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;
public class AlignViewport extends AlignmentViewport
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();
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)
setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+ autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
setPadGaps(Cache.getDefault("PAD_GAPS", true));
setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
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;
if (align != null)
{
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.registerMappings(align.getCodonFrames());
}
if (mappings != null)
{
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
for (AlignedCodonFrame acf : mappings)
{
if (noReferencesTo(acf))
}
/**
- * 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
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.sendSelection(new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()),
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .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);
}
}
{
if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(toAdd, title))
- {
- return;
- }
+ openLinkedAlignment(toAdd, title);
+ return;
}
}
+ addDataToAlignment(toAdd);
+ }
- /*
- * No mappings, or offer declined - add sequences to this alignment
- */
+ /**
+ * adds sequences to this alignment
+ *
+ * @param toAdd
+ */
+ void addDataToAlignment(AlignmentI toAdd)
+ {
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
}
}
- ranges.setEndSeq(getAlignment().getHeight());
- firePropertyChange("alignment", null, getAlignment().getSequences());
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
+ notifyAlignment();
}
/**
* @param al
* @param title
*/
- protected boolean openLinkedAlignment(AlignmentI al, String title)
+ protected void openLinkedAlignment(AlignmentI al, String title)
{
String[] options = new String[] { MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+ final AlignViewport us = this;
+
+ /*
+ * options No, Split Window, New Window correspond to
+ * dialog responses 0, 1, 2 (even though JOptionPane shows them
+ * in reverse order)
+ */
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+ .setResponseHandler(NO_SPLIT, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ 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);
+ }
+ }).setResponseHandler(NEW_WINDOW, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ openLinkedAlignmentAs(null, getAlignment(), al, title,
+ NEW_WINDOW);
+ }
+ });
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
+ }
- if (response != 1 && response != 2)
- {
- return false;
- }
- final boolean openSplitPane = (response == 1);
- final boolean openInNewWindow = (response == 2);
-
+ /**
+ * Open a split frame or a new window
+ *
+ * @param al
+ * @param title
+ * @param mode
+ * SPLIT_FRAME or NEW_WINDOW
+ */
+ public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+ 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 thisAlignment = openSplitPane ? new Alignment(getAlignment())
- : getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
- final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+ AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
/*
* Map sequences. At least one should get mapped as we have already passed
// alignFrame.setFileName(file, format);
// }
- if (openInNewWindow)
+ if (mode == NEW_WINDOW)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
try
{
- newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
- if (openSplitPane)
+ if (mode == SPLIT_FRAME)
{
al.alignAs(thisAlignment);
- protein = openSplitFrame(newAlignFrame, thisAlignment);
+ openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
}
-
- return true;
}
/**
* cdna/protein complement alignment to show in the other split half
* @return the protein alignment in the split frame
*/
- protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement)
+ static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+ AlignFrame newAlignFrame, AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
*/
AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+ copyMe.setTitle(thisFrame.getTitle());
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
}
/**
- * 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()
git://source.jalview.org / jalview.git / blobdiff