import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
true);
localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
true);
localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
// get first non-gaped residue start position
while (jalview.util.Comparison.isGap(seqs[i]
.getCharAt(startIndex)) && startIndex < endIndex)
// get first non-gaped residue start position
while (jalview.util.Comparison.isGap(seqs[i]
.getCharAt(startIndex)) && startIndex < endIndex)
String[] omitHidden, int[] exportRange, ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
getCacheSuffixDefault(format), colSel, null);
}
String[] omitHidden, int[] exportRange, ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
getCacheSuffixDefault(format), colSel, null);
}
String[] omitHidden, int[] exportRange, ColumnSelection colSel,
SequenceGroup sgp)
{
String[] omitHidden, int[] exportRange, ColumnSelection colSel,
SequenceGroup sgp)
{
* defines hidden columns that are edited out of annotation
* @return string representation of the alignment formatted as format
*/
* defines hidden columns that are edited out of annotation
* @return string representation of the alignment formatted as format
*/
String[] omitHidden, int[] exportRange, boolean suffix,
ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
String[] omitHidden, int[] exportRange, boolean suffix,
ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
String[] omitHidden, int[] exportRange, boolean suffix,
String[] omitHidden, int[] exportRange, boolean 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
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);