public static final String PID_NOGAPS = "N";
+ public static final String PROFILE = "P";
+
public static final Hashtable[] calculate(Vector sequences, int start,
int end)
{
+ return calculate(sequences, start, end, false);
+ }
+
+ public static final Hashtable[] calculate(Vector sequences, int start,
+ int end, boolean profile)
+ {
SequenceI[] seqs = new SequenceI[sequences.size()];
int width = 0;
for (int i = 0; i < sequences.size(); i++)
end = width;
}
- calculate(seqs, start, end, reply);
+ calculate(seqs, start, end, reply, profile);
return reply;
}
public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result)
{
+ calculate(sequences, start, end, result, false);
+ }
+
+ public static final void calculate(SequenceI[] sequences, int start,
+ int end, Hashtable[] result, boolean profile)
+ {
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
{
maxResidue = "-";
}
-
+ if (profile)
+ {
+ residueHash.put(PROFILE, new int[][]
+ { values, new int[]
+ { jSize, nongap } });
+ }
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
}
/**
- * Compute all or part of the annotation row from the given consensus hashtable
- * @param consensus - pre-allocated annotation row
+ * Compute all or part of the annotation row from the given consensus
+ * hashtable
+ *
+ * @param consensus
+ * - pre-allocated annotation row
* @param hconsensus
* @param iStart
* @param width
* @param ignoreGapsInConsensusCalculation
+ * @param includeAllConsSymbols
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
- boolean ignoreGapsInConsensusCalculation)
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols)
{
+ completeConsensus(consensus, hconsensus, iStart, width,
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols,
+ null); //new char[]
+ // { 'A', 'C', 'G', 'T', 'U' });
+ }
+
+ public static void completeConsensus(AlignmentAnnotation consensus,
+ Hashtable[] hconsensus, int iStart, int width,
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols, char[] alphabet)
+ {
+ float tval, value;
for (int i = iStart; i < width; i++)
{
- float value = 0;
+ value = 0;
if (ignoreGapsInConsensusCalculation)
{
value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
.floatValue();
}
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
- .toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
- + " ";
-
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
+ int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
+ if (profile != null && includeAllConsSymbols)
+ {
+ mouseOver = "";
+ if (alphabet!=null)
+ {
+ for (int c = 0; c < alphabet.length; c++)
+ {
+ tval = ((float) profile[0][alphabet[c]])
+ * 100f
+ / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
+ mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
+ + ((int) tval) + "%";
+ }
+ }
+ else
+ {
+ Object[] ca = new Object[profile[0].length];
+ float[] vl = new float[profile[0].length];
+ for (int c = 0; c < ca.length; c++)
+ {
+ ca[c] = new char[]
+ { (char) c };
+ vl[c] = (float) profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ {
+ if (((char[]) ca[c])[0] != '-')
+ {
+ tval = ((float) profile[0][((char[]) ca[c])[0]])
+ * 100f
+ / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
+ mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
+ + " " + ((int) tval) + "%";
+ p++;
+
+ }
+ }
- mouseOver += ((int) value + "%");
+ }
+ }
+ else
+ {
+ mouseOver += ((int) value + "%");
+ }
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
}
}
+
+ /**
+ * get the sorted profile for the given position of the consensus
+ *
+ * @param hconsensus
+ * @return
+ */
+ public static int[] extractProfile(Hashtable hconsensus,
+ boolean ignoreGapsInConsensusCalculation)
+ {
+ int[] rtnval = new int[64];
+ int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
+ if (profile == null)
+ return null;
+ Object[] ca = new Object[profile[0].length];
+ float[] vl = new float[profile[0].length];
+ for (int c = 0; c < ca.length; c++)
+ {
+ ca[c] = new char[]
+ { (char) c };
+ vl[c] = (float) profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ rtnval[0] = 1;
+ for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ {
+ if (((char[]) ca[c])[0] != '-')
+ {
+ rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
+ rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ }
+ }
+ return rtnval;
+ }
}