vamsasSeq = new Sequence();
vamsasSeq.setId(id + "");
vamsasSeq.setName(jds.getName());
vamsasSeq = new Sequence();
vamsasSeq.setId(id + "");
vamsasSeq.setName(jds.getName());
if(!pdbfiles.contains(entry.getId()))
{
pdbfiles.addElement(entry.getId());
try
{
File file = new File(entry.getFile());
if(!pdbfiles.contains(entry.getId()))
{
pdbfiles.addElement(entry.getId());
try
{
File file = new File(entry.getFile());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setShowBoxes(av.getShowBoxes());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
view.setWrapAlignment(av.getWrapAlignment());
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
view.setWrapAlignment(av.getWrapAlignment());
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setFont(new java.awt.Font(view.getFontName(),
view.getFontStyle(), view.getFontSize()));
af.alignPanel.fontChanged();
af.viewport.setFont(new java.awt.Font(view.getFontName(),
view.getFontStyle(), view.getFontSize()));
af.alignPanel.fontChanged();
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();