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JAL-3466 higher ‘crummy alignment’ threshold when deciding to create an identity...
[jalview.git]
/
src
/
jalview
/
structure
/
AtomSpecModel.java
diff --git
a/src/jalview/structure/AtomSpecModel.java
b/src/jalview/structure/AtomSpecModel.java
index
1b7d284
..
1ef653e
100644
(file)
--- a/
src/jalview/structure/AtomSpecModel.java
+++ b/
src/jalview/structure/AtomSpecModel.java
@@
-33,9
+33,9
@@
import java.util.TreeMap;
public class AtomSpecModel
{
/*
public class AtomSpecModel
{
/*
- * { modelNo, {chainCode, List<from-to> ranges} }
+ * { modelId, {chainCode, List<from-to> ranges} }
*/
*/
- private Map<Integer, Map<String, BitSet>> atomSpec;
+ private Map<String, Map<String, BitSet>> atomSpec;
/**
* Constructor
/**
* Constructor
@@
-53,7
+53,7
@@
public class AtomSpecModel
* @param endPos
* @param chain
*/
* @param endPos
* @param chain
*/
- public void addRange(int model, int startPos, int endPos, String chain)
+ public void addRange(String model, int startPos, int endPos, String chain)
{
/*
* Get/initialize map of data for the colour and model
{
/*
* Get/initialize map of data for the colour and model
@@
-80,12
+80,17
@@
public class AtomSpecModel
chainData.set(startPos, endPos + 1);
}
chainData.set(startPos, endPos + 1);
}
- public Iterable<Integer> getModels()
+ public Iterable<String> getModels()
{
return atomSpec.keySet();
}
{
return atomSpec.keySet();
}
- public Iterable<String> getChains(Integer model)
+ public int getModelCount()
+ {
+ return atomSpec.size();
+ }
+
+ public Iterable<String> getChains(String model)
{
return atomSpec.containsKey(model) ? atomSpec.get(model).keySet()
: null;
{
return atomSpec.containsKey(model) ? atomSpec.get(model).keySet()
: null;
@@
-99,7
+104,7
@@
public class AtomSpecModel
* @param chain
* @return
*/
* @param chain
* @return
*/
- public List<int[]> getRanges(Integer model, String chain)
+ public List<int[]> getRanges(String model, String chain)
{
List<int[]> ranges = new ArrayList<>();
if (atomSpec.containsKey(model))
{
List<int[]> ranges = new ArrayList<>();
if (atomSpec.containsKey(model))