in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / ControlPanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 471ca78..b58411b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -61,9 +61,11 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.SequenceRelation;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 
 final class ControlPanel extends JPanel implements ActionListener {
@@ -124,6 +126,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private int                  _subtree_cb_item;
     private int                  _color_subtree_cb_item;
     private int                  _open_seq_web_item;
+    private int                  _sort_descendents_item;
     private int                  _open_tax_web_item;
     private int                  _cut_subtree_item;
     private int                  _copy_subtree_item;
@@ -238,8 +241,23 @@ final class ControlPanel extends JPanel implements ActionListener {
                     showWhole();
                 }
                 else if ( e.getSource() == _order ) {
-                    tp.getPhylogeny().orderAppearance( _order_of_appearance );
+                    DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+                    if ( ( !isShowTaxonomyScientificNames() && !isShowTaxonomyCode() && !isShowTaxonomyCommonNames() ) ) {
+                        if ( ( isShowSequenceAcc() || isShowGeneNames() || isShowGeneSymbols() ) ) {
+                            pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+                        }
+                        else if ( isShowNodeNames() ) {
+                            pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+                        }
+                    }
+                    PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri );
                     _order_of_appearance = !_order_of_appearance;
+                    tp.setNodeInPreorderToNull();
+                    tp.getPhylogeny().externalNodesHaveChanged();
+                    tp.getPhylogeny().hashIDs();
+                    tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
+                    tp.resetNodeIdToDistToLeafMap();
+                    tp.setEdited( true );
                     displayedPhylogenyMightHaveChanged( false );
                 }
                 else if ( e.getSource() == _uncollapse_all ) {
@@ -1140,10 +1158,11 @@ final class ControlPanel extends JPanel implements ActionListener {
         else if ( action == _open_seq_web_item ) {
             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
         }
+        else if ( action == _sort_descendents_item ) {
+            setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
+        }
         else if ( action == _blast_item ) {
-            if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
-                setActionWhenNodeClicked( NodeClickAction.BLAST );
-            }
+            setActionWhenNodeClicked( NodeClickAction.BLAST );
         }
         else if ( action == _open_tax_web_item ) {
             setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
@@ -1314,6 +1333,15 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             cb_index++;
         }
+        if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
+            _sort_descendents_item = cb_index;
+            addClickToOption( Configuration.sort_descendents,
+                              _configuration.getClickToTitle( Configuration.sort_descendents ) );
+            if ( default_option == Configuration.sort_descendents ) {
+                selected_index = cb_index;
+            }
+            cb_index++;
+        }
         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
             _color_subtree_cb_item = cb_index;
             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
@@ -1338,6 +1366,14 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             cb_index++;
         }
+        if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
+            _blast_item = cb_index;
+            addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
+            if ( default_option == Configuration.blast ) {
+                selected_index = cb_index;
+            }
+            cb_index++;
+        }
         if ( getOptions().isEditable() ) {
             if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
                 _cut_subtree_item = cb_index;
@@ -1392,16 +1428,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                 }
                 cb_index++;
             }
-            if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
-                if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
-                    _blast_item = cb_index;
-                    addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
-                    if ( default_option == Configuration.blast ) {
-                        selected_index = cb_index;
-                    }
-                    cb_index++;
-                }
-            }
         }
         // Set default selection and its action
         _click_to_combobox.setSelectedIndex( selected_index );
@@ -1689,7 +1715,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         if ( _mainpanel.getCurrentScrollPane() == null ) {
             return;
         }
-        displayedPhylogenyMightHaveChanged( false );
+        getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+        displayedPhylogenyMightHaveChanged( true );
         _mainpanel.getCurrentTreePanel().updateOvSettings();
         _mainpanel.getCurrentTreePanel().validate();
         _mainpanel.validate();
@@ -1784,8 +1811,15 @@ final class ControlPanel extends JPanel implements ActionListener {
     void uncollapseAll( final TreePanel tp ) {
         final Phylogeny t = tp.getPhylogeny();
         if ( ( t != null ) && !t.isEmpty() ) {
-            t.setAllNodesToNotCollapse();
+            for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
+                final PhylogenyNode node = iter.next();
+                node.setCollapse( false );
+            }
+            tp.resetNodeIdToDistToLeafMap();
+            tp.updateSetOfCollapsedExternalNodes();
             t.recalculateNumberOfExternalDescendants( false );
+            tp.setNodeInPreorderToNull();
+            t.hashIDs();
             showWhole();
         }
     }
@@ -1921,6 +1955,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         PASTE_SUBTREE,
         ADD_NEW_NODE,
         EDIT_NODE_DATA,
+        SORT_DESCENDENTS,
         BLAST;
     }
 }