X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=505f60919fdf154d7be0f893482dccb5bc63a7f3;hb=99ece0eec17dfa6afa515adb441f280a2fcf26cc;hp=67559b938ee0642b066330f86fef6e200d82b115;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 67559b9..505f609 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 - * + * * 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 $Revision$ */ @@ -42,47 +46,51 @@ 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" }; // , "SimpleBLAST" }; + { "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" }; + { "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", - "jvp", "sto,stk", "jar" }; + { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", + "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT }; /** * 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" }; + { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", + "STH", "Jalview", PhylipFile.FILE_DESC }; /** * 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" + { "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" };// , + { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", + "Stockholm", "RNAML", PhylipFile.FILE_DESC, "HTML" };// , // "SimpleBLAST" // }; @@ -94,7 +102,7 @@ public class AppletFormatAdapter + prettyPrint(READABLE_FORMATS); /** - * + * * @param els * @return grammatically correct(ish) list consisting of els elements. */ @@ -104,7 +112,7 @@ 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 +126,21 @@ 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 +162,7 @@ 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 +174,7 @@ 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 +188,9 @@ 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 +201,14 @@ 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 +254,8 @@ 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 +267,14 @@ public class AppletFormatAdapter { afile = new SimpleBlastFile(inFile, type); } + else if (format.equals(PhylipFile.FILE_DESC)) + { + afile = new PhylipFile(inFile, type); + } + // else if (format.equals(HtmlFile.FILE_DESC)) + // { + // afile = new HtmlFile(inFile, type); + // } else if (format.equals("RNAML")) { afile = new RnamlFile(inFile, type); @@ -294,12 +326,12 @@ 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 +380,8 @@ 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")) { @@ -362,7 +395,14 @@ public class AppletFormatAdapter { afile = new SimpleBlastFile(source); } - + else if (format.equals(PhylipFile.FILE_DESC)) + { + afile = new PhylipFile(source); + } + // else if (format.equals(HtmlFile.FILE_DESC)) + // { + // afile = new HtmlFile(source); + // } Alignment al = new Alignment(afile.getSeqsAsArray()); afile.addAnnotations(al); @@ -409,7 +449,7 @@ 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 +472,15 @@ 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 +488,7 @@ 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, @@ -494,6 +534,14 @@ public class AppletFormatAdapter { 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 = new RnamlFile(); @@ -569,7 +617,7 @@ 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); } } @@ -579,8 +627,8 @@ 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 @@ -599,7 +647,7 @@ 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 @@ -646,7 +694,7 @@ public class AppletFormatAdapter } catch (Exception ex) { System.err - .println("Exception checking resources: " + file + " " + ex); + .println("Exception checking resources: " + file + " " + ex); } if (file.indexOf("://") > -1) @@ -748,7 +796,7 @@ 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;