if ((i > -1) && (i < sSize))
{
- sq = sequences[i].getSequence();
+ sq = sequences[i].getSequenceAsString();
if (seqNums.size() <= i)
{
seqNums.setElementAt(sqnum, i);
}
else
- System.out.println("NEVER THE EXCEPTION");
+ System.out.println("SEQUENCE HAS BEEN DELETED!!!");
}
else
{
//loop over all the found residues
resultHash = new Hashtable();
- for (int v = '-'; v < 'Z'; v++)
+ for (char v = '-'; v < 'Z'; v++)
{
if (values[v] > thresh)
{
- res = String.valueOf( (char) v);
+ res = String.valueOf( v );
//Now loop over the properties
enumeration2 = propHash.keys();
Hashtable resultHash ;
Enumeration enumeration;
+ //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
+ //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
+ //DOES NOT EXIST IN JALVIEW 2.1.2
+ for(int i=0; i<start; i++)
+ consString.append('-');
+
for (int i = start; i <= end; i++)
{
}
else
{
- consString.append("-");
+ consString.append('-');
}
}