/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
/*
* Set of any registered mappings between (dataset) sequences.
*/
- Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
-
- /*
- * Reference counters for the above mappings. Remove mappings when ref count
- * goes to zero.
- */
- private Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+ public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ if (tmp.alignmentMapping >= -1)
+ {
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
+ mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+ mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ }
}
index++;
{
results = MappingUtils.buildSearchResults(seq, index,
seqmappings);
- }
+ }
if (handlingVamsasMo)
{
results.addResult(seq, index, index);
}
/**
- * Decrement the reference counter for each of the given mappings, and remove
- * it entirely if its reference counter reduces to zero.
- *
- * @param set
- */
- public void removeMappings(Set<AlignedCodonFrame> set)
- {
- if (set != null)
- {
- for (AlignedCodonFrame acf : set)
- {
- removeMapping(acf);
- }
- }
- }
-
- /**
- * Decrement the reference counter for the given mapping, and remove it
- * entirely if its reference counter reduces to zero.
+ * Remove the given mapping
*
* @param acf
*/
- public void removeMapping(AlignedCodonFrame acf)
+ public void deregisterMapping(AlignedCodonFrame acf)
{
- if (acf != null && seqmappings.contains(acf))
+ if (acf != null)
{
- int count = seqMappingRefCounts.get(acf);
- count--;
- if (count > 0)
- {
- seqMappingRefCounts.put(acf, count);
- }
- else
- {
- seqmappings.remove(acf);
- seqMappingRefCounts.remove(acf);
- if (seqmappings.isEmpty())
- { // debug
- System.out.println("All mappings removed");
- }
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
}
}
}
/**
- * Add each of the given codonFrames to the stored set. If not aready present,
- * increments its reference count instead.
+ * Add each of the given codonFrames to the stored set, if not aready present.
*
* @param set
*/
- public void addMappings(Set<AlignedCodonFrame> set)
+ public void registerMappings(Set<AlignedCodonFrame> set)
{
if (set != null)
{
for (AlignedCodonFrame acf : set)
{
- addMapping(acf);
+ registerMapping(acf);
}
}
}
/**
- * Add the given mapping to the stored set, or if already stored, increment
- * its reference counter.
+ * Add the given mapping to the stored set, unless already stored.
*/
- public void addMapping(AlignedCodonFrame acf)
+ public void registerMapping(AlignedCodonFrame acf)
{
if (acf != null)
{
- if (seqmappings.contains(acf))
- {
- seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
- }
- else
+ if (!seqmappings.contains(acf))
{
seqmappings.add(acf);
- seqMappingRefCounts.put(acf, 1);
}
}
}
{
seqmappings.clear();
}
- if (seqMappingRefCounts != null)
- {
- seqMappingRefCounts.clear();
- }
if (sel_listeners != null)
{
sel_listeners.clear();
}
return null;
}
-
- /**
- * Returns the reference count for a mapping
- *
- * @param acf
- * @return
- */
- protected int getMappingReferenceCount(AlignedCodonFrame acf)
- {
- if (seqMappingRefCounts == null)
- {
- return 0;
- }
- Integer count = seqMappingRefCounts.get(acf);
- return (count == null ? 0 : count.intValue());
- }
}