X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=55bb03db516eaea6fc82b00b16cd61739778ec2a;hb=ccc31f21ed36c2e43b5a1b450846284151c680bb;hp=02de02e0580939ed9626b62d3e1617ae0bd4d6a6;hpb=72738726bce0733f652a5dbcc9db7c5a13bc2d80;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 02de02e..55bb03d 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -26,9 +26,12 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; +import jalview.datamodel.PDBEntry.Type; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; import java.io.File; +import java.io.IOException; import java.io.InputStream; import java.util.List; @@ -82,52 +85,51 @@ 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, JSONFile.FILE_DESC, IdentifyFile.GFF3File, - "HTML" }; + 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.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", + 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, - ".gff2,gff3", - "jar,jvp", HtmlFile.FILE_EXT }; + ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT, "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", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview", - HtmlFile.FILE_DESC }; + public static final String[] READABLE_FNAMES = new String[] { "Fasta", + "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML", + PhylipFile.FILE_DESC, JSONFile.FILE_DESC, 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", PhylipFile.FILE_DESC, JSONFile.FILE_DESC }; + public static final String[] WRITEABLE_FORMATS = new String[] { "BLC", + "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH", + PhylipFile.FILE_DESC, JSONFile.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", + 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" }; /** * 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", + public static final String[] WRITABLE_FNAMES = new String[] { "Fasta", + "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -169,7 +171,6 @@ public class AppletFormatAdapter return list.toString(); } - public void setNewlineString(String nl) { newline = nl; @@ -278,10 +279,38 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - alignFile = new MCview.PDBfile(annotFromStructure, + // TODO obtain config value from preference settings. + // Set value to 'true' to test PDB processing with Jmol: JAL-1213 + boolean isParseWithJMOL = StructureImportSettings + .getDefaultPDBFileParser().equalsIgnoreCase( + StructureImportSettings.StructureParser.JMOL_PARSER + .toString()); + if (isParseWithJMOL) + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, inFile, + type); + } + else + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + StructureImportSettings.setShowSeqFeatures(true); + alignFile = new MCview.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, inFile, + type); + } + ((StructureFile) alignFile).setDbRefType(format); + } + else if (format.equalsIgnoreCase("mmCIF")) + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, type); - // Uncomment to test Jmol data based PDB processing: JAL-1213 - // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type); + ((StructureFile) alignFile).setDbRefType(format); } else if (format.equals("STH")) { @@ -307,9 +336,9 @@ public class AppletFormatAdapter { alignFile = new RnamlFile(inFile, type); } - else if (format.equals(IdentifyFile.GFF3File)) + else if (format.equals(IdentifyFile.FeaturesFile)) { - alignFile = new Gff3File(inFile, type); + alignFile = new FeaturesFile(true, inFile, type); } return buildAlignmentFrom(alignFile); } catch (Exception e) @@ -343,7 +372,10 @@ public class AppletFormatAdapter ex.printStackTrace(); } } - + if (format.equalsIgnoreCase("HTML")) + { + throw new IOException(e.getMessage()); + } // If we get to this stage, the format was not supported throw new java.io.IOException(SUPPORTED_FORMATS); } @@ -405,8 +437,30 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - alignFile = new MCview.PDBfile(annotFromStructure, + // TODO obtain config value from preference settings + boolean isParseWithJMOL = false; + if (isParseWithJMOL) + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, source); + } + else + { + StructureImportSettings.setShowSeqFeatures(true); + alignFile = new MCview.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, source); + } + ((StructureFile) alignFile).setDbRefType(Type.PDB); + } + else if (format.equalsIgnoreCase("mmCIF")) + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); + ((StructureFile) alignFile).setDbRefType(Type.MMCIF); } else if (format.equals("STH")) { @@ -424,9 +478,9 @@ public class AppletFormatAdapter { alignFile = new PhylipFile(source); } - else if (format.equals(IdentifyFile.GFF3File)) + else if (format.equals(IdentifyFile.FeaturesFile)) { - alignFile = new Gff3File(inFile, type); + alignFile = new FeaturesFile(inFile, type); } else if (format.equals(JSONFile.FILE_DESC)) { @@ -476,7 +530,6 @@ public class AppletFormatAdapter } } - /** * boilerplate method to handle data from an AlignFile and construct a new * alignment or import to an existing alignment @@ -500,6 +553,7 @@ public class AppletFormatAdapter /** * create an alignment flatfile from a Jalview alignment view + * * @param format * @param jvsuffix * @param av @@ -588,10 +642,10 @@ public class AppletFormatAdapter { afile = new PhylipFile(); } - else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) - { + else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) + { afile = new JSONFile(); - } + } else if (format.equalsIgnoreCase("RNAML")) { afile = new RnamlFile(); @@ -599,7 +653,9 @@ public class AppletFormatAdapter else { - throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string")); + throw new Exception( + MessageManager + .getString("error.implementation_error_unknown_file_format_string")); } afile.setNewlineString(newline); @@ -665,7 +721,7 @@ public class AppletFormatAdapter long memf = -r.totalMemory() + r.freeMemory(); long t1 = -System.currentTimeMillis(); AlignmentI al = afa.readFile(args[i], FILE, - new IdentifyFile().Identify(args[i], FILE)); + new IdentifyFile().identify(args[i], FILE)); t1 += System.currentTimeMillis(); System.gc(); memf += r.totalMemory() - r.freeMemory(); @@ -680,7 +736,7 @@ public class AppletFormatAdapter } 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); } } @@ -690,8 +746,8 @@ 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 @@ -757,7 +813,7 @@ public class AppletFormatAdapter } catch (Exception ex) { System.err - .println("Exception checking resources: " + file + " " + ex); + .println("Exception checking resources: " + file + " " + ex); } if (file.indexOf("://") > -1) @@ -831,7 +887,7 @@ public class AppletFormatAdapter { try { - String idformat = new jalview.io.IdentifyFile().Identify(file, + String idformat = new jalview.io.IdentifyFile().identify(file, protocol); if (idformat == null) { @@ -859,7 +915,7 @@ 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;