X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=9695891e566bad7f332692a2cf64e68d476e2110;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=de9e6bdd63d70f61249150f2a11f3376225845b9;hpb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index de9e6bd..9695891 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -20,18 +20,22 @@ */ package jalview.io; -import java.io.File; -import java.io.InputStream; -import java.util.List; - -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.datamodel.SequenceGroup; +import jalview.datamodel.PDBEntry.Type; +import jalview.ext.jmol.JmolParser; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.util.List; + /** * A low level class for alignment and feature IO with alignment formatting * methods used by both applet and application for generating flat alignment @@ -43,7 +47,7 @@ import jalview.util.MessageManager; */ public class AppletFormatAdapter { - private AlignViewportI viewport; + private AlignmentViewPanel viewpanel; public static String FILE = "File"; @@ -77,55 +81,56 @@ 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", 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"; @@ -138,9 +143,16 @@ public class AppletFormatAdapter { } - public AppletFormatAdapter(AlignViewportI viewport) + public AppletFormatAdapter(AlignmentViewPanel viewpanel) { - this.viewport = viewport; + this.viewpanel = viewpanel; + } + + public AppletFormatAdapter(AlignmentViewPanel alignPanel, + AlignExportSettingI settings) + { + viewpanel = alignPanel; + exportSettings = settings; } /** @@ -160,7 +172,6 @@ public class AppletFormatAdapter return list.toString(); } - public void setNewlineString(String nl) { newline = nl; @@ -196,6 +207,10 @@ public class AppletFormatAdapter public static final boolean isValidFormat(String format, boolean forwriting) { + if (format == null) + { + return false; + } boolean valid = false; String[] format_list = (forwriting) ? WRITEABLE_FORMATS : READABLE_FORMATS; @@ -222,7 +237,7 @@ public class AppletFormatAdapter * * @return DOCUMENT ME! */ - public Alignment readFile(String inFile, String type, String format) + public AlignmentI readFile(String inFile, String type, String format) throws java.io.IOException { // TODO: generalise mapping between format string and io. class instances @@ -230,7 +245,6 @@ public class AppletFormatAdapter this.inFile = inFile; try { - Alignment al; if (format.equals("FASTA")) { alignFile = new FastaFile(inFile, type); @@ -266,10 +280,35 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - alignFile = 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); + // 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(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(inFile, type); + ((StructureFile) alignFile).setDbRefType(format); } else if (format.equals("STH")) { @@ -286,41 +325,20 @@ public class AppletFormatAdapter else if (format.equals(JSONFile.FILE_DESC)) { alignFile = new JSONFile(inFile, type); - al = new Alignment(alignFile.getSeqsAsArray()); - alignFile.addAnnotations(al); - ((JSONFile) alignFile).setViewport(viewport); - for (SequenceGroup sg : alignFile.getSeqGroups()) - { - al.addGroup(sg); - } - - return al; } else if (format.equals(HtmlFile.FILE_DESC)) { alignFile = new HtmlFile(inFile, type); - al = new Alignment(alignFile.getSeqsAsArray()); - alignFile.addAnnotations(al); - for (SequenceGroup sg : alignFile.getSeqGroups()) - { - al.addGroup(sg); - } - return al; } else if (format.equals("RNAML")) { 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); } - - al = new Alignment(alignFile.getSeqsAsArray()); - - alignFile.addAnnotations(al); - - return al; + return buildAlignmentFrom(alignFile); } catch (Exception e) { e.printStackTrace(); @@ -340,11 +358,7 @@ public class AppletFormatAdapter { // Possible sequence is just residues with no label alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); - Alignment al = new Alignment(alignFile.getSeqsAsArray()); - - alignFile.addSeqGroups(al); - alignFile.addAnnotations(al); - return al; + return buildAlignmentFrom(alignFile); } catch (Exception ex) { @@ -356,7 +370,10 @@ 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); } @@ -383,7 +400,6 @@ public class AppletFormatAdapter String type = source.type; try { - Alignment al; if (format.equals("FASTA")) { alignFile = new FastaFile(source); @@ -419,8 +435,28 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - alignFile = new MCview.PDBfile(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, 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.equalsIgnoreCase("mmCIF")) + { + StructureImportSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); + alignFile = new JmolParser(source); + ((StructureFile) alignFile).setDbRefType(Type.MMCIF); } else if (format.equals("STH")) { @@ -438,26 +474,21 @@ 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)) { alignFile = new JSONFile(source); - al = new Alignment(alignFile.getSeqsAsArray()); - alignFile.addAnnotations(al); - alignFile.addSeqGroups(al); - return al; } else if (format.equals(HtmlFile.FILE_DESC)) { alignFile = new HtmlFile(source); } - al = new Alignment(alignFile.getSeqsAsArray()); - alignFile.addAnnotations(al); - return al; + return buildAlignmentFrom(alignFile); + } catch (Exception e) { e.printStackTrace(); @@ -477,10 +508,7 @@ public class AppletFormatAdapter { // Possible sequence is just residues with no label alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); - Alignment al = new Alignment(alignFile.getSeqsAsArray()); - alignFile.addAnnotations(al); - alignFile.addSeqGroups(al); - return al; + return buildAlignmentFrom(alignFile); } catch (Exception ex) { @@ -498,9 +526,30 @@ public class AppletFormatAdapter } } + /** + * boilerplate method to handle data from an AlignFile and construct a new + * alignment or import to an existing alignment + * + * @param alignFile2 + * @return AlignmentI instance ready to pass to a UI constructor + */ + private AlignmentI buildAlignmentFrom(AlignFile alignFile2) + { + // 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 @@ -508,13 +557,14 @@ public class AppletFormatAdapter * @return flatfile in a string */ public String formatSequences(String format, boolean jvsuffix, - AlignViewportI av, boolean selectedOnly) + 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) { @@ -523,7 +573,7 @@ public class AppletFormatAdapter aselview.addAnnotation(aa); } } - + viewpanel = ap; return formatSequences(format, aselview, jvsuffix); } @@ -588,26 +638,10 @@ public class AppletFormatAdapter { afile = new PhylipFile(); } - else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) - { + else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) + { afile = new JSONFile(); - afile.setViewport(viewport); - // Add groups to AlignFile - afile.seqGroups = alignment.getGroups(); - - // Add non auto calculated annotation to AlignFile - for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation()) - { - if (annot != null && !annot.autoCalculated) - { - if (annot.label.equals("PDB.CATempFactor")) - { - continue; - } - afile.annotations.add(annot); - } - } - } + } else if (format.equalsIgnoreCase("RNAML")) { afile = new RnamlFile(); @@ -615,13 +649,27 @@ 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); afile.addJVSuffix(jvsuffix); + afile.setExportSettings(exportSettings); + afile.configureForView(viewpanel); - afile.setSeqs(alignment.getSequencesArray()); - + // check whether we were given a specific alignment to export, rather than + // the one in the viewpanel + if (viewpanel == null || viewpanel.getAlignment() == null + || viewpanel.getAlignment() != alignment) + { + afile.setSeqs(alignment.getSequencesArray()); + } + else + { + afile.setSeqs(viewpanel.getAlignment().getSequencesArray()); + } String afileresp = afile.print(); if (afile.hasWarningMessage()) @@ -668,8 +716,8 @@ 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], FILE, + new IdentifyFile().identify(args[i], FILE)); t1 += System.currentTimeMillis(); System.gc(); memf += r.totalMemory() - r.freeMemory(); @@ -684,7 +732,7 @@ 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); } } @@ -694,8 +742,8 @@ 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 @@ -761,7 +809,7 @@ public class AppletFormatAdapter } catch (Exception ex) { System.err - .println("Exception checking resources: " + file + " " + ex); + .println("Exception checking resources: " + file + " " + ex); } if (file.indexOf("://") > -1) @@ -835,7 +883,7 @@ public class AppletFormatAdapter { try { - String idformat = new jalview.io.IdentifyFile().Identify(file, + String idformat = new jalview.io.IdentifyFile().identify(file, protocol); if (idformat == null) { @@ -863,7 +911,7 @@ 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;