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JAL-4061 JAL-4062 button in Find dialog to copy highlighted regions to clipboard
[jalview.git]
/
src
/
jalview
/
analysis
/
StructureFrequency.java
diff --git
a/src/jalview/analysis/StructureFrequency.java
b/src/jalview/analysis/StructureFrequency.java
index
546a214
..
c04df6c
100644
(file)
--- a/
src/jalview/analysis/StructureFrequency.java
+++ b/
src/jalview/analysis/StructureFrequency.java
@@
-27,7
+27,6
@@
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.Comparison;
import jalview.util.Format;
-import java.util.ArrayList;
import java.util.Hashtable;
/**
import java.util.Hashtable;
/**
@@
-94,11
+93,11
@@
public class StructureFrequency
* @param rnaStruc
*/
public static final void calculate(SequenceI[] sequences, int start,
* @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)
{
AlignmentAnnotation rnaStruc)
{
- Hashtable residueHash;
+ Hashtable<String, Object> residueHash;
String maxResidue;
char[] struc = rnaStruc.getRNAStruc().toCharArray();
String maxResidue;
char[] struc = rnaStruc.getRNAStruc().toCharArray();
@@
-191,7
+190,7
@@
public class StructureFrequency
}
}
}
}
- residueHash = new Hashtable();
+ residueHash = new Hashtable<>();
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
@@
-227,14
+226,14
@@
public class StructureFrequency
maxResidue = "{";
}
}
maxResidue = "{";
}
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
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;
percentage = ((float) count * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
if (result[i] == null)
{
if (result[i] == null)
{
@@
-251,7
+250,7
@@
public class StructureFrequency
maxResidue = maxResidue.equals("(") ? ")"
: maxResidue.equals("[") ? "]" : "}";
maxResidue = maxResidue.equals("(") ? ")"
: maxResidue.equals("[") ? "]" : "}";
- residueHash = new Hashtable();
+ residueHash = new Hashtable<>();
if (profile)
{
residueHash.put(PROFILE,
if (profile)
{
residueHash.put(PROFILE,
@@
-261,14
+260,14
@@
public class StructureFrequency
residueHash.put(PAIRPROFILE, pairs);
}
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(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;
percentage = ((float) count * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
result[bpEnd] = residueHash;
}
result[bpEnd] = residueHash;
}
@@
-288,7
+287,7
@@
public class StructureFrequency
* @param includeAllConsSymbols
*/
public static void completeConsensus(AlignmentAnnotation consensus,
* @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)
{
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, long nseq)
{
@@
-315,7
+314,7
@@
public class StructureFrequency
for (int i = iStart; i < width; i++)
{
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
if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
{
// happens if sequences calculated over were shorter than alignment
@@
-415,7
+414,7
@@
public class StructureFrequency
* @param hconsensus
* @return profile of the given column
*/
* @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
boolean ignoreGapsInConsensusCalculation)
{
int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2