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Get and set PDBEntrys
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
8e821a2
..
d90c231
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-39,7
+39,7
@@
public class Sequence implements SequenceI
int start;
\r
int end;
\r
Color color = Color.white;
\r
int start;
\r
int end;
\r
Color color = Color.white;
\r
- String pdbId;
\r
+ Vector pdbIds;
\r
String vamsasId;
\r
Vector dbrefs;
\r
\r
String vamsasId;
\r
Vector dbrefs;
\r
\r
@@
-96,6
+96,7
@@
public class Sequence implements SequenceI
{
\r
if (st.countTokens() == 2)
\r
{
\r
{
\r
if (st.countTokens() == 2)
\r
{
\r
+
\r
shortName = st.nextToken();
\r
\r
limits = st.nextToken();
\r
shortName = st.nextToken();
\r
\r
limits = st.nextToken();
\r
@@
-108,6
+109,10
@@
public class Sequence implements SequenceI
setEnd(Integer.valueOf(st.nextToken()).intValue());
\r
}
\r
}
\r
setEnd(Integer.valueOf(st.nextToken()).intValue());
\r
}
\r
}
\r
+
\r
+ // If we're still in this loop, parsing of start and end was ok
\r
+ // Therefore remove it from the sequence name
\r
+ name = name.substring(0, name.indexOf("/"));
\r
}
\r
catch (NumberFormatException ex)
\r
{
\r
}
\r
catch (NumberFormatException ex)
\r
{
\r
@@
-116,6
+121,7
@@
public class Sequence implements SequenceI
shortName += "/" + limits;
\r
}
\r
}
\r
shortName += "/" + limits;
\r
}
\r
}
\r
+
\r
}
\r
\r
void checkValidRange()
\r
}
\r
\r
void checkValidRange()
\r
@@
-196,9
+202,9
@@
public class Sequence implements SequenceI
*
\r
* @param id DOCUMENT ME!
\r
*/
\r
*
\r
* @param id DOCUMENT ME!
\r
*/
\r
- public void setPDBId(String id)
\r
+ public void setPDBId(Vector id)
\r
{
\r
{
\r
- pdbId = id;
\r
+ pdbIds = id;
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-206,9
+212,9
@@
public class Sequence implements SequenceI
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public String getPDBId()
\r
+ public Vector getPDBId()
\r
{
\r
{
\r
- return pdbId;
\r
+ return pdbIds;
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r