import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
+import jalview.gui.OverviewPanel;
import jalview.gui.PCAPanel;
import jalview.gui.PaintRefresher;
import jalview.gui.SplitFrame;
import jalview.xml.binding.jalview.JalviewModel.Viewport;
import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
private static final String UTF_8 = "UTF-8";
/**
+ * used in decision if quit confirmation should be issued
+ */
+ private static boolean stateSavedUpToDate = false;
+
+ /**
* prefix for recovering datasets for alignments with multiple views where
* non-existent dataset IDs were written for some views
*/
{
AlignFrame[] frames = Desktop.getAlignFrames();
+ setStateSavedUpToDate(true);
+
if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
{
- int n = 20;
+ int n = debugDelaySave;
int i = 0;
while (i < n)
{
FileOutputStream fos = new FileOutputStream(
doBackup ? backupfiles.getTempFilePath() : jarFile);
+ if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+ {
+ int n = debugDelaySave;
+ int i = 0;
+ while (i < n)
+ {
+ Console.debug("***** debugging save sleep " + i + "/" + n);
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ i++;
+ }
+ }
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
view.setStartRes(vpRanges.getStartRes());
view.setStartSeq(vpRanges.getStartSeq());
+ OverviewPanel ov = ap.getOverviewPanel();
+ if (ov != null)
+ {
+ Overview overview = new Overview();
+ overview.setTitle(ov.getTitle());
+ Rectangle bounds = ov.getFrameBounds();
+ overview.setXpos(bounds.x);
+ overview.setYpos(bounds.y);
+ overview.setWidth(bounds.width);
+ overview.setHeight(bounds.height);
+ overview.setShowHidden(ov.isShowHiddenRegions());
+ overview.setGapColour(ov.getCanvas().getGapColour().getRGB());
+ overview.setResidueColour(
+ ov.getCanvas().getResidueColour().getRGB());
+ overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
+ view.setOverview(overview);
+ }
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
}
/*
- * Load any trees, PDB structures and viewers
+ * Load any trees, PDB structures and viewers, Overview
*
* Not done if flag is false (when this method is used for New View)
*/
loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
+ loadOverview(view, jalviewModel.getVersion(), af);
}
// and finally return.
return af;
}
/**
+ * Load Overview window, restoring colours, 'show hidden regions' flag, title
+ * and geometry as saved
+ *
+ * @param view
+ * @param af
+ */
+ protected void loadOverview(Viewport view, String version, AlignFrame af)
+ {
+ if (!isVersionStringLaterThan("2.11.3",
+ version) && view.getOverview()==null)
+ {
+ return;
+ }
+ /*
+ * first close any Overview that was opened automatically
+ * (if so configured in Preferences) so that the view is
+ * restored in the same state as saved
+ */
+ af.alignPanel.closeOverviewPanel();
+
+ Overview overview = view.getOverview();
+ if (overview != null)
+ {
+ OverviewPanel overviewPanel = af
+ .openOverviewPanel(overview.isShowHidden());
+ overviewPanel.setTitle(overview.getTitle());
+ overviewPanel.setFrameBounds(overview.getXpos(), overview.getYpos(),
+ overview.getWidth(), overview.getHeight());
+ Color gap = new Color(overview.getGapColour());
+ Color residue = new Color(overview.getResidueColour());
+ Color hidden = new Color(overview.getHiddenColour());
+ overviewPanel.getCanvas().setColours(gap, residue, hidden);
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
* - minimum version we are comparing against
* @param version
* - version of data being processsed
- * @return
+ * @return true if version is equal to or later than supported
*/
public static boolean isVersionStringLaterThan(String supported,
String version)
{
splitFrameCandidates.put(view, af);
}
+
return af;
}
+ annotationId);
return null;
}
- if (matchedAnnotation.getThreshold() == null)
+ // belt-and-braces create a threshold line if the
+ // colourscheme needs one but the matchedAnnotation doesn't have one
+ if (safeInt(viewAnnColour.getAboveThreshold()) != 0
+ && matchedAnnotation.getThreshold() == null)
{
matchedAnnotation.setThreshold(
new GraphLine(safeFloat(viewAnnColour.getThreshold()),
return colour;
}
+
+ public static void setStateSavedUpToDate(boolean s)
+ {
+ Console.debug("Setting overall stateSavedUpToDate to " + s);
+ stateSavedUpToDate = s;
+ }
+
+ public static boolean stateSavedUpToDate()
+ {
+ Console.debug("Returning overall stateSavedUpToDate value: "
+ + stateSavedUpToDate);
+ return stateSavedUpToDate;
+ }
+
+ public static boolean allSavedUpToDate()
+ {
+ if (stateSavedUpToDate()) // nothing happened since last project save
+ return true;
+
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null)
+ {
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] == null)
+ continue;
+ if (!frames[i].getViewport().savedUpToDate())
+ return false; // at least one alignment is not individually saved
+ }
+ }
+ return true;
+ }
+
+ // used for debugging and tests
+ private static int debugDelaySave = 20;
+
+ public static void setDebugDelaySave(int n)
+ {
+ debugDelaySave = n;
+ }
}