git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Send gapChar to print original Data
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentAnnotation.java
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
d75683c
..
5a2c46e
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-139,6
+139,8
@@
public class AlignmentAnnotation
this.annotations = annotations;
\r
graph = graphType;
\r
\r
this.annotations = annotations;
\r
graph = graphType;
\r
\r
+ boolean drawValues = true;
\r
+
\r
if (min == max)
\r
{
\r
min = 999999999;
\r
if (min == max)
\r
{
\r
min = 999999999;
\r
@@
-149,6
+151,11
@@
public class AlignmentAnnotation
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
+ if(drawValues && annotations[i].displayCharacter.length() > 1 )
\r
+ {
\r
+ drawValues = false;
\r
+ }
\r
+
\r
if (annotations[i].value > max)
\r
{
\r
max = annotations[i].value;
\r
if (annotations[i].value > max)
\r
{
\r
max = annotations[i].value;
\r
@@
-166,19
+173,30
@@
public class AlignmentAnnotation
\r
for (int i = 0; i < annotations.length; i++)
\r
{
\r
\r
for (int i = 0; i < annotations.length; i++)
\r
{
\r
- if ((annotations[i] != null) &&
\r
- ((annotations[i].secondaryStructure == 'H') ||
\r
+ if (!hasIcons
\r
+ && annotations[i] != null
\r
+ && ((annotations[i].secondaryStructure == 'H') ||
\r
(annotations[i].secondaryStructure == 'E')))
\r
{
\r
hasIcons = true;
\r
}
\r
\r
(annotations[i].secondaryStructure == 'E')))
\r
{
\r
hasIcons = true;
\r
}
\r
\r
- if ((annotations[i] != null) &&
\r
- (annotations[i].displayCharacter.length() > 0))
\r
+ if (!hasText
\r
+ && annotations[i]!=null
\r
+ && annotations[i].displayCharacter.length() > 0)
\r
{
\r
hasText = true;
\r
}
\r
}
\r
{
\r
hasText = true;
\r
}
\r
}
\r
+
\r
+ if(!drawValues && graphType!=NO_GRAPH)
\r
+ {
\r
+ for (int i = 0; i < annotations.length; i++)
\r
+ {
\r
+ if (annotations[i] != null)
\r
+ annotations[i].displayCharacter = "";
\r
+ }
\r
+ }
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-254,7
+272,7
@@
public class AlignmentAnnotation
if(startRes < sequenceRef.getStart())
\r
startRes = sequenceRef.getStart();
\r
\r
if(startRes < sequenceRef.getStart())
\r
startRes = sequenceRef.getStart();
\r
\r
- int seqPos, seqIndex;
\r
+ int seqPos;
\r
\r
int fileOffset = 0;
\r
if(startRes > sequenceRef.getStart())
\r
\r
int fileOffset = 0;
\r
if(startRes > sequenceRef.getStart())
\r
@@
-264,16
+282,13
@@
public class AlignmentAnnotation
\r
for(int i = 0; i < annotations.length; i++)
\r
{
\r
\r
for(int i = 0; i < annotations.length; i++)
\r
{
\r
- seqPos = sequenceRef.findPosition(i - fileOffset)-1;
\r
+ seqPos = sequenceRef.findPosition(i + fileOffset);
\r
if(seqPos<annotations.length)
\r
{
\r
if(seqPos<annotations.length)
\r
{
\r
- if (annotations[seqPos] != null)
\r
+ if (annotations[i] != null)
\r
{
\r
{
\r
- seqIndex = sequenceRef.findIndex(i) + 1;
\r
-
\r
- if(seqIndex>=startRes)
\r
- sequenceMapping.put(new Integer(seqIndex),
\r
- annotations[seqPos]);
\r
+ sequenceMapping.put(new Integer(seqPos),
\r
+ annotations[i]);
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
@@
-286,9
+301,16
@@
public class AlignmentAnnotation
{
\r
int a=0, aSize = sequenceRef.getLength();
\r
\r
{
\r
int a=0, aSize = sequenceRef.getLength();
\r
\r
+ if(aSize == 0)
\r
+ {
\r
+ //Its been deleted
\r
+ return;
\r
+ }
\r
+
\r
int position;
\r
Annotation[] temp = new Annotation[aSize];
\r
Integer index;
\r
int position;
\r
Annotation[] temp = new Annotation[aSize];
\r
Integer index;
\r
+
\r
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
\r
{
\r
index = new Integer(a);
\r
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
\r
{
\r
index = new Integer(a);
\r