X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=907ff462a39f6d1ad14f5d7874128aa01120bb22;hb=c4b90e7ff57436d6bb96d316eed24c887b241f4d;hp=e0a607beae7d4bbb51d4bc4c9de6eeb59ed45c50;hpb=74b531f56bbaad5c5e06a4744980256fe8110923;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index e0a607b..907ff46 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -64,7 +64,7 @@ public class AppletFormatAdapter */ boolean serviceSecondaryStruct = false; - private AlignmentFileI alignFile = null; + private AlignmentFileReaderI alignFile = null; String inFile; @@ -75,63 +75,18 @@ public class AppletFormatAdapter private AlignExportSettingI exportSettings; - /** - * 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", "PHYLIP", "JSON", - // IdentifyFile.FeaturesFile, "HTML", "mmCIF" }; - - /** - * 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", "phy", "json", ".gff2,gff3", "jar,jvp", - // "html", "cif" }; - - // - // /** - // * 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", - // "PHYLIP", "JSON", IdentifyFile.FeaturesFile, - // "Jalview", HtmlFile.FILE_DESC, "mmCIF" }; - - /** - * 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", - // "PHYLIP", "JSON" }; - - /** - * 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", - // "sto,stk", "phy", "json", "jvp" }; + public static String INVALID_CHARACTERS = "Contains invalid characters"; /** - * List of writable formats by the application. Order must correspond with the - * WRITABLE_EXTENSIONS list of formats. + * Returns an error message with a list of supported readable file formats + * + * @return */ - // public static final String[] WRITABLE_FNAMES = new String[] { "Fasta", - // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP", - // "JSON", "Jalview" }; - - public static String INVALID_CHARACTERS = "Contains invalid characters"; - - // TODO: make these messages dynamic - public static String SUPPORTED_FORMATS = "Formats currently supported are\n" - + prettyPrint(FileFormat.getReadableFormats()); - + public static String getSupportedFormats() + { + return "Formats currently supported are\n" + + prettyPrint(FileFormats.getInstance().getReadableFormats()); + } public AppletFormatAdapter() { } @@ -194,55 +149,36 @@ public class AppletFormatAdapter this.inFile = file; try { - if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif) + if (fileFormat.isStructureFile()) { - // TODO obtain config value from preference settings. - // Set value to 'true' to test PDB processing with Jmol: JAL-1213 - boolean isParseWithJMOL = StructureImportSettings - .getDefaultPDBFileParser().equalsIgnoreCase( + String structureParser = StructureImportSettings + .getDefaultPDBFileParser(); + boolean isParseWithJMOL = structureParser.equalsIgnoreCase( StructureImportSettings.StructureParser.JMOL_PARSER .toString()); + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); if (isParseWithJMOL) { - StructureImportSettings.addSettings(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct); - alignFile = new JmolParser(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, inFile, - sourceType); + alignFile = new JmolParser(inFile, sourceType); } else { - StructureImportSettings.addSettings(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct); + // todo is MCview parsing obsolete yet? JAL-2120 StructureImportSettings.setShowSeqFeatures(true); alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, sourceType); } - ((StructureFile) alignFile) - .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB - : Type.MMCIF); + ((StructureFile) alignFile).setDbRefType(FileFormat.PDB + .equals(fileFormat) ? Type.PDB : Type.MMCIF); } else { - alignFile = fileFormat.getAlignmentFile(inFile, sourceType); + // alignFile = fileFormat.getAlignmentFile(inFile, sourceType); + alignFile = fileFormat.getReader(new FileParse(inFile, + sourceType)); } - // new FastaFile(inFile, sourceType); - // new MSFfile(inFile, sourceType); - // new PileUpfile(inFile, sourceType); - // new ClustalFile(inFile, sourceType); - // new BLCFile(inFile, sourceType); - // new PIRFile(inFile, sourceType); - // new PfamFile(inFile, sourceType); - // alignFile = new JPredFile(inFile, sourceType); - // ((JPredFile) alignFile).removeNonSequences(); - // new StockholmFile(inFile, sourceType); - // new SimpleBlastFile(inFile, sourceType); - // new PhylipFile(inFile, sourceType); - // new JSONFile(inFile, sourceType); - // new HtmlFile(inFile, sourceType); - // new RnamlFile(inFile, sourceType); - // alignFile = new FeaturesFile(true, inFile, sourceType); return buildAlignmentFromFile(); } catch (Exception e) { @@ -276,12 +212,12 @@ public class AppletFormatAdapter ex.printStackTrace(); } } - if (fileFormat == FileFormat.Html) + if (FileFormat.Html.equals(fileFormat)) { throw new IOException(e.getMessage()); } } - throw new FileFormatException(SUPPORTED_FORMATS); + throw new FileFormatException(getSupportedFormats()); } /** @@ -301,7 +237,7 @@ public class AppletFormatAdapter DataSourceType type = source.dataSourceType; try { - if (format == FileFormat.PDB || format == FileFormat.MMCif) + if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format)) { // TODO obtain config value from preference settings boolean isParseWithJMOL = false; @@ -309,8 +245,7 @@ public class AppletFormatAdapter { StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); - alignFile = new JmolParser(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, source); + alignFile = new JmolParser(source); } else { @@ -322,7 +257,7 @@ public class AppletFormatAdapter } else { - alignFile = format.getAlignmentFile(source); + alignFile = format.getReader(source); } return buildAlignmentFromFile(); @@ -361,7 +296,7 @@ public class AppletFormatAdapter } // If we get to this stage, the format was not supported - throw new FileFormatException(SUPPORTED_FORMATS); + throw new FileFormatException(getSupportedFormats()); } } @@ -435,7 +370,7 @@ public class AppletFormatAdapter { try { - AlignmentFileI afile = format.getAlignmentFile(); + AlignmentFileWriterI afile = format.getWriter(alignment); afile.setNewlineString(newline); afile.setExportSettings(exportSettings); @@ -463,7 +398,8 @@ public class AppletFormatAdapter return afileresp; } catch (Exception e) { - System.err.println("Failed to write alignment as a '" + format + System.err.println("Failed to write alignment as a '" + + format.getName() + "' file\n"); e.printStackTrace(); } @@ -471,15 +407,26 @@ public class AppletFormatAdapter return null; } - public static DataSourceType checkProtocol(String file) + /** + * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input + * data + * + * @param data + * @return the protocol for the input data + */ + public static DataSourceType checkProtocol(String data) { - DataSourceType protocol = DataSourceType.FILE; - String ft = file.toLowerCase().trim(); + DataSourceType protocol = DataSourceType.PASTE; + String ft = data.toLowerCase().trim(); if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0 || ft.indexOf("file:") == 0) { protocol = DataSourceType.URL; } + else if (new File(data).exists()) + { + protocol = DataSourceType.FILE; + } return protocol; } @@ -712,7 +659,7 @@ public class AppletFormatAdapter return null; } - public AlignmentFileI getAlignFile() + public AlignmentFileReaderI getAlignFile() { return alignFile; }