import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
* is protocol for accessing data referred to by file
* @param autoenabledisplay
* when true, display features flag will be automatically enabled if
* features are loaded
* @return true if data parsed as a features file
*/
* is protocol for accessing data referred to by file
* @param autoenabledisplay
* when true, display features flag will be automatically enabled if
* features are loaded
* @return true if data parsed as a features file
*/
.getFeatureRenderer().getFeatureColours();
boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
"relaxedidmatch", false);
.getFeatureRenderer().getFeatureColours();
boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
"relaxedidmatch", false);
viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
{
for (AlignmentAnnotation aa : alignPanel.getAlignment()
if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
{
for (AlignmentAnnotation aa : alignPanel.getAlignment()
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
- features = formatter.printJalviewFormat(viewport
- .getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols());
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
- // make a note of the access mode and add
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- }
- pdbentry.getProperty().put("protocol", protocol);
+ pdbentry.setProperty("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
alignPanel.getStructureSelectionManager()
.registerPDBEntry(pdbentry);
toaddpdb.addPDBId(pdbentry);
alignPanel.getStructureSelectionManager()
.registerPDBEntry(pdbentry);
{
// Scrub any null sequences from the array
Object[] sqch = cleanSeqChainArrays(seqs, chains);
{
// Scrub any null sequences from the array
Object[] sqch = cleanSeqChainArrays(seqs, chains);
- protocol = (String) pdb.getProperty().get("protocol");
+ String sourceType = (String) pdb.getProperty("protocol");
+ try
+ {
+ protocol = DataSourceType.valueOf(sourceType);
+ } catch (IllegalArgumentException e)
+ {
+ // ignore
+ }
- jalview.appletgui.AppletJmol ajm = null, tajm;
- Vector jmols = applet
- .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ AppletJmol ajm = null, tajm;
+ Vector jmols = applet.getAppletWindow(AppletJmol.class);
// otherwise, create a new window
if (applet.jmolAvailable)
{
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ new AppletJmol(pdb, seqs, chains, alignPanel,