X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=de9e6bdd63d70f61249150f2a11f3376225845b9;hb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;hp=505f60919fdf154d7be0f893482dccb5bc63a7f3;hpb=d6802cb21c694ab6a971fa568f6686660559a5d5;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 505f609..de9e6bd 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 2.8.2) - * 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. * @@ -20,17 +20,18 @@ */ package jalview.io; +import java.io.File; +import java.io.InputStream; +import java.util.List; + import jalview.api.AlignViewportI; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; +import jalview.datamodel.SequenceGroup; import jalview.util.MessageManager; -import java.io.File; -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 @@ -42,58 +43,90 @@ import java.util.List; */ public class AppletFormatAdapter { + private AlignViewportI viewport; + + public static String FILE = "File"; + + public static String URL = "URL"; + + public static String PASTE = "Paste"; + + public static String CLASSLOADER = "ClassLoader"; + /** - * List of valid format strings used in the isValidFormat method + * add jalview-derived non-secondary structure annotation from PDB structure */ - public static final String[] READABLE_FORMATS = new String[] - { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", - "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, "HTML" }; // , - // "SimpleBLAST" - // }; + boolean annotFromStructure = false; /** - * List of valid format strings for use by callers of the formatSequences - * method + * add secondary structure from PDB data with built-in algorithms */ - public static final String[] WRITEABLE_FORMATS = new String[] - { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", - "STH", PhylipFile.FILE_DESC }; + boolean localSecondaryStruct = false; /** - * List of extensions corresponding to file format types in WRITABLE_FNAMES - * that are writable by the application. + * process PDB data with web services */ - public static final String[] WRITABLE_EXTENSIONS = new String[] - { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", - "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT }; + boolean serviceSecondaryStruct = false; + + private AlignFile alignFile = null; + + String inFile; /** - * List of writable formats by the application. Order must correspond with the - * WRITABLE_EXTENSIONS list of formats. + * character used to write newlines */ - public static final String[] WRITABLE_FNAMES = new String[] - { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", - "STH", "Jalview", PhylipFile.FILE_DESC }; + protected String newline = System.getProperty("line.separator"); + + /** + * 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" }; /** * 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" + { "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 }; /** * 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" };// , + { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", + "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview", + HtmlFile.FILE_DESC }; - // "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, 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", + "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", + PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -101,6 +134,15 @@ public class AppletFormatAdapter public static String SUPPORTED_FORMATS = "Formats currently supported are\n" + prettyPrint(READABLE_FORMATS); + public AppletFormatAdapter() + { + } + + public AppletFormatAdapter(AlignViewportI viewport) + { + this.viewport = viewport; + } + /** * * @param els @@ -118,37 +160,6 @@ public class AppletFormatAdapter return list.toString(); } - public static String FILE = "File"; - - public static String URL = "URL"; - - public static String PASTE = "Paste"; - - public static String CLASSLOADER = "ClassLoader"; - - /** - * add jalview-derived non-secondary structure annotation from PDB structure - */ - boolean annotFromStructure = false; - - /** - * add secondary structure from PDB data with built-in algorithms - */ - boolean localSecondaryStruct = false; - - /** - * process PDB data with web services - */ - boolean serviceSecondaryStruct = false; - - AlignFile afile = null; - - String inFile; - - /** - * character used to write newlines - */ - protected String newline = System.getProperty("line.separator"); public void setNewlineString(String nl) { @@ -219,70 +230,95 @@ public class AppletFormatAdapter this.inFile = inFile; try { + Alignment al; if (format.equals("FASTA")) { - afile = new FastaFile(inFile, type); + alignFile = new FastaFile(inFile, type); } else if (format.equals("MSF")) { - afile = new MSFfile(inFile, type); + alignFile = new MSFfile(inFile, type); } else if (format.equals("PileUp")) { - afile = new PileUpfile(inFile, type); + alignFile = new PileUpfile(inFile, type); } else if (format.equals("CLUSTAL")) { - afile = new ClustalFile(inFile, type); + alignFile = new ClustalFile(inFile, type); } else if (format.equals("BLC")) { - afile = new BLCFile(inFile, type); + alignFile = new BLCFile(inFile, type); } else if (format.equals("PIR")) { - afile = new PIRFile(inFile, type); + alignFile = new PIRFile(inFile, type); } else if (format.equals("PFAM")) { - afile = new PfamFile(inFile, type); + alignFile = new PfamFile(inFile, type); } else if (format.equals("JnetFile")) { - afile = new JPredFile(inFile, type); - ((JPredFile) afile).removeNonSequences(); + alignFile = new JPredFile(inFile, type); + ((JPredFile) alignFile).removeNonSequences(); } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(annotFromStructure, + 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); } else if (format.equals("STH")) { - afile = new StockholmFile(inFile, type); + alignFile = new StockholmFile(inFile, type); } else if (format.equals("SimpleBLAST")) { - afile = new SimpleBlastFile(inFile, type); + alignFile = new SimpleBlastFile(inFile, type); } else if (format.equals(PhylipFile.FILE_DESC)) { - afile = new PhylipFile(inFile, type); + alignFile = new PhylipFile(inFile, type); + } + 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(HtmlFile.FILE_DESC)) - // { - // afile = new HtmlFile(inFile, type); - // } else if (format.equals("RNAML")) { - afile = new RnamlFile(inFile, type); + alignFile = new RnamlFile(inFile, type); + } + else if (format.equals(IdentifyFile.GFF3File)) + { + alignFile = new Gff3File(inFile, type); } - Alignment al = new Alignment(afile.getSeqsAsArray()); + al = new Alignment(alignFile.getSeqsAsArray()); - afile.addAnnotations(al); + alignFile.addAnnotations(al); return al; } catch (Exception e) @@ -303,9 +339,11 @@ public class AppletFormatAdapter 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); + alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); + Alignment al = new Alignment(alignFile.getSeqsAsArray()); + + alignFile.addSeqGroups(al); + alignFile.addAnnotations(al); return al; } catch (Exception ex) @@ -345,67 +383,79 @@ public class AppletFormatAdapter String type = source.type; try { + Alignment al; if (format.equals("FASTA")) { - afile = new FastaFile(source); + alignFile = new FastaFile(source); } else if (format.equals("MSF")) { - afile = new MSFfile(source); + alignFile = new MSFfile(source); } else if (format.equals("PileUp")) { - afile = new PileUpfile(source); + alignFile = new PileUpfile(source); } else if (format.equals("CLUSTAL")) { - afile = new ClustalFile(source); + alignFile = new ClustalFile(source); } else if (format.equals("BLC")) { - afile = new BLCFile(source); + alignFile = new BLCFile(source); } else if (format.equals("PIR")) { - afile = new PIRFile(source); + alignFile = new PIRFile(source); } else if (format.equals("PFAM")) { - afile = new PfamFile(source); + alignFile = new PfamFile(source); } else if (format.equals("JnetFile")) { - afile = new JPredFile(source); - ((JPredFile) afile).removeNonSequences(); + alignFile = new JPredFile(source); + ((JPredFile) alignFile).removeNonSequences(); } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(annotFromStructure, + alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); } else if (format.equals("STH")) { - afile = new StockholmFile(source); + alignFile = new StockholmFile(source); } else if (format.equals("RNAML")) { - afile = new RnamlFile(source); + alignFile = new RnamlFile(source); } else if (format.equals("SimpleBLAST")) { - afile = new SimpleBlastFile(source); + alignFile = new SimpleBlastFile(source); } else if (format.equals(PhylipFile.FILE_DESC)) { - afile = new PhylipFile(source); + alignFile = new PhylipFile(source); } - // else if (format.equals(HtmlFile.FILE_DESC)) - // { - // afile = new HtmlFile(source); - // } - Alignment al = new Alignment(afile.getSeqsAsArray()); - - afile.addAnnotations(al); + else if (format.equals(IdentifyFile.GFF3File)) + { + alignFile = new Gff3File(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; } catch (Exception e) @@ -426,9 +476,10 @@ public class AppletFormatAdapter 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); + alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); + Alignment al = new Alignment(alignFile.getSeqsAsArray()); + alignFile.addAnnotations(al); + alignFile.addSeqGroups(al); return al; } catch (Exception ex) @@ -497,7 +548,6 @@ public class AppletFormatAdapter try { AlignFile afile = null; - if (format.equalsIgnoreCase("FASTA")) { afile = new FastaFile(); @@ -538,10 +588,26 @@ public class AppletFormatAdapter { afile = new PhylipFile(); } - // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC)) - // { - // afile = new HtmlFile(); - // } + 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(); @@ -556,6 +622,7 @@ public class AppletFormatAdapter afile.setSeqs(alignment.getSequencesArray()); + String afileresp = afile.print(); if (afile.hasWarningMessage()) { @@ -814,4 +881,14 @@ public class AppletFormatAdapter } return null; } + + public AlignFile getAlignFile() + { + return alignFile; + } + + public void setAlignFile(AlignFile alignFile) + { + this.alignFile = alignFile; + } }