*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+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.gui.Preferences;
+import jalview.util.Comparison;
+import java.io.File;
import java.io.IOException;
/**
}
public FormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
super(alignPanel, settings);
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true))
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ annotFromStructure = jalview.bin.Cache.getDefault(
+ Preferences.ADD_TEMPFACT_ANN,
true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ localSecondaryStruct = jalview.bin.Cache.getDefault(
+ Preferences.ADD_SS_ANN,
true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ serviceSecondaryStruct = jalview.bin.Cache
+ .getDefault(Preferences.USE_RNAVIEW,
true);
}
else
}
}
- public String formatSequences(String format, SequenceI[] seqs,
+ public String formatSequences(FileFormatI format, SequenceI[] seqs,
String[] omitHiddenColumns, int[] exportRange)
{
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--;
*
*
* @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() + "_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
*/
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)
{
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);
}
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
}
/**
- * 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
*
selectedOnly);
}
+ public AlignmentI readFromFile(AlignmentFileReaderI source,
+ FileFormatI format) throws IOException
+ {
+ FileParse fp = new FileParse(source.getInFile(),
+ source.getDataSourceType());
+ return readFromFile(fp, format);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff