X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=6d3c18aef394432234a8f9071afb9aec6f1f8b20;hb=8c5cefb3ac80bd094a8dab7ce6735a11583b1772;hp=63a14d71502b5099a23eec46b25648108c119237;hpb=80300778ebd2107d12371d5073ccb8870f875eda;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 63a14d7..6d3c18a 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -22,13 +22,17 @@ package jalview.io; 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. @@ -63,9 +67,9 @@ public class FormatAdapter extends AppletFormatAdapter 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); + true); + serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW", + true); } else { @@ -76,7 +80,7 @@ public class FormatAdapter extends AppletFormatAdapter } } - public String formatSequences(String format, SequenceI[] seqs, + public String formatSequences(FileFormatI format, SequenceI[] seqs, String[] omitHiddenColumns, int[] exportRange) { @@ -107,30 +111,26 @@ public class FormatAdapter extends AppletFormatAdapter { 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 (jalview.util.Comparison.isGap(seqs[i] - .getCharAt(startIndex)) && startIndex < endIndex) + while (Comparison.isGap(seqs[i].getCharAt(startIndex)) + && startIndex < endIndex) { startIndex++; } // get last non-gaped residue end position - while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex)) + while (Comparison.isGap(seqs[i].getCharAt(endIndex)) && endIndex > startIndex) { endIndex--; } startRes = seqs[i].findPosition(startIndex); - startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart() - : startRes; - endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart(); + endRes = seqs[i].findPosition(endIndex); } tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i], @@ -148,114 +148,32 @@ 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) - { - - 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) + public String formatSequences(FileFormatI format, SequenceI[] seqs) { - 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, int[] exportRange, ColumnSelection colSel) + public boolean getCacheSuffixDefault(FileFormatI format) { - return formatSequences(format, alignment, omitHidden, exportRange, - getCacheSuffixDefault(format), colSel, null); + return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX", + true); } - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, int[] exportRange, ColumnSelection colSel, - SequenceGroup sgp) + public String formatSequences(FileFormatI format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, HiddenColumns hidden) { return formatSequences(format, alignment, omitHidden, exportRange, - getCacheSuffixDefault(format), colSel, sgp); + 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 @@ -266,19 +184,17 @@ 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, + public String formatSequences(FileFormatI format, AlignmentI alignment, String[] omitHidden, int[] exportRange, boolean suffix, - ColumnSelection colSel) + HiddenColumns hidden) { return formatSequences(format, alignment, omitHidden, exportRange, - suffix, colSel, - null); + suffix, hidden, null); } - public String formatSequences(String format, AlignmentI alignment, + public String formatSequences(FileFormatI format, AlignmentI alignment, String[] omitHidden, int[] exportRange, boolean suffix, - ColumnSelection colSel, - jalview.datamodel.SequenceGroup selgp) + HiddenColumns hidden, SequenceGroup selgp) { if (omitHidden != null) { @@ -296,12 +212,12 @@ public class FormatAdapter extends AppletFormatAdapter AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); if (selgp != null) { - colSel.makeVisibleAnnotation(selgp.getStartRes(), - selgp.getEndRes(), na); + na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(), + hidden); } else { - colSel.makeVisibleAnnotation(na); + na.makeVisibleAnnotation(hidden); } alv.addAnnotation(na); } @@ -311,43 +227,23 @@ public class FormatAdapter extends AppletFormatAdapter return this.formatSequences(format, alignment, suffix); } - public AlignmentI readFile(String inFile, String type, String format) - throws java.io.IOException + @Override + public AlignmentI readFile(String file, DataSourceType sourceType, + FileFormatI fileFormat) throws IOException { - AlignmentI 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 { 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'. - * - * @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 - */ - public static final boolean isValidIOFormat(String format, - boolean forwriting) - { - if (format.equalsIgnoreCase("jalview")) - { - return true; - } - return AppletFormatAdapter.isValidFormat(format, forwriting); - } - - /** * Create a flat file representation of a given view or selected region of a * view * @@ -356,12 +252,19 @@ public class FormatAdapter extends AppletFormatAdapter * alignment panel originating the view * @return String containing flat file */ - public String formatSequences(String format, AlignmentViewPanel ap, + public String formatSequences(FileFormatI format, AlignmentViewPanel ap, boolean selectedOnly) { return formatSequences(format, getCacheSuffixDefault(format), ap, selectedOnly); } + public AlignmentI readFromFile(AlignmentFileReaderI source, + FileFormatI format) throws IOException + { + FileParse fp = new FileParse(source.getInFile(), + source.getDataSourceType()); + return readFromFile(fp, format); + } }