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Merge branch 'develop' into releases/Release_2_11_3_Branch
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
8b1525c
..
9a4e982
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-30,7
+30,6
@@
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
@@
-164,15
+163,11
@@
public class AppletFormatAdapter
public AlignmentI readFile(File selectedFile, String file,
DataSourceType sourceType, FileFormatI fileFormat,
public AlignmentI readFile(File selectedFile, String file,
DataSourceType sourceType, FileFormatI fileFormat,
- AlignmentAnnotation.TFType tempfacType) throws IOException
+ StructureImportSettings.TFType tempfacType) throws IOException
{
this.selectedFile = selectedFile;
{
this.selectedFile = selectedFile;
- if (selectedFile != null)
- {
- this.inFile = selectedFile.getPath();
- }
- this.inFile = file;
+ this.inFile = selectedFile != null ? selectedFile.getPath() : file;
try
{
if (fileFormat.isStructureFile())
try
{
if (fileFormat.isStructureFile())
@@
-184,12
+179,16
@@
public class AppletFormatAdapter
.toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
.toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
+ if (tempfacType != null)
+ {
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+ }
if (isParseWithJMOL)
{
// needs a File option
alignFile = new JmolParser(
selectedFile == null ? inFile : selectedFile, sourceType,
if (isParseWithJMOL)
{
// needs a File option
alignFile = new JmolParser(
selectedFile == null ? inFile : selectedFile, sourceType,
- tempfacType);
+ StructureImportSettings.getTemperatureFactorType());
}
else
{
}
else
{