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JAL-3438 spotless for 2.11.2.0
[jalview.git]
/
src
/
jalview
/
io
/
StructureFile.java
diff --git
a/src/jalview/io/StructureFile.java
b/src/jalview/io/StructureFile.java
index
3025907
..
6b623a1
100644
(file)
--- a/
src/jalview/io/StructureFile.java
+++ b/
src/jalview/io/StructureFile.java
@@
-38,7
+38,7
@@
import java.lang.reflect.Constructor;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
-import MCview.PDBChain;
+import mc_view.PDBChain;
public abstract class StructureFile extends AlignFile
{
public abstract class StructureFile extends AlignFile
{
@@
-68,7
+68,7
@@
public abstract class StructureFile extends AlignFile
private boolean pdbIdAvailable;
private boolean pdbIdAvailable;
- public StructureFile(String inFile, DataSourceType sourceType)
+ public StructureFile(Object inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
throws IOException
{
super(inFile, sourceType);
@@
-98,7
+98,7
@@
public abstract class StructureFile extends AlignFile
}
}
- public StructureFile(boolean parseImmediately, String dataObject,
+ public StructureFile(boolean parseImmediately, Object dataObject,
DataSourceType sourceType) throws IOException
{
super(parseImmediately, dataObject, sourceType);
DataSourceType sourceType) throws IOException
{
super(parseImmediately, dataObject, sourceType);
@@
-119,6
+119,7
@@
public abstract class StructureFile extends AlignFile
pdbSequence.setName(getId() + "|" + pdbSequence.getName());
PDBEntry entry = new PDBEntry();
entry.setId(getId());
pdbSequence.setName(getId() + "|" + pdbSequence.getName());
PDBEntry entry = new PDBEntry();
entry.setId(getId());
+ entry.setFakedPDBId(!isPPDBIdAvailable());
entry.setType(getStructureFileType());
if (chain.id != null)
{
entry.setType(getStructureFileType());
if (chain.id != null)
{
@@
-342,7
+343,14
@@
public abstract class StructureFile extends AlignFile
StructureImportSettings.setShowSeqFeatures(true);
}
StructureImportSettings.setShowSeqFeatures(true);
}
- public PDBChain findChain(String id) throws Exception
+ /**
+ * Answers the first PDBChain found matching the given id, or null if none is
+ * found
+ *
+ * @param id
+ * @return
+ */
+ public PDBChain findChain(String id)
{
for (PDBChain chain : getChains())
{
{
for (PDBChain chain : getChains())
{
@@
-351,7
+359,7
@@
public abstract class StructureFile extends AlignFile
return chain;
}
}
return chain;
}
}
- throw new Exception("PDB chain not Found!");
+ return null;
}
public void makeResidueList()
}
public void makeResidueList()