import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport
+public class AlignViewport extends AlignmentViewport<AlignmentPanel>
implements SelectionSource
{
-
public final static int NO_SPLIT = 0;
public final static int SPLIT_FRAME = 1;
public final static int NEW_WINDOW = 2;
-
-
Font font;
boolean cursorMode = false;
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
init();
* @param hiddenColumns
* @param seqsetid
* (may be null)
-f */
+ */
public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid)
{
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug(
+ Console.debug(
"Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
if (hiddenColumns != null)
schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
ResidueColourScheme.NONE);
}
- ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(this, alignment, schemeName);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+ alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
}
setColourAppliesToAllGroups(true);
}
+
boolean validCharWidth;
}
/**
- * Returns an iterator over the visible column regions of the alignment
- *
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the selected
- * area
- * @return
- */
- public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
- {
- int start = 0;
- int end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- end = alignment.getWidth();
- }
-
- return (alignment.getHiddenColumns().getVisContigsIterator(start,
- end, false));
- }
-
- /**
* get hash of undo and redo list for the alignment
*
* @return long[] { historyList.hashCode, redoList.hashCode };
}
public boolean followSelection = true;
-
+
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
new HiddenColumns(getAlignment().getHiddenColumns()),
this);
}
-
- /**
- * return the alignPanel containing the given viewport. Use this to get the
- * components currently handling the given viewport.
- *
- * @param av
- * @return null or an alignPanel guaranteed to have non-null alignFrame
- * reference
- */
- public AlignmentPanel getAlignPanel()
- {
- AlignmentPanel[] aps = PaintRefresher
- .getAssociatedPanels(this.getSequenceSetId());
- for (int p = 0; aps != null && p < aps.length; p++)
- {
- if (aps[p].av == this)
- {
- return aps[p];
- }
- }
- return null;
- }
-
+
public boolean getSortByTree()
{
return sortByTree;
return StructureSelectionManager
.getStructureSelectionManager(Desktop.getInstance());
}
+
@Override
public boolean isNormaliseSequenceLogo()
normaliseSequenceLogo = state;
}
-
/**
*
* @return true if alignment characters should be displayed
{
return validCharWidth;
}
+
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Console.debug("trigger update for " + calcId);
}
}
ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
notifyAlignment();
-
}
/**
@Override
public void run()
{
- addDataToAlignment(al);
+ addDataToAlignment(al);
}
}).setResponseHandler(SPLIT_FRAME, new Runnable()
{
@Override
public void run()
{
+ // Make a copy of this one to open it in a splitframe
openLinkedAlignmentAs(getAlignPanel().alignFrame,
new Alignment(getAlignment()), al, title,
SPLIT_FRAME);
-// us.openLinkedAlignmentAs(al, title, true);
}
}).setResponseHandler(NEW_WINDOW, new Runnable()
{
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
}
+
/**
* Open a split frame or a new window
*
AlignmentI thisAlignment, AlignmentI al, String title, int mode)
{
/*
- * Identify protein and dna alignments. Make a copy of this one if opening
- * in a new split pane.
+ * Identify protein and dna alignments.
*/
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
/*
* Map sequences. At least one should get mapped as we have already passed
* the test for 'mappability'. Any mappings made will be added to the
try
{
- newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
AlignFrame.DEFAULT_HEIGHT);
copyMe.setTitle(thisFrame.getTitle());
-
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
: newAlignFrame;
}
/**
- * Applies the supplied feature settings descriptor to currently known features.
- * This supports an 'initial configuration' of feature colouring based on a
- * preset or user favourite. This may then be modified in the usual way using
- * the Feature Settings dialogue.
+ * Applies the supplied feature settings descriptor to currently known
+ * features. This supports an 'initial configuration' of feature colouring
+ * based on a preset or user favourite. This may then be modified in the usual
+ * way using the Feature Settings dialogue.
*
* @param featureSettings
*/
/**
* when mergeOnly is set, then group and feature visibility or feature colours
* are not modified for features and groups already known to the feature
- * renderer. Feature ordering is always adjusted, and transparency is always set
- * regardless.
+ * renderer. Feature ordering is always adjusted, and transparency is always
+ * set regardless.
*
* @param featureSettings
* @param mergeOnly
{
return;
}
-
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
List<String> origRenderOrder = new ArrayList(),
origGroups = new ArrayList();
- // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+ // preserve original render order - allows differentiation between user
+ // configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
.getFeatureColour(type);
FeatureMatcherSetI preferredFilters = featureSettings
.getFeatureFilters(type);
-
FeatureColourI origColour = fr.getFeatureStyle(type);
if (!mergeOnly || (!origRenderOrder.contains(type)
|| origColour == null
&& origColour.getColour().equals(
ColorUtils.createColourFromName(type)))))
{
- // if we are merging, only update if there wasn't already a colour defined for
+ // if we are merging, only update if there wasn't already a colour
+ // defined for
// this type
if (preferredColour != null)
{
{
displayed.setVisible(type);
}
+ else if (featureSettings.isFeatureHidden(type))
+ {
+ displayed.setHidden(type);
+ }
}
}
{
if (!mergeOnly || !origGroups.contains(group))
{
- // when merging, display groups only if the aren't already marked as not visible
+ // when merging, display groups only if the aren't already marked as not
+ // visible
fr.setGroupVisibility(group,
featureSettings.isGroupDisplayed(group));
}
fr.orderFeatures(featureSettings);
}
fr.setTransparency(featureSettings.getTransparency());
+
+ fr.notifyFeaturesChanged();
}
public String getViewName()
{
this.viewName = viewName;
}
-
}
git://source.jalview.org / jalview.git / blobdiff