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isGap method added to utils
author
amwaterhouse
<Andrew Waterhouse>
Wed, 15 Dec 2004 17:11:34 +0000
(17:11 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 15 Dec 2004 17:11:34 +0000
(17:11 +0000)
src/jalview/analysis/Conservation.java
patch
|
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|
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src/jalview/datamodel/Sequence.java
patch
|
blob
|
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src/jalview/datamodel/SequenceFeature.java
patch
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src/jalview/util/Comparison.java
patch
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diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
f99661e
..
eed6d0a
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-119,17
+119,19
@@
public class Conservation {
}
\r
}
\r
\r
}
\r
}
\r
\r
- public int countGaps(int j) {
\r
+ public int countGaps(int j)
\r
+ {
\r
int count = 0;
\r
\r
int count = 0;
\r
\r
- for (int i = 0; i < sequences.size();i++) {
\r
+ for (int i = 0; i < sequences.size();i++)
\r
+ {
\r
if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())
\r
{ count++; continue;}
\r
\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
+ char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
\r
+ if (jalview.util.Comparison.isGap((c)))
\r
count++;
\r
count++;
\r
- }
\r
+
\r
}
\r
return count;
\r
}
\r
}
\r
return count;
\r
}
\r
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
cc5d760
..
d35cbe8
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-144,19
+144,18
@@
public class Sequence implements SequenceI
\r
while (i< sequence.length() && j <= end && j <= pos) {
\r
\r
\r
while (i< sequence.length() && j <= end && j <= pos) {
\r
\r
- String s = sequence.substring(i,i+1);
\r
+ char c = sequence.charAt(i);
\r
\r
\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
\r
+ if (!jalview.util.Comparison.isGap((c)))
\r
j++;
\r
j++;
\r
- }
\r
+
\r
i++;
\r
}
\r
i++;
\r
}
\r
- if (j == end && j < pos) {
\r
+ if (j == end && j < pos)
\r
return end+1;
\r
return end+1;
\r
- } else {
\r
-
\r
+ else
\r
return i;
\r
return i;
\r
- }
\r
+
\r
}
\r
\r
public int findPosition(int i) {
\r
}
\r
\r
public int findPosition(int i) {
\r
@@
-164,12
+163,13
@@
public class Sequence implements SequenceI
int j = 0;
\r
int pos = start;
\r
\r
int j = 0;
\r
int pos = start;
\r
\r
- while (j < i) {
\r
- String s = sequence.substring(j,j+1);
\r
+ while (j < i)
\r
+ {
\r
+ char c = sequence.charAt(j);
\r
\r
\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
\r
+ if (!jalview.util.Comparison.isGap((c)))
\r
pos++;
\r
pos++;
\r
- }
\r
+
\r
j++;
\r
}
\r
return pos;
\r
j++;
\r
}
\r
return pos;
\r
diff --git
a/src/jalview/datamodel/SequenceFeature.java
b/src/jalview/datamodel/SequenceFeature.java
index
2512978
..
cba91df
100755
(executable)
--- a/
src/jalview/datamodel/SequenceFeature.java
+++ b/
src/jalview/datamodel/SequenceFeature.java
@@
-161,12
+161,12
@@
public class SequenceFeature {
}
\r
\r
for (int i = fstart; i <= fend; i++) {
\r
}
\r
\r
for (int i = fstart; i <= fend; i++) {
\r
- String s = sequence.sequence.substring(i,i+1);
\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
\r
+ char c = sequence.sequence.charAt(i);
\r
+ if (!jalview.util.Comparison.isGap((c)))
\r
g.fillRect(x1+(i-fstart)*width,y1,width,height);
\r
g.fillRect(x1+(i-fstart)*width,y1,width,height);
\r
- } else {
\r
+ else
\r
g.drawString("-",x1+(i-fstart)*width,y1+height);
\r
g.drawString("-",x1+(i-fstart)*width,y1+height);
\r
- }
\r
+
\r
}
\r
\r
}
\r
}
\r
\r
}
\r
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
72fb1d1
..
d8e599b
100755
(executable)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-16,27
+16,22
@@
public class Comparison {
int ilen = end-start+1;
\r
int jlen = end-start+1;
\r
\r
int ilen = end-start+1;
\r
int jlen = end-start+1;
\r
\r
- if ( si.substring(start + ilen).equals("-") ||
\r
- si.substring(start + ilen).equals(".") ||
\r
- si.substring(start + ilen).equals(" ")) {
\r
-
\r
+ if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
\r
+ {
\r
ilen--;
\r
\r
ilen--;
\r
\r
- while (si.substring(start + ilen,start + ilen+1).equals("-") ||
\r
- si.substring(start + ilen,start + ilen+1).equals(".") ||
\r
- si.substring(start + ilen,start + ilen+1).equals(" ")) {
\r
+ while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))
\r
+ {
\r
ilen--;
\r
}
\r
}
\r
\r
ilen--;
\r
}
\r
}
\r
\r
- if ( sj.substring(start + jlen).equals("-") ||
\r
- sj.substring(start + jlen).equals(".") ||
\r
- sj.substring(start + jlen).equals(" ")) {
\r
+ if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )
\r
+ {
\r
jlen--;
\r
\r
jlen--;
\r
\r
- while (sj.substring(start + jlen,start + jlen+1).equals("-") ||
\r
- sj.substring(start + jlen,start + jlen+1).equals(".") ||
\r
- sj.substring(start + jlen,start + jlen+1).equals(" ")) {
\r
+ while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))
\r
+ {
\r
jlen--;
\r
}
\r
}
\r
jlen--;
\r
}
\r
}
\r
@@
-68,47
+63,47
@@
public class Comparison {
}
\r
\r
/** */
\r
}
\r
\r
/** */
\r
- public static float PID(Sequence s1 , Sequence s2) {
\r
- int res = 0;
\r
+ public static float PID(Sequence s1 , Sequence s2)
\r
+ {
\r
int len;
\r
\r
int len;
\r
\r
- if (s1.getSequence().length() > s2.getSequence().length()) {
\r
+ if (s1.getSequence().length() > s2.getSequence().length())
\r
len = s1.getSequence().length();
\r
len = s1.getSequence().length();
\r
- } else {
\r
+ else
\r
len = s2.getSequence().length();
\r
len = s2.getSequence().length();
\r
- }
\r
+
\r
\r
int bad = 0;
\r
\r
\r
int bad = 0;
\r
\r
- for (int i = 0; i < len; i++) {
\r
- String str1 = "";
\r
- String str2 = "";
\r
+ for (int i = 0; i < len; i++)
\r
+ {
\r
+ char chr1;
\r
+ char chr2;
\r
\r
\r
- if (i < s1.getSequence().length()) {
\r
- str1 = s1.getSequence().substring(i,i+1);
\r
- } else {
\r
- str1 = ".";
\r
- }
\r
+ if (i < s1.getSequence().length())
\r
+ chr1 = s1.getSequence().charAt(i);
\r
+ else
\r
+ chr1 = '.';
\r
\r
\r
- if (i < s2.getSequence().length()) {
\r
- str2 = s2.getSequence().substring(i,i+1);
\r
- } else {
\r
- str2 = ".";
\r
- }
\r
\r
\r
- if (!(str1.equals(".") ||
\r
- str1.equals("-") ||
\r
- str1.equals(" ")) &&
\r
- !(str2.equals(".") ||
\r
- str2.equals("-") ||
\r
- str2.equals(" "))) {
\r
+ if (i < s2.getSequence().length())
\r
+ chr2 = s2.getSequence().charAt(i);
\r
+ else
\r
+ chr2 = '.';
\r
+
\r
\r
\r
- if (!str1.equals(str2)) {
\r
+ if (!(jalview.util.Comparison.isGap( chr1 )) && !(jalview.util.Comparison.isGap( chr2 )))
\r
+ {
\r
+ if (chr1!=chr2)
\r
bad++;
\r
bad++;
\r
- }
\r
}
\r
}
\r
\r
return (float)100*(len-bad)/len;
\r
}
\r
}
\r
}
\r
\r
return (float)100*(len-bad)/len;
\r
}
\r
+
\r
+ public static boolean isGap(char c)
\r
+ {
\r
+ return (c != '.' && c != '-' && c != ' ') ? false : true;
\r
+ }
\r
}
\r
}
\r