X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=649aad377b3db6361a279762d21b248e061c7a97;hb=2a42323bc7b92e39c676fc46768f28d032f2f686;hp=3f9a425ce82e7086458f4ffb94aad8c53068c782;hpb=4b8e37b39d6599396ea8538e1737b65eb869aa21;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 3f9a425..649aad3 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -1,38 +1,42 @@ /* - * 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. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; +import jalview.api.AlignViewportI; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.util.MessageManager; + import java.io.File; import java.io.InputStream; import java.util.List; -import jalview.api.AlignViewportI; -import jalview.datamodel.*; - /** * A low level class for alignment and feature IO with alignment formatting * methods used by both applet and application for generating flat alignment * files. It also holds the lists of magic format names that the applet and * application will allow the user to read or write files with. - * + * * @author $author$ * @version $Revision$ */ @@ -43,14 +47,33 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FORMATS = new String[] { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", - "PDB", "JnetFile", "RNAML" }; // , "SimpleBLAST" }; + "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, + "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", + "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, + "jar,jvp", "html" }; + + /** + * 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, "Jalview", "HTML" }; /** * 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" }; + { "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 @@ -58,34 +81,15 @@ public class AppletFormatAdapter */ public static final String[] WRITABLE_EXTENSIONS = new String[] { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", - "jvp", "sto,stk", "jar" }; + "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", "Jalview", - "STH", "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" }; // ".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" };// , - - // "SimpleBLAST" - // }; + { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", + PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -94,7 +98,7 @@ public class AppletFormatAdapter + prettyPrint(READABLE_FORMATS); /** - * + * * @param els * @return grammatically correct(ish) list consisting of els elements. */ @@ -104,7 +108,7 @@ public class AppletFormatAdapter for (int i = 0, iSize = els.length - 1; i < iSize; i++) { list.append(els[i]); - list.append(","); + list.append(", "); } list.append(" and " + els[els.length - 1] + "."); return list.toString(); @@ -118,6 +122,21 @@ public class AppletFormatAdapter 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; @@ -139,7 +158,7 @@ public class AppletFormatAdapter /** * 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 @@ -151,7 +170,7 @@ public class AppletFormatAdapter /** * validate format is valid for IO - * + * * @param format * a format string to be compared with either READABLE_FORMATS or * WRITEABLE_FORMATS @@ -165,9 +184,9 @@ public class AppletFormatAdapter boolean valid = false; String[] format_list = (forwriting) ? WRITEABLE_FORMATS : READABLE_FORMATS; - for (int i = 0; i < format_list.length; i++) + for (String element : format_list) { - if (format_list[i].equalsIgnoreCase(format)) + if (element.equalsIgnoreCase(format)) { return true; } @@ -178,14 +197,14 @@ public class AppletFormatAdapter /** * Constructs the correct filetype parser for a characterised datasource - * + * * @param inFile * data/data location * @param type * type of datasource * @param format * File format of data provided by datasource - * + * * @return DOCUMENT ME! */ public Alignment readFile(String inFile, String type, String format) @@ -231,7 +250,8 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(inFile, type); + 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); } @@ -243,6 +263,14 @@ public class AppletFormatAdapter { afile = new SimpleBlastFile(inFile, type); } + else if (format.equals(PhylipFile.FILE_DESC)) + { + afile = new PhylipFile(inFile, type); + } + else if (format.equals(JSONFile.FILE_DESC)) + { + afile = new JSONFile(inFile, type); + } else if (format.equals("RNAML")) { afile = new RnamlFile(inFile, type); @@ -251,6 +279,7 @@ public class AppletFormatAdapter Alignment al = new Alignment(afile.getSeqsAsArray()); afile.addAnnotations(al); + afile.addSeqGroups(al); return al; } catch (Exception e) @@ -273,6 +302,8 @@ public class AppletFormatAdapter // Possible sequence is just residues with no label afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); Alignment al = new Alignment(afile.getSeqsAsArray()); + + afile.addSeqGroups(al); afile.addAnnotations(al); return al; @@ -294,12 +325,12 @@ public class AppletFormatAdapter /** * Constructs the correct filetype parser for an already open datasource - * + * * @param source * an existing datasource * @param format * File format of data that will be provided by datasource - * + * * @return DOCUMENT ME! */ public AlignmentI readFromFile(FileParse source, String format) @@ -348,7 +379,8 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(source); + afile = new MCview.PDBfile(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct, source); } else if (format.equals("STH")) { @@ -362,10 +394,18 @@ public class AppletFormatAdapter { afile = new SimpleBlastFile(source); } - + else if (format.equals(PhylipFile.FILE_DESC)) + { + afile = new PhylipFile(source); + } + else if (format.equals(JSONFile.FILE_DESC)) + { + afile = new JSONFile(source); + } Alignment al = new Alignment(afile.getSeqsAsArray()); afile.addAnnotations(al); + afile.addSeqGroups(al); return al; } catch (Exception e) @@ -389,6 +429,7 @@ public class AppletFormatAdapter afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); Alignment al = new Alignment(afile.getSeqsAsArray()); afile.addAnnotations(al); + afile.addSeqGroups(al); return al; } catch (Exception ex) @@ -409,7 +450,7 @@ public class AppletFormatAdapter /** - * create an alignment flatfile from a Jalview alignment view + * create an alignment flatfile from a Jalview alignment view * @param format * @param jvsuffix * @param av @@ -432,15 +473,15 @@ public class AppletFormatAdapter aselview.addAnnotation(aa); } } - + return formatSequences(format, aselview, jvsuffix); } - + /** * Construct an output class for an alignment in a particular filetype TODO: * allow caller to detect errors and warnings encountered when generating * output - * + * * @param format * string name of alignment format * @param alignment @@ -448,7 +489,7 @@ public class AppletFormatAdapter * @param jvsuffix * passed to AlnFile class controls whether /START-END is added to * sequence names - * + * * @return alignment flat file contents */ public String formatSequences(String format, AlignmentI alignment, @@ -457,7 +498,6 @@ public class AppletFormatAdapter try { AlignFile afile = null; - if (format.equalsIgnoreCase("FASTA")) { afile = new FastaFile(); @@ -494,6 +534,29 @@ public class AppletFormatAdapter { afile = new AMSAFile(alignment); } + else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC)) + { + afile = new PhylipFile(); + } + else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) + { + afile = new JSONFile(); + // 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(); @@ -501,14 +564,14 @@ public class AppletFormatAdapter else { - throw new Exception( - "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.setSeqs(alignment.getSequencesArray()); + String afileresp = afile.print(); if (afile.hasWarningMessage()) { @@ -570,7 +633,7 @@ 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); } } @@ -580,8 +643,8 @@ 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 @@ -600,7 +663,7 @@ public class AppletFormatAdapter /** * try to discover how to access the given file as a valid datasource that * will be identified as the given type. - * + * * @param file * @param format * @return protocol that yields the data parsable as the given type @@ -647,7 +710,7 @@ public class AppletFormatAdapter } catch (Exception ex) { System.err - .println("Exception checking resources: " + file + " " + ex); + .println("Exception checking resources: " + file + " " + ex); } if (file.indexOf("://") > -1) @@ -749,7 +812,7 @@ 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;