X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=00fcb9c39c598d12dc6d285b5b9720bb080ba129;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=0c99d260deb10bb621ce4d9c3aaa01821ab93a47;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 0c99d26..00fcb9c 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -20,14 +20,19 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; +import java.util.Locale; + +import jalview.api.AlignExportSettingsI; import jalview.api.AlignmentViewPanel; 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 jalview.util.Platform; import java.io.File; import java.io.IOException; @@ -62,7 +67,7 @@ public class AppletFormatAdapter */ boolean serviceSecondaryStruct = false; - private AlignmentFileI alignFile = null; + private AlignmentFileReaderI alignFile = null; String inFile; @@ -71,63 +76,22 @@ public class AppletFormatAdapter */ protected String newline = System.getProperty("line.separator"); - 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" }; + private AlignExportSettingsI exportSettings; - /** - * 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" }; + private File selectedFile; - /** - * 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(READABLE_FORMATS); + public static String getSupportedFormats() + { + return "Formats currently supported are\n" + + prettyPrint(FileFormats.getInstance().getReadableFormats()); + } public AppletFormatAdapter() { @@ -139,26 +103,28 @@ public class AppletFormatAdapter } public AppletFormatAdapter(AlignmentViewPanel alignPanel, - AlignExportSettingI settings) + AlignExportSettingsI settings) { viewpanel = alignPanel; exportSettings = settings; } /** - * - * @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(); } @@ -186,41 +152,63 @@ public class AppletFormatAdapter public AlignmentI readFile(String file, DataSourceType sourceType, FileFormatI fileFormat) throws IOException { + return readFile(null, file, sourceType, fileFormat); + } + + public AlignmentI readFile(File selectedFile, String file, + DataSourceType sourceType, FileFormatI fileFormat) + throws IOException + { + + this.selectedFile = selectedFile; + if (selectedFile != null) + { + this.inFile = selectedFile.getPath(); + } 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) + { + // needs a File option + alignFile = new JmolParser( + selectedFile == null ? inFile : selectedFile, sourceType); + } + else + { + // todo is mc_view parsing obsolete yet? JAL-2120 + StructureImportSettings.setShowSeqFeatures(true); + alignFile = new mc_view.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, inFile, + sourceType); + } + ((StructureFile) alignFile).setDbRefType( + FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF); + } + else if (selectedFile != null) + { + alignFile = fileFormat + .getReader(new FileParse(selectedFile, sourceType)); } 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) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" - + fileFormat + System.err.println("Failed to read alignment using the '" + fileFormat + "' reader.\n" + e); if (e.getMessage() != null @@ -249,12 +237,12 @@ 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()); } /** @@ -274,15 +262,27 @@ 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 mc_view.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, source); + } + ((StructureFile) alignFile).setDbRefType(Type.PDB); } else { - alignFile = format.getAlignmentFile(source); + alignFile = format.getReader(source); } return buildAlignmentFromFile(); @@ -321,7 +321,7 @@ public class AppletFormatAdapter } // If we get to this stage, the format was not supported - throw new FileFormatException(SUPPORTED_FORMATS); + throw new FileFormatException(getSupportedFormats()); } } @@ -358,10 +358,10 @@ public class AppletFormatAdapter AlignmentViewPanel ap, boolean selectedOnly) { - AlignmentView selvew = ap.getAlignViewport().getAlignmentView( - selectedOnly, false); - AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport() - .getGapCharacter()); + AlignmentView selvew = ap.getAlignViewport() + .getAlignmentView(selectedOnly, false); + AlignmentI aselview = selvew + .getVisibleAlignment(ap.getAlignViewport().getGapCharacter()); List ala = (ap.getAlignViewport() .getVisibleAlignmentAnnotation(selectedOnly)); if (ala != null) @@ -395,7 +395,7 @@ public class AppletFormatAdapter { try { - AlignmentFileI afile = format.getAlignmentFile(); + AlignmentFileWriterI afile = format.getWriter(alignment); afile.setNewlineString(newline); afile.setExportSettings(exportSettings); @@ -423,26 +423,54 @@ public class AppletFormatAdapter return afileresp; } catch (Exception e) { - System.err.println("Failed to write alignment as a '" + format - + "' file\n"); + System.err.println("Failed to write alignment as a '" + + format.getName() + "' file\n"); e.printStackTrace(); } return null; } - public static DataSourceType checkProtocol(String file) + /** + * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input + * data + * + * BH 2018 allows File or String, and can return RELATIVE_URL + * + * @param dataObject + * File or String + * @return the protocol for the input data + */ + public static DataSourceType checkProtocol(Object dataObject) { - DataSourceType protocol = DataSourceType.FILE; - String ft = file.toLowerCase().trim(); + if (dataObject instanceof File) + { + return DataSourceType.FILE; + } + + String data = dataObject.toString(); + DataSourceType protocol = DataSourceType.PASTE; + String ft = data.toLowerCase(Locale.ROOT).trim(); if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0 || ft.indexOf("file:") == 0) { protocol = DataSourceType.URL; } + else if (Platform.isJS()) + { + protocol = DataSourceType.RELATIVE_URL; + } + else if (new File(data).exists()) + { + protocol = DataSourceType.FILE; + } return protocol; } + /** + * @param args + * @j2sIgnore + */ public static void main(String[] args) { int i = 0; @@ -459,10 +487,9 @@ public class AppletFormatAdapter System.gc(); long memf = -r.totalMemory() + r.freeMemory(); long t1 = -System.currentTimeMillis(); - AlignmentI al = afa - .readFile(args[i], DataSourceType.FILE, - new IdentifyFile().identify(args[i], - DataSourceType.FILE)); + AlignmentI al = afa.readFile(args[i], DataSourceType.FILE, + new IdentifyFile().identify(args[i], + DataSourceType.FILE)); t1 += System.currentTimeMillis(); System.gc(); memf += r.totalMemory() - r.freeMemory(); @@ -472,12 +499,12 @@ public class AppletFormatAdapter + " sequences and " + al.getWidth() + " columns."); try { - System.out.println(new AppletFormatAdapter().formatSequences( - FileFormat.Fasta, al, true)); + System.out.println(new AppletFormatAdapter() + .formatSequences(FileFormat.Fasta, al, true)); } catch (Exception e) { - System.err - .println("Couln't format the alignment for output as a FASTA file."); + System.err.println( + "Couln't format the alignment for output as a FASTA file."); e.printStackTrace(System.err); } } @@ -486,8 +513,8 @@ public class AppletFormatAdapter System.out.println("Couldn't read alignment"); } System.out.println("Read took " + (t1 / 1000.0) + " seconds."); - System.out - .println("Difference between free memory now and before is " + System.out.println( + "Difference between free memory now and before is " + (memf / (1024.0 * 1024.0) * 1.0) + " MB"); } catch (Exception e) { @@ -571,8 +598,8 @@ public class AppletFormatAdapter { if (debug) { - System.out.println("Trying to get contents of resource as " - + protocol + ":"); + System.out.println( + "Trying to get contents of resource as " + protocol + ":"); } fp = new FileParse(file, protocol); if (!fp.isValid()) @@ -628,8 +655,7 @@ public class AppletFormatAdapter { try { - FileFormatI idformat = new IdentifyFile().identify(file, - protocol); + FileFormatI idformat = new IdentifyFile().identify(file, protocol); if (idformat == null) { if (debug) @@ -673,7 +699,7 @@ public class AppletFormatAdapter return null; } - public AlignmentFileI getAlignFile() + public AlignmentFileReaderI getAlignFile() { return alignFile; }