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Removed spaces
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
db572ac
..
4a93eef
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-64,7
+64,7
@@
public class Conservation {
if (sequences.elementAt(j) instanceof Sequence) {
\r
Sequence s = (Sequence)sequences.elementAt(j);
\r
\r
if (sequences.elementAt(j) instanceof Sequence) {
\r
Sequence s = (Sequence)sequences.elementAt(j);
\r
\r
- if (s.getSequence().length() > i) {
\r
+ if (s.getLength() > i) {
\r
String res = s.getSequence().substring(i,i+1);
\r
\r
if (residueHash.containsKey(res)) {
\r
String res = s.getSequence().substring(i,i+1);
\r
\r
if (residueHash.containsKey(res)) {
\r
@@
-125,6
+125,9
@@
public class Conservation {
int count = 0;
\r
\r
for (int i = 0; i < sequences.size();i++) {
\r
int count = 0;
\r
\r
for (int i = 0; i < sequences.size();i++) {
\r
+ if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())
\r
+ { count++; continue;}
\r
+
\r
String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);
\r
if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {
\r
count++;
\r
String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);
\r
if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {
\r
count++;
\r
@@
-140,42
+143,46
@@
public class Conservation {
int totGaps = countGaps(i);
\r
float pgaps = (float)totGaps*100/(float)sequences.size();
\r
\r
int totGaps = countGaps(i);
\r
float pgaps = (float)totGaps*100/(float)sequences.size();
\r
\r
- if (percentageGaps > pgaps) {
\r
+ if (percentageGaps > pgaps)
\r
+ {
\r
Hashtable resultHash = (Hashtable)total.elementAt(i);
\r
\r
//Now find the verdict
\r
int count = 0;
\r
Enumeration e3 = resultHash.keys();
\r
\r
Hashtable resultHash = (Hashtable)total.elementAt(i);
\r
\r
//Now find the verdict
\r
int count = 0;
\r
Enumeration e3 = resultHash.keys();
\r
\r
- while (e3.hasMoreElements()) {
\r
+ while (e3.hasMoreElements())
\r
+ {
\r
String type = (String)e3.nextElement();
\r
Integer result = (Integer)resultHash.get(type);
\r
\r
//Do we want to count +ve conservation or +ve and -ve cons.?
\r
\r
String type = (String)e3.nextElement();
\r
Integer result = (Integer)resultHash.get(type);
\r
\r
//Do we want to count +ve conservation or +ve and -ve cons.?
\r
\r
- if (consflag) {
\r
- if (result.intValue() == 1) {
\r
+ if (consflag)
\r
+ {
\r
+ if (result.intValue() == 1)
\r
count++;
\r
count++;
\r
- }
\r
- } else {
\r
- if (result.intValue() != -1) {
\r
+ }
\r
+ else
\r
+ {
\r
+ if (result.intValue() != -1)
\r
count++;
\r
count++;
\r
- }
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
- if (count < 10) {
\r
+ if (count < 10)
\r
consString = consString + String.valueOf(count);
\r
consString = consString + String.valueOf(count);
\r
- } else {
\r
+ else
\r
consString = consString + "*";
\r
consString = consString + "*";
\r
- }
\r
- } else {
\r
+
\r
+ }
\r
+ else
\r
+ {
\r
consString = consString + "-";
\r
}
\r
}
\r
\r
consSequence = new DrawableSequence(name,consString,start,end);
\r
consString = consString + "-";
\r
}
\r
}
\r
\r
consSequence = new DrawableSequence(name,consString,start,end);
\r
-
\r
}
\r
\r
public jalview.gui.DrawableSequence getConsSequence() {
\r
}
\r
\r
public jalview.gui.DrawableSequence getConsSequence() {
\r