$ */ +@J2SIgnoreImport({java.io.File.class}) public class AppletFormatAdapter { private AlignmentViewPanel viewpanel; @@ -84,7 +90,7 @@ 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, JSONFile.FILE_DESC, IdentifyFile.GFF3File, + "PDB", "JnetFile", "RNAML", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, IdentifyFile.GFF3File, "HTML" }; /** @@ -93,9 +99,9 @@ public class AppletFormatAdapter */ 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, + "sto,stk", "xml,rnaml", Constants.Phylip_FILE_EXT, Constants.JSON_FILE_EXT, ".gff2,gff3", - "jar,jvp", HtmlFile.FILE_EXT }; + "jar,jvp", Constants.Html_FILE_EXT }; /** * List of readable formats by application in order corresponding to @@ -103,8 +109,8 @@ public class AppletFormatAdapter */ 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 }; + "RNAML", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, IdentifyFile.GFF3File, "Jalview", + Constants.Html_FILE_DESC }; /** * List of valid format strings for use by callers of the formatSequences @@ -112,7 +118,7 @@ public class AppletFormatAdapter */ public static final String[] WRITEABLE_FORMATS = new String[] { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", - "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC }; + "STH", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC }; /** * List of extensions corresponding to file format types in WRITABLE_FNAMES @@ -120,7 +126,7 @@ public class AppletFormatAdapter */ 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" }; + "sto,stk", Constants.Phylip_FILE_EXT, Constants.JSON_FILE_EXT, "jvp" }; /** * List of writable formats by the application. Order must correspond with the @@ -128,7 +134,7 @@ public class AppletFormatAdapter */ public static final String[] WRITABLE_FNAMES = new String[] { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", - PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" }; + Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, "Jalview" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -241,35 +247,35 @@ public class AppletFormatAdapter { if (format.equals("FASTA")) { - alignFile = new FastaFile(inFile, type); + alignFile = GenericFileAdapter.getFile("FastaFile", inFile, type); } else if (format.equals("MSF")) { - alignFile = new MSFfile(inFile, type); + alignFile = GenericFileAdapter.getFile("MSFfile", inFile, type); } else if (format.equals("PileUp")) { - alignFile = new PileUpfile(inFile, type); + alignFile = GenericFileAdapter.getFile("PileUpfile", inFile, type); } else if (format.equals("CLUSTAL")) { - alignFile = new ClustalFile(inFile, type); + alignFile = GenericFileAdapter.getFile("ClustalFile", inFile, type); } else if (format.equals("BLC")) { - alignFile = new BLCFile(inFile, type); + alignFile = GenericFileAdapter.getFile("BLCFile", inFile, type); } else if (format.equals("PIR")) { - alignFile = new PIRFile(inFile, type); + alignFile = GenericFileAdapter.getFile("PIRFile", inFile, type); } else if (format.equals("PFAM")) { - alignFile = new PfamFile(inFile, type); + alignFile = GenericFileAdapter.getFile("PfamFile", inFile, type); } else if (format.equals("JnetFile")) { - alignFile = new JPredFile(inFile, type); + alignFile = GenericFileAdapter.getFile("JPredFile", inFile, type); ((JPredFile) alignFile).removeNonSequences(); } else if (format.equals("PDB")) @@ -281,31 +287,31 @@ public class AppletFormatAdapter } else if (format.equals("STH")) { - alignFile = new StockholmFile(inFile, type); + alignFile = GenericFileAdapter.getFile("StockholmFile", inFile, type); } else if (format.equals("SimpleBLAST")) { - alignFile = new SimpleBlastFile(inFile, type); + alignFile = GenericFileAdapter.getFile("SimpleBlastFile", inFile, type); } else if (format.equals(PhylipFile.FILE_DESC)) { - alignFile = new PhylipFile(inFile, type); + alignFile = GenericFileAdapter.getFile("PhylipFile", inFile, type); } - else if (format.equals(JSONFile.FILE_DESC)) + else if (format.equals(Constants.JSON_FILE_DESC)) { - alignFile = new JSONFile(inFile, type); + alignFile = GenericFileAdapter.getFile("JSONFile", inFile, type); } - else if (format.equals(HtmlFile.FILE_DESC)) + else if (format.equals(Constants.Html_FILE_DESC)) { - alignFile = new HtmlFile(inFile, type); + alignFile = GenericFileAdapter.getFile("HtmlFile", inFile, type); } else if (format.equals("RNAML")) { - alignFile = new RnamlFile(inFile, type); + alignFile = GenericFileAdapter.getFile("RnamlFile", inFile, type); } else if (format.equals(IdentifyFile.GFF3File)) { - alignFile = new Gff3File(inFile, type); + alignFile = GenericFileAdapter.getFile("Gff3File", inFile, type); } return buildAlignmentFrom(alignFile); } catch (Exception e) @@ -326,7 +332,7 @@ public class AppletFormatAdapter try { // Possible sequence is just residues with no label - alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); + alignFile = GenericFileAdapter.getFile("FastaFile", ">UNKNOWN\n" + inFile, "Paste"); return buildAlignmentFrom(alignFile); } catch (Exception ex) @@ -368,35 +374,35 @@ public class AppletFormatAdapter { if (format.equals("FASTA")) { - alignFile = new FastaFile(source); + alignFile = GenericFileAdapter.getFile("FastaFile", source); } else if (format.equals("MSF")) { - alignFile = new MSFfile(source); + alignFile = GenericFileAdapter.getFile("MSFfile", source); } else if (format.equals("PileUp")) { - alignFile = new PileUpfile(source); + alignFile = GenericFileAdapter.getFile("PileUpfile", source); } else if (format.equals("CLUSTAL")) { - alignFile = new ClustalFile(source); + alignFile = GenericFileAdapter.getFile("ClustalFile", source); } else if (format.equals("BLC")) { - alignFile = new BLCFile(source); + alignFile = GenericFileAdapter.getFile("BLCFile", source); } else if (format.equals("PIR")) { - alignFile = new PIRFile(source); + alignFile = GenericFileAdapter.getFile("PIRFile", source); } else if (format.equals("PFAM")) { - alignFile = new PfamFile(source); + alignFile = GenericFileAdapter.getFile("PfamFile", source); } else if (format.equals("JnetFile")) { - alignFile = new JPredFile(source); + alignFile = GenericFileAdapter.getFile("JPredFile", source); ((JPredFile) alignFile).removeNonSequences(); } else if (format.equals("PDB")) @@ -406,31 +412,31 @@ public class AppletFormatAdapter } else if (format.equals("STH")) { - alignFile = new StockholmFile(source); + alignFile = GenericFileAdapter.getFile("StockholmFile", source); } else if (format.equals("RNAML")) { - alignFile = new RnamlFile(source); + alignFile = GenericFileAdapter.getFile("RnamlFile", source); } else if (format.equals("SimpleBLAST")) { - alignFile = new SimpleBlastFile(source); + alignFile = GenericFileAdapter.getFile("SimpleBlastFile", source); } - else if (format.equals(PhylipFile.FILE_DESC)) + else if (format.equals(Constants.Phylip_FILE_DESC)) { - alignFile = new PhylipFile(source); + alignFile = GenericFileAdapter.getFile("PhylipFile", source); } else if (format.equals(IdentifyFile.GFF3File)) { - alignFile = new Gff3File(inFile, type); + alignFile = GenericFileAdapter.getFile("Gff3File", inFile, type); } - else if (format.equals(JSONFile.FILE_DESC)) + else if (format.equals(Constants.JSON_FILE_DESC)) { - alignFile = new JSONFile(source); + alignFile = GenericFileAdapter.getFile("JSONFile", source); } - else if (format.equals(HtmlFile.FILE_DESC)) + else if (format.equals(Constants.Html_FILE_DESC)) { - alignFile = new HtmlFile(source); + alignFile = GenericFileAdapter.getFile("HtmlFile", source); } return buildAlignmentFrom(alignFile); @@ -453,7 +459,7 @@ public class AppletFormatAdapter try { // Possible sequence is just residues with no label - alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); + alignFile = GenericFileAdapter.getFile("FastaFile", ">UNKNOWN\n" + inFile, "Paste"); return buildAlignmentFrom(alignFile); } catch (Exception ex) @@ -546,51 +552,51 @@ public class AppletFormatAdapter AlignFile afile = null; if (format.equalsIgnoreCase("FASTA")) { - afile = new FastaFile(); + afile = GenericFileAdapter.getFile("FastaFile"); } else if (format.equalsIgnoreCase("MSF")) { - afile = new MSFfile(); + afile = GenericFileAdapter.getFile("MSFfile"); } else if (format.equalsIgnoreCase("PileUp")) { - afile = new PileUpfile(); + afile = GenericFileAdapter.getFile("PileUpfile"); // BH NOTE LOWER CASE "file" } else if (format.equalsIgnoreCase("CLUSTAL")) { - afile = new ClustalFile(); + afile = GenericFileAdapter.getFile("ClustalFile"); } else if (format.equalsIgnoreCase("BLC")) { - afile = new BLCFile(); + afile = GenericFileAdapter.getFile("BLCFile"); } else if (format.equalsIgnoreCase("PIR")) { - afile = new PIRFile(); + afile = GenericFileAdapter.getFile("PIRFile"); } else if (format.equalsIgnoreCase("PFAM")) { - afile = new PfamFile(); + afile = GenericFileAdapter.getFile("PfamFile"); } else if (format.equalsIgnoreCase("STH")) { - afile = new StockholmFile(alignment); + afile = GenericFileAdapter.getFile("StockholmFile", alignment); } else if (format.equalsIgnoreCase("AMSA")) { - afile = new AMSAFile(alignment); + afile = GenericFileAdapter.getFile("AMSAFile", alignment); } - else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC)) + else if (format.equalsIgnoreCase(Constants.Phylip_FILE_DESC)) { - afile = new PhylipFile(); + afile = GenericFileAdapter.getFile("PhylipFile"); } - else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) + else if (format.equalsIgnoreCase(Constants.JSON_FILE_DESC)) { - afile = new JSONFile(); + afile = GenericFileAdapter.getFile("JSONFile"); } else if (format.equalsIgnoreCase("RNAML")) { - afile = new RnamlFile(); + afile = GenericFileAdapter.getFile("RnamlFile"); } else @@ -644,6 +650,11 @@ public class AppletFormatAdapter return protocol; } + /** + * @j2sIgnore + * + * @param args + */ public static void main(String[] args) { int i = 0;