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JAL-2154 use convenience method
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
1aa29e0
..
21d990c
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-20,10
+20,16
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import java.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* Calculates conservation values for a given set of sequences
/**
* Calculates conservation values for a given set of sequences
@@
-108,7
+114,7
@@
public class Conservation
{
for (s = 0; s < sSize; s++)
{
{
for (s = 0; s < sSize; s++)
{
- sarray[s] = (SequenceI) sequences.get(s);
+ sarray[s] = sequences.get(s);
if (sarray[s].getLength() > maxLength)
{
maxLength = sarray[s].getLength();
if (sarray[s].getLength() > maxLength)
{
maxLength = sarray[s].getLength();
@@
-229,10
+235,7
@@
public class Conservation
c = '-';
}
c = '-';
}
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
+ c = toUpperCase(c);
}
values[c]++;
}
}
values[c]++;
}
@@
-274,8
+277,7
@@
public class Conservation
resultHash.put(type, ht.get("-"));
}
}
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals((Integer) ht
- .get(res)) == false)
+ else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
{
resultHash.put(type, new Integer(-1));
}
{
resultHash.put(type, new Integer(-1));
}
@@
-321,6
+323,7
@@
public class Conservation
}
else
{
}
else
{
+ c = toUpperCase(c);
nres++;
if (nres == 1)
nres++;
if (nres == 1)
@@
-342,6
+345,22
@@
public class Conservation
}
/**
}
/**
+ * Returns the upper-cased character if between 'a' and 'z', else the
+ * unchanged value
+ *
+ * @param c
+ * @return
+ */
+ char toUpperCase(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
* @param consflag
* Calculates the conservation sequence
*
* @param consflag
@@
-368,14
+387,14
@@
public class Conservation
{
consString.append('-');
}
{
consString.append('-');
}
- consSymbs = new String[end-start+1];
+ consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
gapcons = countConsNGaps(i);
totGaps = gapcons[1];
for (int i = start; i <= end; i++)
{
gapcons = countConsNGaps(i);
totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.length;
- consSymbs[i-start]=new String();
-
+ pgaps = ((float) totGaps * 100) / sequences.length;
+ consSymbs[i - start] = new String();
+
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
@@
-392,7
+411,7
@@
public class Conservation
{
if (result.intValue() == 1)
{
{
if (result.intValue() == 1)
{
- consSymbs[i-start] = type+" "+consSymbs[i-start];
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
}
count++;
}
}
@@
-400,14
+419,17
@@
public class Conservation
{
if (result.intValue() != -1)
{
{
if (result.intValue() != -1)
{
- {
- if (result.intValue()==0) {
- consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
- } else {
- consSymbs[i-start] = type+" "+consSymbs[i-start];
- }
+ {
+ if (result.intValue() == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
}
}
-
+
count++;
}
}
count++;
}
}
@@
-671,7
+693,7
@@
public class Conservation
qmax = qualityRange[1].floatValue();
}
qmax = qualityRange[1].floatValue();
}
- for (int i = 0; i < alWidth; i++)
+ for (int i = istart; i < alWidth; i++)
{
float value = 0;
{
float value = 0;
@@
-679,7
+701,7
@@
public class Conservation
if (Character.isDigit(c))
{
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
}
else if (c == '*')
{
@@
-692,10
+714,12
@@
public class Conservation
float vprop = value - min;
vprop /= max;
float vprop = value - min;
vprop /= max;
+ int consp = i - start;
+ String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
conservation.annotations[i] = new Annotation(String.valueOf(c),
conservation.annotations[i] = new Annotation(String.valueOf(c),
- consSymbs[i-start], ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
// Quality calc
if (quality2 != null)
// Quality calc
if (quality2 != null)