import java.util.Collection;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
"1.11.2", "1.11.1", "1.11" };
// Missing 1.1 as this has known bug see JAL-2422
- private static String[] CHIMERAX_VERSIONS = new String[] { "1.2.5", "1.0",
- "0.93", "0.92", "0.91", "0.9" };
+ private static String[] CHIMERAX_VERSIONS = new String[] { "1.3", "1.2.5",
+ "1.0", "0.93", "0.92", "0.91", "0.9" };
static final String[] defaultStructureKeys = { "Structure", "pdb",
"pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
/**
* This is called by the selectionListener to let us know that the user has
- * changed their selection in Chimera. We need to go back to Chimera to find out
- * what is currently selected and update our list.
+ * changed their selection in Chimera. We need to go back to Chimera to find
+ * out what is currently selected and update our list.
*/
public void chimeraSelectionChanged()
{
}
/**
- * Add a selection to the selection list. This is called primarily by the Model
- * Navigator Dialog to keep the selections in sync
+ * Add a selection to the selection list. This is called primarily by the
+ * Model Navigator Dialog to keep the selections in sync
*
* @param selectionToAdd
- * the selection to add to our list
+ * the selection to add to our list
*/
public void addChimSelection(ChimeraStructuralObject selectionToAdd)
{
* Model Navigator Dialog to keep the selections in sync
*
* @param selectionToRemove
- * the selection to remove from our list
+ * the selection to remove from our list
*/
public void removeChimSelection(ChimeraStructuralObject selectionToRemove)
{
// Add default installation paths
if (os.startsWith("Linux"))
{
- // ChimeraX .deb and .rpm packages put symbolic link from /usr/bin/chimerax
- pathList.add(String.format("/usr/bin/%s", chimeraExe.toLowerCase()));
+ // ChimeraX .deb and .rpm packages put symbolic link from
+ // /usr/bin/chimerax
+ pathList.add(String.format("/usr/bin/%s",
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("/usr/bin/%s", chimeraExe));
- pathList.add(
- String.format("/usr/local/bin/%s", chimeraExe.toLowerCase()));
+ pathList.add(String.format("/usr/local/bin/%s",
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("/usr/local/bin/%s", chimeraExe));
// these paths also used by .deb and .rpm
pathList.add(String.format("/usr/lib/ucsf-%s/bin/%s",
- chimera.toLowerCase(), chimeraExe));
+ chimera.toLowerCase(Locale.ROOT), chimeraExe));
pathList.add(String.format("/usr/libexec/UCSF-%s/bin/%s", chimera,
chimeraExe));
pathList.add(String.format("/usr/local/chimera/bin/%s", chimeraExe));
// user home paths
- pathList.add(String.format("%s/bin/%s",
- System.getProperty("user.home"), chimeraExe.toLowerCase()));
+ pathList.add(
+ String.format("%s/bin/%s", System.getProperty("user.home"),
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("%s/bin/%s",
System.getProperty("user.home"), chimeraExe));
pathList.add(String.format("%s/opt/bin/%s",
- System.getProperty("user.home"), chimeraExe.toLowerCase()));
+ System.getProperty("user.home"),
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("%s/opt/bin/%s",
System.getProperty("user.home"), chimeraExe));
pathList.add(String.format("%s/local/bin/%s",
- System.getProperty("user.home"), chimeraExe.toLowerCase()));
+ System.getProperty("user.home"),
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("%s/local/bin/%s",
System.getProperty("user.home"), chimeraExe));
}
{
for (String root : new String[] { "\\Program Files",
"C:\\Program Files", "\\Program Files (x86)",
- "C:\\Program Files (x86)" })
+ "C:\\Program Files (x86)", String.format("%s\\AppData\\Local",
+ System.getProperty("user.home")) })
{
String[] candidates = isChimeraX ? CHIMERAX_VERSIONS
: CHIMERA_VERSIONS;