*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
/**
* Creates a new JPredFile object.
*
+ * BH allows File or String
+ *
* @param inFile
* DOCUMENT ME!
* @param sourceType
* @throws IOException
* DOCUMENT ME!
*/
- public JPredFile(String inFile, DataSourceType sourceType)
+ public JPredFile(Object inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
@Override
public void parse() throws IOException
{
- // JBPNote log.System.out.println("all read in ");
+ // JBPNote log.jalview.bin.Console.outPrintln("all read in ");
String line;
QuerySeqPosition = -1;
noSeqs = 0;
}
else if (id.equals("jnetconf"))
{
- // log.debug System.out.println("here");
+ // log.debug jalview.bin.Console.outPrintln("here");
id = "Prediction Confidence";
this.conf = new Vector(numSymbols);
}
/**
- * DOCUMENT ME!
*
* @param args
- * DOCUMENT ME!
+ * @j2sIgnore
*/
public static void main(String[] args)
{
for (int i = 0; i < jpred.seqs.size(); i++)
{
- System.out.println(((Sequence) jpred.seqs.elementAt(i)).getName()
- + "\n"
- + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
- + "\n");
+ jalview.bin.Console
+ .outPrintln(((Sequence) jpred.seqs.elementAt(i)).getName()
+ + "\n" + ((Sequence) jpred.seqs.elementAt(i))
+ .getSequenceAsString()
+ + "\n");
}
} catch (java.io.IOException e)
{
- System.err.println("Exception " + e);
+ jalview.bin.Console.errPrintln("Exception " + e);
// e.printStackTrace(); not java 1.1 compatible!
}
}
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
- if (sq.getName().toUpperCase().startsWith("JPRED"))
+ if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
* out = BLCFile.print(s);
*
* AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
- * System.out.println(out); } catch (java.io.IOException e) {
- * System.out.println("Exception " + e); } } }
+ * jalview.bin.Console.outPrintln(out); } catch (java.io.IOException e) {
+ * jalview.bin.Console.outPrintln("Exception " + e); } } }
*/