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JAL-1990 suggested revision to separate references to UI components from datamodel...
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
fd2de8e
..
8dbe0c2
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-717,10
+717,7
@@
public class StructureChooser extends GStructureChooser implements
@Override
public void ok_ActionPerformed()
{
@Override
public void ok_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
new Thread(new Runnable()
{
@Override
new Thread(new Runnable()
{
@Override
@@
-765,7
+762,8
@@
public class StructureChooser extends GStructureChooser implements
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
}
else if (currentView == VIEWS_LOCAL_PDB)
{
@@
-788,7
+786,8
@@
public class StructureChooser extends GStructureChooser implements
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
else if (currentView == VIEWS_ENTER_ID)
{
@@
-830,7
+829,8
@@
public class StructureChooser extends GStructureChooser implements
jalview.io.AppletFormatAdapter.FILE,
selectedSequence, true, Desktop.instance);
jalview.io.AppletFormatAdapter.FILE,
selectedSequence, true, Desktop.instance);
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ launchStructureViewer(ssm,
+ new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
}
mainFrame.dispose();
new SequenceI[] { selectedSequence });
}
mainFrame.dispose();
@@
-857,12
+857,17
@@
public class StructureChooser extends GStructureChooser implements
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
final StructureViewer sViewer = new StructureViewer(ssm);
final StructureViewer sViewer = new StructureViewer(ssm);
+ setProgressBar(null, progressId);
if (SiftsSettings.isMapWithSifts())
{
if (SiftsSettings.isMapWithSifts())
{
+ // TODO: prompt user if there are lots of sequences without dbrefs.
+ // It can take a long time if we need to fetch all dbrefs for all
+ // sequences!
ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
for (SequenceI seq : sequences)
{
ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
for (SequenceI seq : sequences)
{
@@
-875,10
+880,9
@@
public class StructureChooser extends GStructureChooser implements
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_dbrefs_for_sequences_without_valid_refs",
"status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
+ y), progressId);
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
@@
-886,6
+890,7
@@
public class StructureChooser extends GStructureChooser implements
seqWithoutSrcDBRef[x++] = fSeq;
}
new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
seqWithoutSrcDBRef[x++] = fSeq;
}
new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+ setProgressBar("Fetch complete.", progressId); // todo i18n
}
}
if (pdbEntriesToView.length > 1)
}
}
if (pdbEntriesToView.length > 1)
@@
-896,19
+901,18
@@
public class StructureChooser extends GStructureChooser implements
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
+ setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"), progressId);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
+ pdbEntriesToView[0].getId()),progressId);
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
+ setProgressBar(null, progressId);
}
/**
}
/**