import jalview.xml.binding.jalview.VAMSAS;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
{
if (ds.getCodonFrames() != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerMappings(ds.getCodonFrames());
}
}
{
entry.setProperty(prop.getName(), prop.getValue());
}
- Desktop.getInstance().getStructureSelectionManager()
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
}
AlignFrame loadViewport(String file, List<JSeq> JSEQ,
- List<SequenceI> hiddenSeqs, AlignmentI al,
- JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+ Viewport view, String uniqueSeqSetId, String viewId,
+ List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
safeInt(view.getHeight()), uniqueSeqSetId, viewId)
-// {
-//
-// @Override
-// protected void processKeyEvent(java.awt.event.KeyEvent e) {
-// System.out.println("Jalview2XML AF " + e);
-// super.processKeyEvent(e);
-//
-// }
-//
-// }
+ // {
+ //
+ // @Override
+ // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+ // System.out.println("Jalview2XML AF " + e);
+ // super.processKeyEvent(e);
+ //
+ // }
+ //
+ // }
;
af.alignPanel.setHoldRepaint(true);
af.setFileName(file, FileFormat.Jalview);
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
af.changeColour(cs);
viewport.setColourAppliesToAllGroups(true);
- viewport
- .setShowSequenceFeatures(
- safeBoolean(view.isShowSequenceFeatures()));
+ viewport.setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
viewport.setCentreColumnLabels(view.isCentreColumnLabels());
viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jm.getFeatureSettings()
- .getSetting().size()];
+ String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+ .size()];
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jm.getFeatureSettings()
- .getSetting().size(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+ .size(); fs++)
{
Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
.getMatcherSet();
if (filters != null)
{
- FeatureMatcherSetI filter = Jalview2XML
- .parseFilter(featureType, filters);
+ FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+ filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
FeatureColourI gc = new FeatureColour(maxColour, minColour,
- maxColour,
- noValueColour, min, max);
+ maxColour, noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
gc.setAttributeName(setting.getAttributeName().toArray(
}
else
{
- featureColours.put(featureType,
- new FeatureColour(maxColour));
+ featureColours.put(featureType, new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
if (setting.getOrder() != null)
String complementaryViewId = view.getComplementId();
if (complementaryViewId == null)
{
- Desktop.addInternalFrame(af, view.getTitle(),
+ Dimension dim = Platform.getDimIfEmbedded(af,
safeInt(view.getWidth()), safeInt(view.getHeight()));
+ Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
reorderAutoannotation(af, al, autoAlan);
AlignFrame af = loadFromObject(jm, null, false, null);
af.getAlignPanels().clear();
af.closeMenuItem_actionPerformed(true);
-
- /*
- * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
- * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
- * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
- * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
- * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
- */
+ af.alignPanel.setHoldRepaint(false);
return af.alignPanel;
}
axis.getXPos(), axis.getYPos(), axis.getZPos());
}
+ Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
Desktop.addInternalFrame(panel, MessageManager.formatMessage(
- "label.calc_title", "PCA", modelName), 475, 450);
+ "label.calc_title", "PCA", modelName), dim.width,
+ dim.height);
}
} catch (Exception ex)
{