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
JAL-3725 restrict mapped virtual feature location to mapped region
[jalview.git]
/
src
/
jalview
/
io
/
ModellerDescription.java
diff --git
a/src/jalview/io/ModellerDescription.java
b/src/jalview/io/ModellerDescription.java
index
a7a1efa
..
c1849fc
100755
(executable)
--- a/
src/jalview/io/ModellerDescription.java
+++ b/
src/jalview/io/ModellerDescription.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-61,7
+61,8
@@
public class ModellerDescription
*/
final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
*/
final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
- final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+ final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
+ '.' };
java.util.Hashtable fields = new java.util.Hashtable();
java.util.Hashtable fields = new java.util.Hashtable();
@@
-84,7
+85,7
@@
public class ModellerDescription
resCode(int v)
{
resCode(int v)
{
- val = new Integer(v);
+ val = Integer.valueOf(v);
field = val.toString();
}
};
field = val.toString();
}
};
@@
-244,15
+245,15
@@
public class ModellerDescription
{
// Set start and end before we update the type (in the case of a
// synthesized field set)
{
// Set start and end before we update the type (in the case of a
// synthesized field set)
- if (getStartCode() == null
- || (getStartNum() != seq.getStart() && getStartCode().val != null))
+ if (getStartCode() == null || (getStartNum() != seq.getStart()
+ && getStartCode().val != null))
{
// unset or user updated sequence start position
setStartCode(seq.getStart());
}
{
// unset or user updated sequence start position
setStartCode(seq.getStart());
}
- if (getEndCode() == null
- || (getEndNum() != seq.getEnd() && getStartCode() != null && getStartCode().val != null))
+ if (getEndCode() == null || (getEndNum() != seq.getEnd()
+ && getStartCode() != null && getStartCode().val != null))
{
setEndCode(seq.getEnd());
}
{
setEndCode(seq.getEnd());
}
@@
-268,10
+269,10
@@
public class ModellerDescription
// sets the local reference field
int t = 0; // sequence
if (seq.getDatasetSequence() != null
// sets the local reference field
int t = 0; // sequence
if (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getDBRef() != null)
+ && seq.getDatasetSequence().getDBRefs() != null)
{
jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
{
jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
- .getDBRef();
+ .getDBRefs();
int i, j;
for (i = 0, j = dbr.length; i < j; i++)
{
int i, j;
for (i = 0, j = dbr.length; i < j; i++)
{