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package mc_view; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.Vector; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileParse; |
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import jalview.io.StructureFile; |
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import jalview.util.MessageManager; |
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| 74.4% |
Uncovered Elements: 34 (133) |
Complexity: 34 |
Complexity Density: 0.4 |
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public class PDBfile extends StructureFile |
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{ |
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private static String CALC_ID_PREFIX = "JalviewPDB"; |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public PDBfile(boolean addAlignmentAnnotations,... |
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boolean predictSecondaryStructure, boolean externalSecStr) |
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{ |
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super(); |
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addSettings(addAlignmentAnnotations, predictSecondaryStructure, |
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externalSecStr); |
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} |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,... |
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boolean externalSecStr, String dataObject, |
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DataSourceType sourceType) throws IOException |
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{ |
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super(false, dataObject, sourceType); |
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addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr); |
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doParse(); |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,... |
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boolean externalSecStr, FileParse source) throws IOException |
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{ |
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super(false, source); |
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addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr); |
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doParse(); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public String print(SequenceI[] seqs, boolean jvSuffix) |
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{ |
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return null; |
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} |
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| 80.4% |
Uncovered Elements: 19 (97) |
Complexity: 24 |
Complexity Density: 0.38 |
|
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@Override... |
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public void parse() throws IOException |
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{ |
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setDbRefType(DBRefSource.PDB); |
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setId(safeName(getDataName())); |
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setChains(new Vector<PDBChain>()); |
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List<SequenceI> rna = new ArrayList<SequenceI>(); |
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List<SequenceI> prot = new ArrayList<SequenceI>(); |
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PDBChain tmpchain; |
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String line = null; |
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boolean modelFlag = false; |
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boolean terFlag = false; |
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String lastID = ""; |
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int indexx = 0; |
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String atomnam = null; |
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try |
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{ |
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while ((line = nextLine()) != null) |
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{ |
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55440 |
if (line.indexOf("HEADER") == 0) |
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{ |
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if (line.length() > 62) |
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{ |
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String tid; |
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if (line.length() > 67) |
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{ |
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tid = line.substring(62, 67).trim(); |
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} |
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else |
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{ |
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tid = line.substring(62).trim(); |
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} |
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if (tid.length() > 0) |
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{ |
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setId(tid); |
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} |
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continue; |
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} |
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} |
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if (line.indexOf("SEQRES") == 0) |
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{ |
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} |
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if (line.indexOf("MODEL") == 0) |
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{ |
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modelFlag = true; |
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} |
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55424 |
if (line.indexOf("TER") == 0) |
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{ |
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terFlag = true; |
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} |
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if (modelFlag && line.indexOf("ENDMDL") == 0) |
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{ |
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break; |
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} |
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55424 |
if (line.indexOf("ATOM") == 0 |
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|| (line.indexOf("HETATM") == 0 && !terFlag)) |
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{ |
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46602 |
terFlag = false; |
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atomnam = line.substring(12, 15).trim(); |
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if (!atomnam.equals("CA") && !atomnam.equals("P")) |
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{ |
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39498 |
continue; |
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} |
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7104 |
Atom tmpatom = new Atom(line); |
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7104 |
if (tmpatom.resNumIns.trim().equals(lastID)) |
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{ |
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continue; |
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} |
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tmpchain = findChain(tmpatom.chain); |
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7101 |
if (tmpchain != null) |
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{ |
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7066 |
tmpchain.atoms.addElement(tmpatom); |
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} |
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else |
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{ |
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tmpchain = new PDBChain(getId(), tmpatom.chain); |
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getChains().add(tmpchain); |
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tmpchain.atoms.addElement(tmpatom); |
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} |
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lastID = tmpatom.resNumIns.trim(); |
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} |
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index++; |
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} |
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makeResidueList(); |
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makeCaBondList(); |
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if (getId() == null) |
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{ |
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setId(inFile.getName()); |
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} |
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for (PDBChain chain : getChains()) |
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{ |
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SequenceI chainseq = postProcessChain(chain); |
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if (isRNA(chainseq)) |
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{ |
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rna.add(chainseq); |
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} |
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else |
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{ |
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prot.add(chainseq); |
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} |
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} |
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if (predictSecondaryStructure) |
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{ |
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addSecondaryStructure(rna, prot); |
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} |
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} catch (OutOfMemoryError er) |
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{ |
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System.out.println("OUT OF MEMORY LOADING PDB FILE"); |
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throw new IOException(MessageManager |
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.getString("exception.outofmemory_loading_pdb_file")); |
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} catch (NumberFormatException ex) |
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{ |
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if (line != null) |
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{ |
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System.err.println("Couldn't read number from line:"); |
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System.err.println(line); |
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} |
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} |
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markCalcIds(); |
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} |
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209 |
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@param |
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@return |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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6 |
public static boolean isCalcIdHandled(String calcId)... |
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{ |
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6 |
return calcId != null && (CALC_ID_PREFIX.equals(calcId)); |
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} |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
220 |
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public static boolean isCalcIdForFile(AlignmentAnnotation alan,... |
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String pdbFile) |
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{ |
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return alan.getCalcId() != null |
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&& CALC_ID_PREFIX.equals(alan.getCalcId()) |
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&& pdbFile.equals(alan.getProperty("PDBID")); |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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0 |
public static String relocateCalcId(String calcId,... |
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Hashtable<String, String> alreadyLoadedPDB) throws Exception |
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{ |
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int s = CALC_ID_PREFIX.length(), |
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end = calcId.indexOf(CALC_ID_PREFIX, s); |
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String between = calcId.substring(s, end - 1); |
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return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":" |
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+ calcId.substring(end); |
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} |
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|
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| 84.6% |
Uncovered Elements: 2 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
238 |
16 |
private void markCalcIds()... |
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{ |
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16 |
for (SequenceI sq : seqs) |
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{ |
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35 |
if (sq.getAnnotation() != null) |
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{ |
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18 |
for (AlignmentAnnotation aa : sq.getAnnotation()) |
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{ |
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22 |
String oldId = aa.getCalcId(); |
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22 |
if (oldId == null) |
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{ |
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0 |
oldId = ""; |
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} |
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22 |
aa.setCalcId(CALC_ID_PREFIX); |
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22 |
aa.setProperty("PDBID", getId()); |
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22 |
aa.setProperty("oldCalcId", oldId); |
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} |
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} |
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} |
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} |
258 |
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} |