X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=735619f4b29adf16797f0fe0c5cc7ff1026b7b3e;hb=b09158307712372752e22a0e766b3a5b9b9e15df;hp=eac1041b9d8625cc4fc3f6e3b3263961396637ca;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index eac1041..735619f 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -20,17 +20,21 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; +import java.util.Locale; + +import jalview.api.AlignExportSettingsI; 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.File; import java.io.IOException; /** @@ -54,21 +58,18 @@ public class FormatAdapter extends AppletFormatAdapter } public FormatAdapter(AlignmentViewPanel alignPanel, - AlignExportSettingI settings) + AlignExportSettingsI settings) { super(alignPanel, settings); } private void init() { - if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true)) + if (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); + annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN", true); + localSecondaryStruct = Cache.getDefault("ADD_SS_ANN", true); + serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW", true); } else { @@ -79,7 +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) { @@ -115,14 +116,14 @@ public class FormatAdapter extends AppletFormatAdapter 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--; @@ -147,114 +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) + 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; + boolean withSuffix = getCacheSuffixDefault(format); + return format.getWriter(null).print(seqs, withSuffix); } public boolean getCacheSuffixDefault(FileFormatI format) { - if (isValidFormat(format)) - { - return Cache.getDefault(format.toUpperCase() - + "_JVSUFFIX", true); - } - return false; - } - - public String formatSequences(FileFormatI format, AlignmentI alignment, - String[] omitHidden, int[] exportRange, ColumnSelection colSel) - { - return formatSequences(format, alignment, omitHidden, exportRange, - getCacheSuffixDefault(format), colSel, null); + return Cache.getDefault( + format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX", true); } public String formatSequences(FileFormatI format, AlignmentI alignment, - String[] omitHidden, int[] exportRange, ColumnSelection colSel, - SequenceGroup sgp) + 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 @@ -267,15 +186,15 @@ public class FormatAdapter extends AppletFormatAdapter */ 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(FileFormatI format, AlignmentI alignment, String[] omitHidden, int[] exportRange, boolean suffix, - ColumnSelection colSel, SequenceGroup selgp) + HiddenColumns hidden, SequenceGroup selgp) { if (omitHidden != null) { @@ -293,12 +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); } @@ -316,6 +235,13 @@ public class FormatAdapter extends AppletFormatAdapter return al; } + public AlignmentI readFile(File file, DataSourceType sourceType, + FileFormatI fileFormat) throws IOException + { + AlignmentI al = super.readFile(file, null, sourceType, fileFormat); + return al; + } + @Override public AlignmentI readFromFile(FileParse source, FileFormatI format) throws IOException @@ -325,28 +251,6 @@ public class FormatAdapter extends AppletFormatAdapter } /** - * 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 * @@ -362,4 +266,12 @@ public class FormatAdapter extends AppletFormatAdapter selectedOnly); } + public AlignmentI readFromFile(AlignmentFileReaderI source, + FileFormatI format) throws IOException + { + FileParse fp = new FileParse(source.getInFile(), + source.getDataSourceType()); + return readFromFile(fp, format); + } + }