package jalview.io;
import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
/**
* Additional formatting methods used by the application in a number of places.
public class FormatAdapter extends AppletFormatAdapter
{
+ public FormatAdapter()
+ {
+ super();
+ 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(String format, SequenceI[] seqs,
String[] omitHiddenColumns)
{
public boolean getCacheSuffixDefault(String format)
{
if (isValidFormat(format))
+ {
return jalview.bin.Cache.getDefault(format.toUpperCase()
+ "_JVSUFFIX", true);
+ }
return false;
}
return this.formatSequences(format, alignment, suffix);
}
+ public Alignment readFile(String inFile, String type, String format)
+ throws java.io.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);
+ }
+
+ return al;
+ }
+
+ public AlignmentI readFromFile(FileParse source, String format)
+ throws java.io.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);
+ }
+ return al;
+ }
+
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for