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Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
[jalview.git]
/
src
/
jalview
/
bin
/
Cache.java
diff --git
a/src/jalview/bin/Cache.java
b/src/jalview/bin/Cache.java
index
8493dff
..
4be7830
100755
(executable)
--- a/
src/jalview/bin/Cache.java
+++ b/
src/jalview/bin/Cache.java
@@
-20,6
+20,7
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import jalview.datamodel.PDBEntry;
import jalview.structure.StructureImportSettings;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import jalview.structure.StructureImportSettings;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
@@
-226,11
+227,15
@@
public class Cache
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
-
+
/**
* Allowed values are PDB or mmCIF
*/
/**
* Allowed values are PDB or mmCIF
*/
- private final static String DEFAULT_STRUCTURE_FORMAT = "PDB";
+ private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+ .toString();
+
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString();
/**
* Initialises the Jalview Application Log
/**
* Initialises the Jalview Application Log
@@
-428,12
+433,12
@@
public class Cache
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
- StructureImportSettings.setCurrentDefaultFormat(jalview.bin.Cache
+ StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault(
"DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
.getDefault(
"DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
-
- StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault(
- "PROCESS_HETATM", false));
+ StructureImportSettings
+ .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null