/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequenceNode;
import jalview.io.NewickFile;
import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
/**
- * DOCUMENT ME!
+ * NeighborJoining tree
*
* @author $author$
* @version $Revision$
}
/*
* sequenceString = new String[odata.length]; char gapChar =
- * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
+ * Comparison.GapChars.charAt(0); for (int i = 0; i <
* odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
* sequenceString[i] = oseq_aligned.getSequence(); }
*/
if (one2many.contains(nam))
{
countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // if (Cache.log.isDebugEnabled())
+ // Cache.log.debug("One 2 many relationship for
// "+nam.getName());
}
else
j.setPlaceholder(true);
}
}
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // if (Cache.log.isDebugEnabled() && countOne2Many>0) {
+ // Cache.log.debug("There were "+countOne2Many+" alignment
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
*/
public String toString()
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+ NewickFile fout = new NewickFile(getTopNode());
return fout.print(isHasBootstrap(), isHasDistances(),
isHasRootDistance()); // output all data available for tree
String[] seqdatas = seqData.getSequenceStrings(gapChar);
for (int i = 0; i < seqdatas.length; i++)
{
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
- .getName()));
+ sb.append(new Format("%-" + 15 + "s").form(sequence[i].getName()));
sb.append(" " + seqdatas[i] + "\n");
}
return sb.toString();