X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=c5a80e339fd64c383133e23f29f7f159a91bacd1;hb=35ce4609cc8a776b1d85a1f2c2c70aaa106c1a3b;hp=74ca0b9babe0f38c81bcf48e688cf66f34d56d27;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 74ca0b9..c5a80e3 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,14 +20,19 @@ */ package jalview.io; -import jalview.api.AlignViewportI; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignmentViewPanel; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; -import jalview.util.MessageManager; +import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; +import jalview.structure.StructureImportSettings; import java.io.File; +import java.io.IOException; import java.io.InputStream; import java.util.List; @@ -42,89 +47,7 @@ import java.util.List; */ 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, "HTML" }; // , - // "SimpleBLAST" - // }; - - /** - * 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 }; - - /** - * 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", PhylipFile.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", - PhylipFile.FILE_DESC, "Jalview" }; - - /** - * 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", - "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, - "html" }; // ".blast" - - /** - * 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", "Jalview", - "Stockholm", "RNAML", PhylipFile.FILE_DESC, "HTML" };// , - - // "SimpleBLAST" - // }; - - 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); - - /** - * - * @param els - * @return grammatically correct(ish) list consisting of els elements. - */ - public static String prettyPrint(String[] els) - { - StringBuffer list = new StringBuffer(); - for (int i = 0, iSize = els.length - 1; i < iSize; i++) - { - list.append(els[i]); - list.append(", "); - } - list.append(" and " + els[els.length - 1] + "."); - return list.toString(); - } - - public static String FILE = "File"; - - public static String URL = "URL"; - - public static String PASTE = "Paste"; - - public static String CLASSLOADER = "ClassLoader"; + private AlignmentViewPanel viewpanel; /** * add jalview-derived non-secondary structure annotation from PDB structure @@ -141,7 +64,7 @@ public class AppletFormatAdapter */ boolean serviceSecondaryStruct = false; - AlignFile afile = null; + private AlignmentFileReaderI alignFile = null; String inFile; @@ -150,53 +73,63 @@ public class AppletFormatAdapter */ protected String newline = System.getProperty("line.separator"); - public void setNewlineString(String nl) + private AlignExportSettingI exportSettings; + + public static String INVALID_CHARACTERS = "Contains invalid characters"; + + /** + * Returns an error message with a list of supported readable file formats + * + * @return + */ + public static String getSupportedFormats() + { + return "Formats currently supported are\n" + + prettyPrint(FileFormats.getInstance().getReadableFormats()); + } + public AppletFormatAdapter() { - newline = nl; } - public String getNewlineString() + public AppletFormatAdapter(AlignmentViewPanel viewpanel) { - return newline; + this.viewpanel = viewpanel; } - /** - * check that this format is valid for reading - * - * @param format - * a format string to be compared with READABLE_FORMATS - * @return true if format is readable - */ - public static final boolean isValidFormat(String format) + public AppletFormatAdapter(AlignmentViewPanel alignPanel, + AlignExportSettingI settings) { - return isValidFormat(format, false); + viewpanel = alignPanel; + exportSettings = settings; } /** - * validate format is valid for IO - * - * @param format - * a format string to be compared with either READABLE_FORMATS or - * WRITEABLE_FORMATS - * @param forwriting - * when true, format is checked for containment in WRITEABLE_FORMATS - * @return true if format is valid + * Formats a grammatically correct(ish) list consisting of the given objects + * + * @param things + * @return */ - public static final boolean isValidFormat(String format, - boolean forwriting) + public static String prettyPrint(List things) { - boolean valid = false; - String[] format_list = (forwriting) ? WRITEABLE_FORMATS - : READABLE_FORMATS; - for (String element : format_list) + StringBuffer list = new StringBuffer(); + for (int i = 0, iSize = things.size() - 1; i < iSize; i++) { - if (element.equalsIgnoreCase(format)) - { - return true; - } + list.append(things.get(i).toString()); + list.append(", "); } + // could i18n 'and' here + list.append(" and " + things.get(things.size() - 1).toString() + "."); + return list.toString(); + } - return valid; + public void setNewlineString(String nl) + { + newline = nl; + } + + public String getNewlineString() + { + return newline; } /** @@ -204,124 +137,87 @@ public class AppletFormatAdapter * * @param inFile * data/data location - * @param type + * @param sourceType * type of datasource - * @param format - * File format of data provided by datasource + * @param fileFormat * - * @return DOCUMENT ME! + * @return */ - public Alignment readFile(String inFile, String type, String format) - throws java.io.IOException + public AlignmentI readFile(String file, DataSourceType sourceType, + FileFormatI fileFormat) throws IOException { - // TODO: generalise mapping between format string and io. class instances - // using Constructor.invoke reflection - this.inFile = inFile; + this.inFile = file; try { - if (format.equals("FASTA")) - { - afile = new FastaFile(inFile, type); - } - else if (format.equals("MSF")) - { - afile = new MSFfile(inFile, type); - } - else if (format.equals("PileUp")) - { - afile = new PileUpfile(inFile, type); - } - else if (format.equals("CLUSTAL")) - { - afile = new ClustalFile(inFile, type); - } - else if (format.equals("BLC")) - { - afile = new BLCFile(inFile, type); - } - else if (format.equals("PIR")) - { - afile = new PIRFile(inFile, type); - } - else if (format.equals("PFAM")) - { - afile = new PfamFile(inFile, type); - } - else if (format.equals("JnetFile")) - { - afile = new JPredFile(inFile, type); - ((JPredFile) afile).removeNonSequences(); - } - else if (format.equals("PDB")) - { - afile = new MCview.PDBfile(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, inFile, type); - // Uncomment to test Jmol data based PDB processing: JAL-1213 - // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type); - } - else if (format.equals("STH")) - { - afile = new StockholmFile(inFile, type); - } - else if (format.equals("SimpleBLAST")) - { - afile = new SimpleBlastFile(inFile, type); - } - else if (format.equals(PhylipFile.FILE_DESC)) - { - afile = new PhylipFile(inFile, type); + if (fileFormat.isStructureFile()) + { + String structureParser = StructureImportSettings + .getDefaultPDBFileParser(); + boolean isParseWithJMOL = structureParser.equalsIgnoreCase( + StructureImportSettings.StructureParser.JMOL_PARSER + .toString()); + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + if (isParseWithJMOL) + { + alignFile = new JmolParser(inFile, sourceType); + } + else + { + // todo is MCview parsing obsolete yet? JAL-2120 + StructureImportSettings.setShowSeqFeatures(true); + alignFile = new MCview.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, inFile, + sourceType); + } + ((StructureFile) alignFile).setDbRefType(FileFormat.PDB + .equals(fileFormat) ? Type.PDB : Type.MMCIF); } - // else if (format.equals(HtmlFile.FILE_DESC)) - // { - // afile = new HtmlFile(inFile, type); - // } - else if (format.equals("RNAML")) + else { - afile = new RnamlFile(inFile, type); + // alignFile = fileFormat.getAlignmentFile(inFile, sourceType); + alignFile = fileFormat.getReader(new FileParse(inFile, + sourceType)); } - - Alignment al = new Alignment(afile.getSeqsAsArray()); - - afile.addAnnotations(al); - - return al; + return buildAlignmentFromFile(); } catch (Exception e) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" + format - + "' reader.\n" + e); + System.err.println("Failed to read alignment using the '" + + fileFormat + "' reader.\n" + e); if (e.getMessage() != null && e.getMessage().startsWith(INVALID_CHARACTERS)) { - throw new java.io.IOException(e.getMessage()); + throw new IOException(e.getMessage()); } // Finally test if the user has pasted just the sequence, no id - if (type.equalsIgnoreCase("Paste")) + if (sourceType == DataSourceType.PASTE) { try { // Possible sequence is just residues with no label - afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); - Alignment al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - return al; + alignFile = new FastaFile(">UNKNOWN\n" + inFile, + DataSourceType.PASTE); + return buildAlignmentFromFile(); } catch (Exception ex) { if (ex.toString().startsWith(INVALID_CHARACTERS)) { - throw new java.io.IOException(e.getMessage()); + throw new IOException(e.getMessage()); } ex.printStackTrace(); } } - - // If we get to this stage, the format was not supported - throw new java.io.IOException(SUPPORTED_FORMATS); + if (FileFormat.Html.equals(fileFormat)) + { + throw new IOException(e.getMessage()); + } } + throw new FileFormatException(getSupportedFormats()); } /** @@ -332,82 +228,40 @@ public class AppletFormatAdapter * @param format * File format of data that will be provided by datasource * - * @return DOCUMENT ME! + * @return */ - public AlignmentI readFromFile(FileParse source, String format) - throws java.io.IOException + public AlignmentI readFromFile(FileParse source, FileFormatI format) + throws IOException { - // TODO: generalise mapping between format string and io. class instances - // using Constructor.invoke reflection - // This is exactly the same as the readFile method except we substitute - // 'inFile, type' with 'source' this.inFile = source.getInFile(); - String type = source.type; + DataSourceType type = source.dataSourceType; try { - if (format.equals("FASTA")) - { - afile = new FastaFile(source); - } - else if (format.equals("MSF")) + if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format)) { - afile = new MSFfile(source); - } - else if (format.equals("PileUp")) - { - afile = new PileUpfile(source); - } - else if (format.equals("CLUSTAL")) - { - afile = new ClustalFile(source); - } - else if (format.equals("BLC")) - { - afile = new BLCFile(source); - } - else if (format.equals("PIR")) - { - afile = new PIRFile(source); - } - else if (format.equals("PFAM")) - { - afile = new PfamFile(source); - } - else if (format.equals("JnetFile")) - { - afile = new JPredFile(source); - ((JPredFile) afile).removeNonSequences(); - } - else if (format.equals("PDB")) - { - afile = new MCview.PDBfile(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, source); - } - else if (format.equals("STH")) - { - afile = new StockholmFile(source); - } - else if (format.equals("RNAML")) - { - afile = new RnamlFile(source); - } - else if (format.equals("SimpleBLAST")) - { - afile = new SimpleBlastFile(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 if (format.equals(PhylipFile.FILE_DESC)) + else { - afile = new PhylipFile(source); + alignFile = format.getReader(source); } - // else if (format.equals(HtmlFile.FILE_DESC)) - // { - // afile = new HtmlFile(source); - // } - Alignment al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); + return buildAlignmentFromFile(); - return al; } catch (Exception e) { e.printStackTrace(); @@ -417,25 +271,24 @@ public class AppletFormatAdapter if (e.getMessage() != null && e.getMessage().startsWith(INVALID_CHARACTERS)) { - throw new java.io.IOException(e.getMessage()); + throw new FileFormatException(e.getMessage()); } // Finally test if the user has pasted just the sequence, no id - if (type.equalsIgnoreCase("Paste")) + if (type == DataSourceType.PASTE) { try { // Possible sequence is just residues with no label - afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); - Alignment al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - return al; + alignFile = new FastaFile(">UNKNOWN\n" + inFile, + DataSourceType.PASTE); + return buildAlignmentFromFile(); } catch (Exception ex) { if (ex.toString().startsWith(INVALID_CHARACTERS)) { - throw new java.io.IOException(e.getMessage()); + throw new IOException(e.getMessage()); } ex.printStackTrace(); @@ -443,27 +296,48 @@ public class AppletFormatAdapter } // If we get to this stage, the format was not supported - throw new java.io.IOException(SUPPORTED_FORMATS); + throw new FileFormatException(getSupportedFormats()); } } + /** + * boilerplate method to handle data from an AlignFile and construct a new + * alignment or import to an existing alignment + * + * @return AlignmentI instance ready to pass to a UI constructor + */ + private AlignmentI buildAlignmentFromFile() + { + // Standard boilerplate for creating alignment from parser + // alignFile.configureForView(viewpanel); + + AlignmentI al = new Alignment(alignFile.getSeqsAsArray()); + + alignFile.addAnnotations(al); + + alignFile.addGroups(al); + + return al; + } /** * create an alignment flatfile from a Jalview alignment view + * * @param format * @param jvsuffix * @param av * @param selectedOnly * @return flatfile in a string */ - public String formatSequences(String format, boolean jvsuffix, - AlignViewportI av, boolean selectedOnly) + public String formatSequences(FileFormatI format, boolean jvsuffix, + AlignmentViewPanel ap, boolean selectedOnly) { - AlignmentView selvew = av.getAlignmentView(selectedOnly, false); - AlignmentI aselview = selvew.getVisibleAlignment(av + AlignmentView selvew = ap.getAlignViewport().getAlignmentView( + selectedOnly, false); + AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport() .getGapCharacter()); - List ala = (av + List ala = (ap.getAlignViewport() .getVisibleAlignmentAnnotation(selectedOnly)); if (ala != null) { @@ -472,7 +346,7 @@ public class AppletFormatAdapter aselview.addAnnotation(aa); } } - + viewpanel = ap; return formatSequences(format, aselview, jvsuffix); } @@ -491,72 +365,31 @@ public class AppletFormatAdapter * * @return alignment flat file contents */ - public String formatSequences(String format, AlignmentI alignment, + public String formatSequences(FileFormatI format, AlignmentI alignment, boolean jvsuffix) { try { - AlignFile afile = null; + AlignmentFileWriterI afile = format.getWriter(alignment); - if (format.equalsIgnoreCase("FASTA")) - { - afile = new FastaFile(); - } - else if (format.equalsIgnoreCase("MSF")) - { - afile = new MSFfile(); - } - else if (format.equalsIgnoreCase("PileUp")) - { - afile = new PileUpfile(); - } - else if (format.equalsIgnoreCase("CLUSTAL")) - { - afile = new ClustalFile(); - } - else if (format.equalsIgnoreCase("BLC")) - { - afile = new BLCFile(); - } - else if (format.equalsIgnoreCase("PIR")) - { - afile = new PIRFile(); - } - else if (format.equalsIgnoreCase("PFAM")) - { - afile = new PfamFile(); - } - else if (format.equalsIgnoreCase("STH")) - { - afile = new StockholmFile(alignment); - } - else if (format.equalsIgnoreCase("AMSA")) - { - afile = new AMSAFile(alignment); - } - else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC)) - { - afile = new PhylipFile(); - } - // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC)) - // { - // afile = new HtmlFile(); - // } - else if (format.equalsIgnoreCase("RNAML")) + afile.setNewlineString(newline); + afile.setExportSettings(exportSettings); + afile.configureForView(viewpanel); + + // check whether we were given a specific alignment to export, rather than + // the one in the viewpanel + SequenceI[] seqs = null; + if (viewpanel == null || viewpanel.getAlignment() == null + || viewpanel.getAlignment() != alignment) { - afile = new RnamlFile(); + seqs = alignment.getSequencesArray(); } - else { - throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string")); + seqs = viewpanel.getAlignment().getSequencesArray(); } - afile.setNewlineString(newline); - afile.addJVSuffix(jvsuffix); - afile.setSeqs(alignment.getSequencesArray()); - - String afileresp = afile.print(); + String afileresp = afile.print(seqs, jvsuffix); if (afile.hasWarningMessage()) { System.err.println("Warning raised when writing as " + format @@ -565,7 +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(); } @@ -573,14 +407,14 @@ public class AppletFormatAdapter return null; } - public static String checkProtocol(String file) + public static DataSourceType checkProtocol(String file) { - String protocol = FILE; + DataSourceType protocol = DataSourceType.FILE; String ft = file.toLowerCase().trim(); if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0 || ft.indexOf("file:") == 0) { - protocol = URL; + protocol = DataSourceType.URL; } return protocol; } @@ -601,8 +435,10 @@ public class AppletFormatAdapter System.gc(); long memf = -r.totalMemory() + r.freeMemory(); long t1 = -System.currentTimeMillis(); - Alignment al = afa.readFile(args[i], FILE, - new IdentifyFile().Identify(args[i], 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(); @@ -613,11 +449,11 @@ public class AppletFormatAdapter try { System.out.println(new AppletFormatAdapter().formatSequences( - "FASTA", al, true)); + FileFormat.Fasta, al, true)); } 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); } } @@ -627,8 +463,8 @@ 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 @@ -652,16 +488,17 @@ public class AppletFormatAdapter * @param format * @return protocol that yields the data parsable as the given type */ - public static String resolveProtocol(String file, String format) + public static DataSourceType resolveProtocol(String file, + FileFormatI format) { return resolveProtocol(file, format, false); } - public static String resolveProtocol(String file, String format, - boolean debug) + public static DataSourceType resolveProtocol(String file, + FileFormatI format, boolean debug) { // TODO: test thoroughly! - String protocol = null; + DataSourceType protocol = null; if (debug) { System.out.println("resolving datasource started with:\n>>file\n" @@ -685,26 +522,25 @@ public class AppletFormatAdapter System.err.println("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader."); } - ; if (rtn) { - protocol = AppletFormatAdapter.CLASSLOADER; + protocol = DataSourceType.CLASSLOADER; } } catch (Exception ex) { System.err - .println("Exception checking resources: " + file + " " + ex); + .println("Exception checking resources: " + file + " " + ex); } if (file.indexOf("://") > -1) { - protocol = AppletFormatAdapter.URL; + protocol = DataSourceType.URL; } else { // skipping codebase prepend check. - protocol = AppletFormatAdapter.FILE; + protocol = DataSourceType.FILE; } FileParse fp = null; try @@ -740,7 +576,7 @@ public class AppletFormatAdapter { System.out.println("Accessing as paste."); } - protocol = AppletFormatAdapter.PASTE; + protocol = DataSourceType.PASTE; fp = null; try { @@ -760,7 +596,7 @@ public class AppletFormatAdapter { return null; } - if (format == null || format.length() == 0) + if (format == null) { return protocol; } @@ -768,8 +604,7 @@ public class AppletFormatAdapter { try { - String idformat = new jalview.io.IdentifyFile().Identify(file, - protocol); + FileFormatI idformat = new IdentifyFile().identify(file, protocol); if (idformat == null) { if (debug) @@ -796,7 +631,7 @@ 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; @@ -808,10 +643,13 @@ public class AppletFormatAdapter System.err.println("File deemed not accessible via " + protocol); e.printStackTrace(); } - ; - } } return null; } + + public AlignmentFileReaderI getAlignFile() + { + return alignFile; + } }