*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
*/
protected String newline = System.getProperty("line.separator");
- private AlignExportSettingI exportSettings;
+ private AlignExportSettingsI exportSettings;
+
+ private File selectedFile;
public static String INVALID_CHARACTERS = "Contains invalid characters";
}
public AppletFormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
viewpanel = alignPanel;
exportSettings = settings;
public AlignmentI readFile(String file, DataSourceType sourceType,
FileFormatI fileFormat) throws IOException
{
+ return readFile(null, file, sourceType, fileFormat);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+
+ this.selectedFile = selectedFile;
+ if (selectedFile != null)
+ this.inFile = selectedFile.getPath();
this.inFile = file;
try
{
localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
{
- alignFile = new JmolParser(inFile, sourceType);
+ // needs a File option
+ alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
}
else
{
- // todo is MCview parsing obsolete yet? JAL-2120
+ // todo is mc_view parsing obsolete yet? JAL-2120
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
sourceType);
}
((StructureFile) alignFile).setDbRefType(
FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
}
- else
+ else if (selectedFile != null) {
+ alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
+ } else
{
// alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
else
{
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
((StructureFile) alignFile).setDbRefType(Type.PDB);
return null;
}
+
/**
* Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
* data
+ *
+ * BH 2018 allows File or String, and can return RELATIVE_URL
*
- * @param data
+ * @param dataObject File or String
* @return the protocol for the input data
*/
- public static DataSourceType checkProtocol(String data)
+ public static DataSourceType checkProtocol(Object dataObject)
{
+ if(dataObject instanceof File)
+ return DataSourceType.FILE;
+
+ String data = dataObject.toString();
DataSourceType protocol = DataSourceType.PASTE;
String ft = data.toLowerCase().trim();
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
{
protocol = DataSourceType.URL;
}
- else if (jalview.bin.Jalview.isJS)
+ else if (jalview.bin.Jalview.isJS())
{
protocol = DataSourceType.RELATIVE_URL;
}