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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
TreePanel.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index
5bd03f3
..
befe375
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/
forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@
-411,7
+411,7
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
}
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
}
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
@@
-882,7
+882,7
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
setCopiedAndPastedNodes( null );
setCutOrCopiedTree( _phylogeny.copy( node ) );
_phylogeny.deleteSubtree( node, true );
setCopiedAndPastedNodes( null );
setCutOrCopiedTree( _phylogeny.copy( node ) );
_phylogeny.deleteSubtree( node, true );
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
@@
-948,7
+948,7
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
_phylogeny.deleteSubtree( node, true );
}
_phylogeny.externalNodesHaveChanged();
_phylogeny.deleteSubtree( node, true );
}
_phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
@@
-4243,7
+4243,7
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
getCopiedAndPastedNodes().addAll( node_ids );
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
getCopiedAndPastedNodes().addAll( node_ids );
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
@@
-4546,7
+4546,9
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
}
}
if ( getMainPanel().getOptions().isAntialiasScreen() ) {
}
}
if ( getMainPanel().getOptions().isAntialiasScreen() ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) {
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+ && !getMainPanel().getOptions().isShowDefaultNodeShapes()
+ && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
_rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
}
else {
_rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
}
else {
@@
-4954,7
+4956,7
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
node.swapChildren();
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
node.swapChildren();
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
@@
-4978,7
+4980,7
@@
public final class TreePanel extends JPanel implements ActionListener, MouseWhee
PhylogenyMethods.sortNodeDescendents( node, pri );
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
PhylogenyMethods.sortNodeDescendents( node, pri );
setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );