X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=45d65d61065ddaef9c6f32f21cabbf1ca8d7ca57;hb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;hp=0c99d260deb10bb621ce4d9c3aaa01821ab93a47;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 0c99d26..45d65d6 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -26,7 +26,9 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; +import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; import java.io.File; @@ -73,61 +75,10 @@ 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" }; - - /** - * 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", - "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(READABLE_FORMATS); + + prettyPrint(FileFormat.getReadableFormats()); public AppletFormatAdapter() { @@ -146,19 +97,21 @@ public class AppletFormatAdapter } /** - * - * @param els - * @return grammatically correct(ish) list consisting of els elements. + * Formats a grammatically correct(ish) list consisting of the given objects + * + * @param things + * @return */ - public static String prettyPrint(String[] els) + public static String prettyPrint(List things) { StringBuffer list = new StringBuffer(); - for (int i = 0, iSize = els.length - 1; i < iSize; i++) + for (int i = 0, iSize = things.size() - 1; i < iSize; i++) { - list.append(els[i]); + list.append(things.get(i).toString()); list.append(", "); } - list.append(" and " + els[els.length - 1] + "."); + // could i18n 'and' here + list.append(" and " + things.get(things.size() - 1).toString() + "."); return list.toString(); } @@ -189,39 +142,40 @@ public class AppletFormatAdapter this.inFile = file; try { - if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif) + if (fileFormat.isStructureFile()) { + String structureParser = StructureImportSettings + .getDefaultPDBFileParser(); + boolean isParseWithJMOL = structureParser.equalsIgnoreCase( + StructureImportSettings.StructureParser.JMOL_PARSER + .toString()); StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); - alignFile = fileFormat.getAlignmentFile(inFile, sourceType); + if (isParseWithJMOL) + { + alignFile = new JmolParser(inFile, sourceType); + } + else + { + // todo is MCview parsing obsolete yet? + StructureImportSettings.setShowSeqFeatures(true); + alignFile = new MCview.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, inFile, + sourceType); + } + ((StructureFile) alignFile).setDbRefType(FileFormat.PDB + .equals(fileFormat) ? Type.PDB : Type.MMCIF); } else { alignFile = fileFormat.getAlignmentFile(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) { e.printStackTrace(); System.err.println("Failed to read alignment using the '" - + fileFormat - + "' reader.\n" + e); + + fileFormat + "' reader.\n" + e); if (e.getMessage() != null && e.getMessage().startsWith(INVALID_CHARACTERS)) @@ -249,7 +203,7 @@ public class AppletFormatAdapter ex.printStackTrace(); } } - if (fileFormat == FileFormat.Html) + if (FileFormat.Html.equals(fileFormat)) { throw new IOException(e.getMessage()); } @@ -274,11 +228,23 @@ public class AppletFormatAdapter DataSourceType type = source.dataSourceType; try { - if (format == FileFormat.PDB || format == FileFormat.MMCif) + if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format)) { - StructureImportSettings.addSettings(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct); - alignFile = format.getAlignmentFile(source); + // TODO obtain config value from preference settings + boolean isParseWithJMOL = false; + if (isParseWithJMOL) + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + alignFile = new JmolParser(source); + } + else + { + StructureImportSettings.setShowSeqFeatures(true); + alignFile = new MCview.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, source); + } + ((StructureFile) alignFile).setDbRefType(Type.PDB); } else { @@ -395,7 +361,7 @@ public class AppletFormatAdapter { try { - AlignmentFileI afile = format.getAlignmentFile(); + AlignmentFileI afile = format.getAlignmentFile(alignment); afile.setNewlineString(newline); afile.setExportSettings(exportSettings); @@ -628,8 +594,7 @@ public class AppletFormatAdapter { try { - FileFormatI idformat = new IdentifyFile().identify(file, - protocol); + FileFormatI idformat = new IdentifyFile().identify(file, protocol); if (idformat == null) { if (debug)