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JAL-3253 miscellaneous tidying up before merge to JS-develop
[jalview.git]
/
src
/
jalview
/
structures
/
models
/
AAStructureBindingModel.java
diff --git
a/src/jalview/structures/models/AAStructureBindingModel.java
b/src/jalview/structures/models/AAStructureBindingModel.java
index
ffd865f
..
56d2e9b
100644
(file)
--- a/
src/jalview/structures/models/AAStructureBindingModel.java
+++ b/
src/jalview/structures/models/AAStructureBindingModel.java
@@
-178,7
+178,8
@@
public abstract class AAStructureBindingModel
String chain = (chains != null && chains[pe] != null)
? chains[pe][se]
: null;
String chain = (chains != null && chains[pe] != null)
? chains[pe][se]
: null;
- SequenceI sq = asq.getDatasetSequence();
+ SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+ : asq.getDatasetSequence();
if (sq.getAllPDBEntries() != null)
{
for (PDBEntry pdbentry : sq.getAllPDBEntries())
if (sq.getAllPDBEntries() != null)
{
for (PDBEntry pdbentry : sq.getAllPDBEntries())
@@
-354,8
+355,8
@@
public abstract class AAStructureBindingModel
{ Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
{ Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
+ List<SequenceI> s = new ArrayList<>();
+ List<String> c = new ArrayList<>();
if (getChains() == null)
{
setChains(new String[getPdbCount()][]);
if (getChains() == null)
{
setChains(new String[getPdbCount()][]);
@@
-424,8
+425,8
@@
public abstract class AAStructureBindingModel
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
- List<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
+ List<PDBEntry> v = new ArrayList<>();
+ List<int[]> rtn = new ArrayList<>();
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
@@
-514,9
+515,7
@@
public abstract class AAStructureBindingModel
* Returns a readable description of all mappings for the wrapped pdbfile to
* any mapped sequences
*
* Returns a readable description of all mappings for the wrapped pdbfile to
* any mapped sequences
*
- * @param pdbfile
- * @param seqs
- * @return
+ * @return
*/
public String printMappings()
{
*/
public String printMappings()
{