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JAL-2023 JAL-1681 fixed bug in computing '+' for co-modal codons
[jalview.git]
/
src
/
jalview
/
io
/
StructureFile.java
diff --git
a/src/jalview/io/StructureFile.java
b/src/jalview/io/StructureFile.java
index
af5a1fa
..
97e11eb
100644
(file)
--- a/
src/jalview/io/StructureFile.java
+++ b/
src/jalview/io/StructureFile.java
@@
-9,7
+9,7
@@
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.io.IOException;
import java.awt.Color;
import java.io.IOException;
@@
-67,19
+67,19
@@
public abstract class StructureFile extends AlignFile
public void xferSettings()
{
public void xferSettings()
{
- this.visibleChainAnnotation = StructureViewSettings
+ this.visibleChainAnnotation = StructureImportSettings
.isVisibleChainAnnotation();
.isVisibleChainAnnotation();
- this.predictSecondaryStructure = StructureViewSettings
+ this.predictSecondaryStructure = StructureImportSettings
.isPredictSecondaryStructure();
.isPredictSecondaryStructure();
- this.externalSecondaryStructure = StructureViewSettings
+ this.externalSecondaryStructure = StructureImportSettings
.isExternalSecondaryStructure();
}
.isExternalSecondaryStructure();
}
- public StructureFile(boolean parseImmediately, String inFile, String type)
+ public StructureFile(boolean parseImmediately, String dataObject, String type)
throws IOException
{
throws IOException
{
- super(parseImmediately, inFile, type);
+ super(parseImmediately, dataObject, type);
}
public StructureFile(boolean a, FileParse fp) throws IOException
}
public StructureFile(boolean a, FileParse fp) throws IOException
@@
-270,11
+270,11
@@
public abstract class StructureFile extends AlignFile
predictSecondaryStructure, externalSecondaryStructure,
new FileParse(getDataName(), type) };
predictSecondaryStructure, externalSecondaryStructure,
new FileParse(getDataName(), type) };
- StructureViewSettings.setShowSeqFeatures(false);
- StructureViewSettings.setVisibleChainAnnotation(false);
- StructureViewSettings
+ StructureImportSettings.setShowSeqFeatures(false);
+ StructureImportSettings.setVisibleChainAnnotation(false);
+ StructureImportSettings
.setPredictSecondaryStructure(predictSecondaryStructure);
.setPredictSecondaryStructure(predictSecondaryStructure);
- StructureViewSettings
+ StructureImportSettings
.setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
.setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
@@
-297,13
+297,14
@@
public abstract class StructureFile extends AlignFile
} catch (ClassNotFoundException q)
{
}
} catch (ClassNotFoundException q)
{
}
+ StructureImportSettings.setShowSeqFeatures(true);
}
public PDBChain findChain(String id) throws Exception
{
for (PDBChain chain : getChains())
{
}
public PDBChain findChain(String id) throws Exception
{
for (PDBChain chain : getChains())
{
- if (chain.id.equalsIgnoreCase(id))
+ if (chain.id.equals(id))
{
return chain;
}
{
return chain;
}