import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
- JalviewFileChooser chooser = JalviewFileChooser
+ final JalviewFileChooser chooser = JalviewFileChooser
.forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
-
+ final AlignFrame us = this;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(this);
-
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
{
- currentFileFormat = chooser.getSelectedFormat();
- while (currentFileFormat == null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"),
- JvOptionPane.WARNING_MESSAGE);
+ @Override
+ public void run()
+ {
currentFileFormat = chooser.getSelectedFormat();
- value = chooser.showSaveDialog(this);
- if (value != JalviewFileChooser.APPROVE_OPTION)
+ while (currentFileFormat == null)
{
- return;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.select_file_format_before_saving"),
+ MessageManager
+ .getString("label.file_format_not_specified"),
+ JvOptionPane.WARNING_MESSAGE);
+ currentFileFormat = chooser.getSelectedFormat();
+ chooser.showSaveDialog(us);
}
- }
- fileName = chooser.getSelectedFile().getPath();
+ fileName = chooser.getSelectedFile().getPath();
- Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat.getName());
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
- }
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
+ }).showSaveDialog(this);
}
public boolean saveAlignment(String file, FileFormatI format)
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
- // Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(filePath, DataSourceType.FILE);
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
- } catch (Exception ex)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- if (fin != null && fin.hasWarningMessage())
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
- }
+ chooser.response(
+ new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ {
+ @Override
+ public void run()
+ {
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
+ try
+ {
+ fin = new NewickFile(new FileParse(
+ chooser.getSelectedFile(), DataSourceType.FILE));
+ viewport.setCurrentTree(
+ showNewickTree(fin, filePath).getTree());
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ ex.getMessage(),
+ MessageManager.getString(
+ "label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager.getString(
+ "label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }).openDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file or a File object
* @param sourceType
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
- public boolean parseFeaturesFile(String file, DataSourceType sourceType)
+ public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
+ // BH 2018
return avc.parseFeaturesFile(file, sourceType,
Cache.getDefault("RELAXEDSEQIDMATCHING", false));
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
+
+
final AlignFrame thisaf = this;
- final List<String> files = new ArrayList<>();
+ final List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
* Object[] { String,SequenceI}
*/
ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<String> filesnotmatched = new ArrayList<>();
+ ArrayList<Object> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018
+ Object file = files.get(i);
+ String fileName = file.toString();
String pdbfn = "";
- DataSourceType protocol = FormatAdapter.checkProtocol(file);
+ DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = new File(file);
+ File fl = (file instanceof File ? (File) file : new File(fileName));
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
{
- URL url = new URL(file);
+ URL url = new URL(fileName);
pdbfn = url.getFile();
}
if (pdbfn.length() > 0)
}
if (mtch != null)
{
- FileFormatI type = null;
+ FileFormatI type;
try
{
type = new IdentifyFile().identify(file, protocol);
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add((String) o[0]);
+ filesnotmatched.add(o[0]);
}
}
}
{
return;
}
- for (String fn : filesnotmatched)
+ for (Object fn : filesnotmatched)
{
loadJalviewDataFile(fn, null, null, null);
}
* @param file
* either a filename or a URL string.
*/
- public void loadJalviewDataFile(String file, DataSourceType sourceType,
+ public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
+ // BH 2018 was String file
try
{
if (sourceType == null)
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+ final AlignFrame us = this;
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ {
+ @Override
+ public void run()
+ {
- int value = chooser.showOpenDialog(null);
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ };
+ }).openDialog(null);
}