*/
package jalview.gui;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
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;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-
/**
* DOCUMENT ME!
*
boolean antiAlias = false;
- private Rectangle explodedGeometry;
+ private Rectangle explodedGeometry = null;
- private String viewName;
+ private String viewName = null;
/*
* Flag set true on the view that should 'gather' multiple views of the same
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)
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+ antiAlias = Cache.getDefault("ANTI_ALIAS", true);
viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", 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)
}
/**
- * returns 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 };
// 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
al.addSequence(seq);
}
}
-
- ranges.setEndSeq(getAlignment().getHeight());
+ for (ContactMatrixI cm : toAdd.getContactMaps())
+ {
+ al.addContactList(cm);
+ }
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}
* @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.desktop)
+ .setResponseHandler(0, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ addDataToAlignment(al);
+ }
+ }).setResponseHandler(1, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ us.openLinkedAlignmentAs(al, title, true);
+ }
+ }).setResponseHandler(2, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ us.openLinkedAlignmentAs(al, title, false);
+ }
+ });
+ 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);
-
+ protected void openLinkedAlignmentAs(AlignmentI al, String title,
+ boolean newWindowOrSplitPane)
+ {
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
*/
- AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ AlignmentI thisAlignment = newWindowOrSplitPane
+ ? new Alignment(getAlignment())
: getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
// alignFrame.setFileName(file, format);
// }
- if (openInNewWindow)
+ if (!newWindowOrSplitPane)
{
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 (newWindowOrSplitPane)
{
al.alignAs(thisAlignment);
protein = openSplitFrame(newAlignFrame, thisAlignment);
}
-
- return true;
}
/**
}
/**
- * 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
+ List<String> origRenderOrder = new ArrayList<>();
+ List<String> origGroups = new ArrayList<>();
+ // preserve original render order - allows differentiation between user
+ // configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
if (!mergeOnly)
{
// only clear displayed features if we are mergeing
- displayed.clear();
+ // displayed.clear();
}
// TODO this clears displayed.featuresRegistered - do we care?
//
&& 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