X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=3027ab1bb1cb83bb9077afda60194196ab96e248;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=416773d9035986e9b59ee92537fa3f415a616332;hpb=68c26e8852772be21fdb5b091fa9083d8cdb6eec;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 416773d..3027ab1 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.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. * @@ -20,14 +20,19 @@ */ package jalview.io; -import jalview.api.AlignViewportI; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.util.Comparison; + +import java.io.IOException; /** * Additional formatting methods used by the application in a number of places. @@ -37,12 +42,50 @@ import jalview.datamodel.SequenceI; */ public class FormatAdapter extends AppletFormatAdapter { + public FormatAdapter(AlignmentViewPanel viewpanel) + { + super(viewpanel); + init(); + } - public String formatSequences(String format, SequenceI[] seqs, - String[] omitHiddenColumns) + public FormatAdapter() { + super(); + init(); + } - return formatSequences(format, replaceStrings(seqs, omitHiddenColumns)); + public FormatAdapter(AlignmentViewPanel alignPanel, + AlignExportSettingI settings) + { + super(alignPanel, settings); + } + + private void init() + { + if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true)) + { + annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN", + true); + localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN", + true); + serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW", + true); + } + else + { + // disable all PDB annotation options + annotFromStructure = false; + localSecondaryStruct = false; + serviceSecondaryStruct = false; + } + } + + public String formatSequences(FileFormatI format, SequenceI[] seqs, + String[] omitHiddenColumns, int[] exportRange) + { + + return formatSequences(format, + replaceStrings(seqs, omitHiddenColumns, exportRange)); } /** @@ -54,15 +97,44 @@ public class FormatAdapter extends AppletFormatAdapter * @return new sequences */ public SequenceI[] replaceStrings(SequenceI[] seqs, - String[] omitHiddenColumns) + String[] omitHiddenColumns, int[] startEnd) { if (omitHiddenColumns != null) { SequenceI[] tmp = new SequenceI[seqs.length]; + + int startRes; + int endRes; + int startIndex; + int endIndex; for (int i = 0; i < seqs.length; i++) { + startRes = seqs[i].getStart(); + endRes = seqs[i].getEnd(); + if (startEnd != null) + { + startIndex = startEnd[0]; + endIndex = startEnd[1]; + // get first non-gaped residue start position + while (Comparison.isGap(seqs[i].getCharAt(startIndex)) + && startIndex < endIndex) + { + startIndex++; + } + + // get last non-gaped residue end position + while (Comparison.isGap(seqs[i].getCharAt(endIndex)) + && endIndex > startIndex) + { + endIndex--; + } + + startRes = seqs[i].findPosition(startIndex); + endRes = seqs[i].findPosition(endIndex); + } + tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i], - seqs[i].getStart(), seqs[i].getEnd()); + startRes, endRes); tmp[i].setDescription(seqs[i].getDescription()); } seqs = tmp; @@ -76,113 +148,31 @@ public class FormatAdapter extends AppletFormatAdapter * * * @param format - * Format string as givien in the AppletFormatAdaptor list (exact - * match to name of class implementing file io for that format) * @param seqs * vector of sequences to write * * @return String containing sequences in desired format */ - public String formatSequences(String format, SequenceI[] seqs) + public String formatSequences(FileFormatI format, SequenceI[] seqs) { - - try - { - AlignFile afile = null; - - if (format.equalsIgnoreCase("FASTA")) - { - afile = new FastaFile(); - afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", - true)); - } - else if (format.equalsIgnoreCase("MSF")) - { - afile = new MSFfile(); - afile.addJVSuffix(jalview.bin.Cache - .getDefault("MSF_JVSUFFIX", true)); - } - else if (format.equalsIgnoreCase("PileUp")) - { - afile = new PileUpfile(); - afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", - true)); - } - else if (format.equalsIgnoreCase("CLUSTAL")) - { - afile = new ClustalFile(); - afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", - true)); - } - else if (format.equalsIgnoreCase("BLC")) - { - afile = new BLCFile(); - afile.addJVSuffix(jalview.bin.Cache - .getDefault("BLC_JVSUFFIX", true)); - } - else if (format.equalsIgnoreCase("PIR")) - { - afile = new PIRFile(); - afile.addJVSuffix(jalview.bin.Cache - .getDefault("PIR_JVSUFFIX", true)); - } - else if (format.equalsIgnoreCase("PFAM")) - { - afile = new PfamFile(); - afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", - true)); - } - /* - * amsa is not supported by this function - it requires an alignment - * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA")) - * { afile = new AMSAFile(); afile.addJVSuffix( - * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); } - */ - - afile.setSeqs(seqs); - String afileresp = afile.print(); - if (afile.hasWarningMessage()) - { - System.err.println("Warning raised when writing as " + format - + " : " + afile.getWarningMessage()); - } - return afileresp; - } catch (Exception e) - { - System.err.println("Failed to write alignment as a '" + format - + "' file\n"); - e.printStackTrace(); - } - - return null; - } - - public boolean getCacheSuffixDefault(String format) - { - if (isValidFormat(format)) - { - return jalview.bin.Cache.getDefault(format.toUpperCase() - + "_JVSUFFIX", true); - } - return false; + boolean withSuffix = getCacheSuffixDefault(format); + return format.getWriter(null).print(seqs, withSuffix); } - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, ColumnSelection colSel) + public boolean getCacheSuffixDefault(FileFormatI format) { - return formatSequences(format, alignment, omitHidden, - getCacheSuffixDefault(format), colSel, null); + return Cache.getDefault(format.getName() + "_JVSUFFIX", true); } - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp) + public String formatSequences(FileFormatI format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, HiddenColumns hidden) { - return formatSequences(format, alignment, omitHidden, - getCacheSuffixDefault(format), colSel, sgp); + return formatSequences(format, alignment, omitHidden, exportRange, + getCacheSuffixDefault(format), hidden, null); } /** - * hack function to replace seuqences with visible sequence strings before + * hack function to replace sequences with visible sequence strings before * generating a string of the alignment in the given format. * * @param format @@ -193,16 +183,17 @@ public class FormatAdapter extends AppletFormatAdapter * defines hidden columns that are edited out of annotation * @return string representation of the alignment formatted as format */ - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, boolean suffix, ColumnSelection colSel) + public String formatSequences(FileFormatI format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, boolean suffix, + HiddenColumns hidden) { - return formatSequences(format, alignment, omitHidden, suffix, colSel, - null); + return formatSequences(format, alignment, omitHidden, exportRange, + suffix, hidden, null); } - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, boolean suffix, ColumnSelection colSel, - jalview.datamodel.SequenceGroup selgp) + public String formatSequences(FileFormatI format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, boolean suffix, + HiddenColumns hidden, SequenceGroup selgp) { if (omitHidden != null) { @@ -211,7 +202,7 @@ public class FormatAdapter extends AppletFormatAdapter // TODO: JAL-1486 - set start and end for output correctly. basically, // AlignmentView.getVisibleContigs does this. Alignment alv = new Alignment(replaceStrings( - alignment.getSequencesArray(), omitHidden)); + alignment.getSequencesArray(), omitHidden, exportRange)); AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation(); if (ala != null) { @@ -220,12 +211,12 @@ public class FormatAdapter extends AppletFormatAdapter AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); if (selgp != null) { - colSel.makeVisibleAnnotation(selgp.getStartRes(), + hidden.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(), na); } else { - colSel.makeVisibleAnnotation(na); + hidden.makeVisibleAnnotation(na); } alv.addAnnotation(na); } @@ -235,72 +226,44 @@ public class FormatAdapter extends AppletFormatAdapter return this.formatSequences(format, alignment, suffix); } - public Alignment readFile(String inFile, String type, String format) - throws java.io.IOException + @Override + public AlignmentI readFile(String file, DataSourceType sourceType, + FileFormatI fileFormat) throws IOException { - Alignment al; - if (format.equals("HTML")) - { - afile = new HtmlFile(inFile, type); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - } - else - { - al = super.readFile(inFile, type, format); - } - + AlignmentI al = super.readFile(file, sourceType, fileFormat); return al; } - public AlignmentI readFromFile(FileParse source, String format) - throws java.io.IOException + @Override + public AlignmentI readFromFile(FileParse source, FileFormatI format) + throws IOException { - Alignment al; - if (format.equals("HTML")) - { - afile = new HtmlFile(source); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - } - else - { - al = (Alignment) super.readFromFile(source, format); - } + AlignmentI al = super.readFromFile(source, format); return al; } /** - * validate format is valid for IO in Application. This is basically the - * AppletFormatAdapter.isValidFormat call with additional checks for - * Application only formats like 'Jalview'. + * Create a flat file representation of a given view or selected region of a + * view * * @param format - * a format string to be compared with list of readable or writable - * formats (READABLE_FORMATS or WRITABLE_FORMATS) - * @param forwriting - * when true, format is checked against list of writable formats. - * @return true if format is valid + * @param ap + * alignment panel originating the view + * @return String containing flat file */ - public static final boolean isValidIOFormat(String format, - boolean forwriting) + public String formatSequences(FileFormatI format, AlignmentViewPanel ap, + boolean selectedOnly) { - if (format.equalsIgnoreCase("jalview")) - { - return true; - } - return AppletFormatAdapter.isValidFormat(format, forwriting); + return formatSequences(format, getCacheSuffixDefault(format), ap, + selectedOnly); } - /** - * Create a flat file representation of a given view or selected region of a view - * @param format - * @param av - * @return String containing flat file - */ - public String formatSequences(String format, AlignViewportI av, boolean selectedOnly) + public AlignmentI readFromFile(AlignmentFileReaderI source, + FileFormatI format) throws IOException { - return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly); + FileParse fp = new FileParse(source.getInFile(), + source.getDataSourceType()); + return readFromFile(fp, format); } }