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JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
6d3c18a
..
00920db
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-20,7
+20,9
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
@@
-32,6
+34,7
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
+import java.io.File;
import java.io.IOException;
/**
import java.io.IOException;
/**
@@
-55,20
+58,20
@@
public class FormatAdapter extends AppletFormatAdapter
}
public FormatAdapter(AlignmentViewPanel alignPanel,
}
public FormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
super(alignPanel, settings);
}
private void init()
{
{
super(alignPanel, settings);
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
true);
true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
true);
true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
true);
}
else
true);
}
else
@@
-161,7
+164,7
@@
public class FormatAdapter extends AppletFormatAdapter
public boolean getCacheSuffixDefault(FileFormatI format)
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
true);
}
true);
}
@@
-235,6
+238,13
@@
public class FormatAdapter extends AppletFormatAdapter
return al;
}
return al;
}
+ public AlignmentI readFile(File file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+ return al;
+ }
+
@Override
public AlignmentI readFromFile(FileParse source, FileFormatI format)
throws IOException
@Override
public AlignmentI readFromFile(FileParse source, FileFormatI format)
throws IOException