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JAL-3390 pull-up refactoring towards functional changes...
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
6c934c8
..
b28b81c
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-20,6
+20,7
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
@@
-326,7
+327,7
@@
public class AppJmol extends StructureViewerBase
for (String s : files)
{
fileList.append(SPACE).append(QUOTE)
for (String s : files)
{
fileList.append(SPACE).append(QUOTE)
- .append(Platform.escapeString(s)).append(QUOTE);
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
String filesString = fileList.toString();
}
String filesString = fileList.toString();
@@
-396,9
+397,9
@@
public class AppJmol extends StructureViewerBase
}
// refresh the sequence colours for the new structure(s)
}
// refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentViewPanel avp : _colourwith)
{
{
- jmb.updateColours(ap);
+ jmb.updateColours(avp);
}
// do superposition if asked to
if (alignAddedStructures)
}
// do superposition if asked to
if (alignAddedStructures)
@@
-515,7
+516,7
@@
public class AppJmol extends StructureViewerBase
addingStructures = true; // already files loaded.
for (int c = 0; c < filesInViewer.length; c++)
{
addingStructures = true; // already files loaded.
for (int c = 0; c < filesInViewer.length; c++)
{
- if (filesInViewer[c].equals(file))
+ if (Platform.pathEquals(filesInViewer[c], file))
{
file = null;
break;
{
file = null;
break;