import jalview.util.Comparison;
import jalview.util.Format;
-import java.util.ArrayList;
import java.util.Hashtable;
/**
* @param rnaStruc
*/
public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result, boolean profile,
+ int end, Hashtable<String, Object>[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
- Hashtable residueHash;
+ Hashtable<String, Object> residueHash;
String maxResidue;
char[] struc = rnaStruc.getRNAStruc().toCharArray();
{
if (sequences[j] == null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
}
}
- residueHash = new Hashtable();
+ residueHash = new Hashtable<>();
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
maxResidue = "{";
}
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
+ residueHash.put(PID_GAPS, Float.valueOf(percentage));
percentage = ((float) count * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
if (result[i] == null)
{
maxResidue = maxResidue.equals("(") ? ")"
: maxResidue.equals("[") ? "]" : "}";
- residueHash = new Hashtable();
+ residueHash = new Hashtable<>();
if (profile)
{
residueHash.put(PROFILE,
residueHash.put(PAIRPROFILE, pairs);
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
+ residueHash.put(PID_GAPS, Float.valueOf(percentage));
percentage = ((float) count * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
result[bpEnd] = residueHash;
}
* @param includeAllConsSymbols
*/
public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
+ Hashtable<String, Object>[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, long nseq)
{
for (int i = iStart; i < width; i++)
{
- Hashtable hci;
+ Hashtable<String, Object> hci;
if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
{
// happens if sequences calculated over were shorter than alignment
* @param hconsensus
* @return profile of the given column
*/
- public static int[] extractProfile(Hashtable hconsensus,
+ public static int[] extractProfile(Hashtable<String, Object> hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2
System.arraycopy(rtnval, 0, result, 1, rtnval.length);
return result;
}
-
- public static void main(String args[])
- {
- // Short test to see if checkBpType works
- ArrayList<String> test = new ArrayList<String>();
- test.add("A");
- test.add("c");
- test.add("g");
- test.add("T");
- test.add("U");
- for (String i : test)
- {
- for (String j : test)
- {
- System.out.println(i + "-" + j + ": "
- + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
- }
- }
- }
}