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JAL-1807 explicit imports (jalview.viewmodel)
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
015cd8e
..
afadbea
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-22,9
+22,13
@@
package jalview.gui;
package jalview.gui;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
import jalview.jbgui.GStructureChooser;
import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
import jalview.jbgui.GStructureChooser;
import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
@@
-100,9
+104,13
@@
public class StructureChooser extends GStructureChooser
public void run()
{
long startTime = System.currentTimeMillis();
public void run()
{
long startTime = System.currentTimeMillis();
- String msg = MessageManager.getString("status.fetching_db_refs");
- updateProgressIndicator(msg, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.loading_cached_pdb_entries"), startTime);
loadLocalCachedPDBEntries();
loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.searching_for_pdb_structures"),
+ startTime);
fetchStructuresMetaData();
populateFilterComboBox();
updateProgressIndicator(null, startTime);
fetchStructuresMetaData();
populateFilterComboBox();
updateProgressIndicator(null, startTime);
@@
-418,8
+426,7
@@
public class StructureChooser extends GStructureChooser
+ totalTime + ")");
if (errors.size() > 0)
{
+ totalTime + ")");
if (errors.size() > 0)
{
- StringBuilder errorMsg = new StringBuilder(
- "Operation unsucessful due to the following: \n");
+ StringBuilder errorMsg = new StringBuilder();
for (String error : errors)
{
errorMsg.append(error).append("\n");
for (String error : errors)
{
errorMsg.append(error).append("\n");
@@
-443,9
+450,9
@@
public class StructureChooser extends GStructureChooser
*/
public void pdbFromFile_actionPerformed()
{
*/
public void pdbFromFile_actionPerformed()
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
"label.select_pdb_file_for", new String[]
{ selectedSequence.getDisplayId(false) }));
chooser.setDialogTitle(MessageManager.formatMessage(
"label.select_pdb_file_for", new String[]
{ selectedSequence.getDisplayId(false) }));
@@
-454,10
+461,10
@@
public class StructureChooser extends GStructureChooser
{ selectedSequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
{ selectedSequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ if (value == JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
validateSelections();
}
}
@@
-730,7
+737,7
@@
public class StructureChooser extends GStructureChooser
}
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(
}
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(
- selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+ selectedPdbFileName, AppletFormatAdapter.FILE,
selectedSequence, true, Desktop.instance);
launchStructureViewer(ap.getStructureSelectionManager(),
selectedSequence, true, Desktop.instance);
launchStructureViewer(ap.getStructureSelectionManager(),
@@
-743,17
+750,17
@@
public class StructureChooser extends GStructureChooser
private void launchStructureViewer(StructureSelectionManager ssm,
PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
private void launchStructureViewer(StructureSelectionManager ssm,
PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
- SequenceI[] selectedSequences)
+ SequenceI[] sequences)
{
StructureViewer sViewer = new StructureViewer(ssm);
if (pdbEntriesToView.length > 1)
{
{
StructureViewer sViewer = new StructureViewer(ssm);
if (pdbEntriesToView.length > 1)
{
- sViewer.viewStructures(alignPanel, pdbEntriesToView,
- alignPanel.av.collateForPDB(pdbEntriesToView));
+ sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView),
+ alignPanel);
}
else
{
}
else
{
- sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+ sViewer.viewStructures(pdbEntriesToView[0], sequences,
alignPanel);
}
}
alignPanel);
}
}
@@
-825,13
+832,10
@@
public class StructureChooser extends GStructureChooser
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
- // JOptionPane.showMessageDialog(this, e.getMessage(),
- // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
errorWarning.append(e.getMessage());
return;
} finally
{
errorWarning.append(e.getMessage());
return;
} finally
{
- // System.out.println(">>>>> executing finally block");
validateSelections();
}
if (resultList.getSearchSummary() != null
validateSelections();
}
if (resultList.getSearchSummary() != null