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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
structure
/
StructureSelectionManager.java
diff --git
a/src/jalview/structure/StructureSelectionManager.java
b/src/jalview/structure/StructureSelectionManager.java
index
db0b47e
..
fbfa486
100644
(file)
--- a/
src/jalview/structure/StructureSelectionManager.java
+++ b/
src/jalview/structure/StructureSelectionManager.java
@@
-161,8
+161,8
@@
public class StructureSelectionManager
}
else
{
}
else
{
- System.err.println("reportMapping: There are " + mappings.size()
- + " mappings.");
+ System.err.println(
+ "reportMapping: There are " + mappings.size() + " mappings.");
int i = 0;
for (StructureMapping sm : mappings)
{
int i = 0;
for (StructureMapping sm : mappings)
{
@@
-214,9
+214,8
@@
public class StructureSelectionManager
{
if (instances != null)
{
{
if (instances != null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_structure_selection_manager_null"),
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_structure_selection_manager_null"),
new NullPointerException(MessageManager
.getString("exception.ssm_context_is_null")));
}
new NullPointerException(MessageManager
.getString("exception.ssm_context_is_null")));
}
@@
-433,8
+432,8
@@
public class StructureSelectionManager
}
else if (seq.getName().indexOf("|") > -1)
{
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChainId = seq.getName().substring(
- seq.getName().lastIndexOf("|") + 1);
+ targetChainId = seq.getName()
+ .substring(seq.getName().lastIndexOf("|") + 1);
if (targetChainId.length() > 1)
{
if (targetChainId.trim().length() == 0)
if (targetChainId.length() > 1)
{
if (targetChainId.trim().length() == 0)
@@
-577,8
+576,8
@@
public class StructureSelectionManager
setProgressBar(null);
setProgressBar(MessageManager
.getString("status.obtaining_mapping_with_nw_alignment"));
setProgressBar(null);
setProgressBar(MessageManager
.getString("status.obtaining_mapping_with_nw_alignment"));
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
seqToStrucMapping.add(nwMapping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
@@
-637,8
+636,8
@@
public class StructureSelectionManager
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append(
- "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE)
+ .append("Sequence \u27f7 Structure mapping details");
mappingDetails.append(NEWLINE);
mappingDetails
.append("Method: inferred with Needleman & Wunsch alignment");
mappingDetails.append(NEWLINE);
mappingDetails
.append("Method: inferred with Needleman & Wunsch alignment");
@@
-670,11
+669,12
@@
public class StructureSelectionManager
.append(" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
mappingDetails.append(NEWLINE).append("SEQ start/end ");
.append(" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
mappingDetails.append(NEWLINE).append("SEQ start/end ");
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ mappingDetails
+ .append(String
+ .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
.append(" ");
.append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + (seq.getStart() - 1)));
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1)));
mappingDetails.append(NEWLINE);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
mappingDetails.append(NEWLINE);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
@@
-696,8
+696,9
@@
public class StructureSelectionManager
insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
- mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
- tmp.atomIndex });
+ mapping.put(tmp.alignmentMapping + 1,
+ new int[]
+ { tmp.resNumber, tmp.atomIndex });
}
}
}
}
@@
-775,7
+776,8
@@
public class StructureSelectionManager
* @param chain
* @param pdbfile
*/
* @param chain
* @param pdbfile
*/
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ public void mouseOverStructure(int pdbResNum, String chain,
+ String pdbfile)
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
@@
-807,7
+809,8
@@
public class StructureSelectionManager
return;
}
return;
}
- SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(
+ atoms);
for (Object li : listeners)
{
if (li instanceof SequenceListener)
for (Object li : listeners)
{
if (li instanceof SequenceListener)
@@
-950,8
+953,7
@@
public class StructureSelectionManager
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
- if (sm.sequence == seq
- || sm.sequence == seq.getDatasetSequence()
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
|| (sm.sequence.getDatasetSequence() != null && sm.sequence
.getDatasetSequence() == seq.getDatasetSequence()))
{
|| (sm.sequence.getDatasetSequence() != null && sm.sequence
.getDatasetSequence() == seq.getDatasetSequence()))
{
@@
-961,8
+963,8
@@
public class StructureSelectionManager
if (atomNo > 0)
{
if (atomNo > 0)
{
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
}
}
}
}
}
}
@@
-1328,8
+1330,8
@@
public class StructureSelectionManager
{
if (command instanceof EditCommand)
{
{
if (command instanceof EditCommand)
{
- return MappingUtils.mapEditCommand((EditCommand) command, undo,
- mapTo, gapChar, seqmappings);
+ return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo,
+ gapChar, seqmappings);
}
else if (command instanceof OrderCommand)
{
}
else if (command instanceof OrderCommand)
{