for (int i = start; i < end; i++) // foreach column
{
- int canonicalOrWobblePairCount = 0;
+ int canonicalOrWobblePairCount = 0, canonical = 0;
int otherPairCount = 0;
int nongap = 0;
maxResidue = "-";
{
if (sequences[j] == null)
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ System.err.println(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
}
if (Rna.isCanonicalOrWobblePair(c, cEnd))
{
- values['(']++;
- maxResidue = "(";
canonicalOrWobblePairCount++;
+ if (Rna.isCanonicalPair(c, cEnd))
+ {
+ canonical++;
+ }
}
else
{
- values['[']++;
- maxResidue = "[";
otherPairCount++;
}
pairs[c][cEnd]++;
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
-
+ values['('] = canonicalOrWobblePairCount;
+ values['['] = canonical;
+ values['{'] = otherPairCount;
/*
* the count is the number of valid pairs (as a percentage, determines
* the relative size of the profile logo)
int count = canonicalOrWobblePairCount;
/*
- * currently displaying as '(' if most pairs are valid, or as
- * '[' if there are more invalid than valid pairs
+ * display '(' if most pairs are canonical, or as
+ * '[' if there are more wobble pairs.
*/
- if (!maxResidue.equals("-"))
+ if (canonicalOrWobblePairCount > 0 || otherPairCount > 0)
{
- maxResidue = canonicalOrWobblePairCount >= otherPairCount ? "("
- : "[";
+ if (canonicalOrWobblePairCount >= otherPairCount)
+ {
+ maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+ ? "("
+ : "[";
+ }
+ else
+ {
+ maxResidue = "{";
+ }
}
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
{
values[')'] = values['('];
values[']'] = values['['];
+ values['}'] = values['{'];
values['('] = 0;
values['['] = 0;
- maxResidue = maxResidue.equals("(") ? ")" : "]";
+ values['{'] = 0;
+ maxResidue = maxResidue.equals("(") ? ")"
+ : maxResidue.equals("[") ? "]" : "}";
residueHash = new Hashtable();
if (profile)
{
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
int valuesCount = 0;
rtnval[1] = 0;
int offset = 2;
- final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)