public class PAEContactMatrix extends
MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
{
+
+
int maxrow = 0, maxcol = 0;
+
float[][] elements;
float maxscore;
+
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
throws FileFormatException
while (scores.hasNext())
{
Object d = scores.next();
-
if (d instanceof Double)
{
elements[row][col++] = ((Double) d).longValue();
@Override
public ContactListI getContactList(final int column)
{
- // final int _column;
- // if (toSeq != null)
- // {
- // int[] word = toSeq.locateInTo(column, column);
- // if (word == null)
- // {
- // return null;
- // }
- // _column = word[0];
- // }
- // else
- // {
- // _column = column;
- // }
if (column < 0 || column >= elements.length)
{
return null;
{
return length;
}
-
public static void validateContactMatrixFile(String fileName)
throws FileFormatException, IOException
{
{
new IOException("Couldn't open " + fileName, t);
}
-
JSONObject paeDict = null;
try
{
"No data in PAE matrix read from '" + fileName + "'");
}
}
-
@Override
protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
MapList newFromMapList)