Adjust branch lengths toggle

marbl · Dec 31, 2014 · 9baf419 · 9baf419
1 parent a2dada2
commit 9baf419
Show file tree

Hide file tree

Showing 5 changed files with 41 additions and 2 deletions.
diff --git a/html/index.html b/html/index.html
@@ -53,6 +53,7 @@ <h2 id="menu">Menus (<a href="#">back to Contents</a>)</h2>
 			<li><strong>Tree</strong>
 				<ul>
 					<li><p><strong>Reroot at midpoint</strong> - Balances the tree at the center of the longest path.</p>
+					<li><p><strong>Adjust branch lengths</strong> - Toggles whether the branch lengths shown in the status bar (or exported to Newick) are adjusted to account for total core size (since trees are typically generated with variant columns only). Note that this option will only be available for Gingr files generated by Parsnp version 1.1 or later, or with harvesttools using the -u flag.</p>
 					</li>
 				</ul>
 			<li><strong>View</strong>

diff --git a/src/MainWindow.cpp b/src/MainWindow.cpp
@@ -715,6 +715,18 @@ void MainWindow::saveSnapshot(const QString & fileName, bool tree, bool alignmen
 	pixmap.save(fileName);
 }
 
+void MainWindow::setAdjustBranchLengths(bool adjust)
+{
+	if ( adjust )
+	{
+		treeStatus->setMultiplier(hio.phylogenyTree.getMult());
+	}
+	else
+	{
+		treeStatus->setMultiplier(1);
+	}
+}
+
 void MainWindow::setDocumentChanged()
 {
 	actionSave->setDisabled(false);
@@ -1192,7 +1204,7 @@ void MainWindow::exportFileBackground(const QString & fileName, ImportWindow::Fi
 			hio.writeXmfa(out);
 			break;
 		case ImportWindow::TRE_NWK:
-			hio.writeNewick(out);
+			hio.writeNewick(out, actionToggleAdjustBranchLengths->isChecked());
 			break;
 		case ImportWindow::VAR_MFA:
 			hio.writeSnp(out);
@@ -1348,6 +1360,7 @@ void MainWindow::initializeAlignment()
 	actionExportVariantsVcf->setDisabled(false);
 }
 
+
 void MainWindow::initializeLayout()
 {
 	trackFocus = -1;
@@ -1379,6 +1392,12 @@ void MainWindow::initializeLayout()
 	actionMidpointReroot->setDisabled(true);
 	connect(actionMidpointReroot, SIGNAL(triggered()), this, SLOT(rerootTreeMidpoint()));
 
+	actionToggleAdjustBranchLengths = new QAction(tr("Adjust branch lengths"), this);
+	actionToggleAdjustBranchLengths->setCheckable(true);
+	actionToggleAdjustBranchLengths->setDisabled(true);
+	menuTree->addAction(actionToggleAdjustBranchLengths);
+	connect(actionToggleAdjustBranchLengths, SIGNAL(toggled(bool)), this, SLOT(setAdjustBranchLengths(bool)));
+
 	actionToggleSynteny = new QAction(tr("Synten&y"), this);
 	actionToggleSynteny->setCheckable(true);
 	actionToggleSynteny->setShortcut(QKeySequence("Ctrl+Y"));
@@ -1669,6 +1688,17 @@ void MainWindow::initializeTree()
 		hio.phylogenyTree.getLeafIds(leafIds);
 		treeViewMain->setPhylogenyTree(&hio.phylogenyTree);
 		treeViewMap->setPhylogenyTree(&hio.phylogenyTree);
+
+		if ( hio.phylogenyTree.getMult() == 1 )
+		{
+			actionToggleAdjustBranchLengths->setChecked(false);
+			actionToggleAdjustBranchLengths->setDisabled(true);
+		}
+		else
+		{
+			actionToggleAdjustBranchLengths->setEnabled(true);
+			actionToggleAdjustBranchLengths->setChecked(true);
+		}
 	}
 	else
 	{

diff --git a/src/MainWindow.h b/src/MainWindow.h
@@ -84,6 +84,7 @@ public slots:
 	void setNode(const PhylogenyTreeNode * node);
 	void setPosition(int gapped);
 	void toggleSynteny();
+	void setAdjustBranchLengths(bool adjust);
 	void setTrackFocus(int track);
 	void setTrackHover(int track, int trackEnd);
 	void setTrackListViewFocus(TrackListView * view);
@@ -185,6 +186,7 @@ public slots:
 	QAction * actionSaveAs;
 	QAction * actionSnps;
 	QAction * actionSearch;
+	QAction * actionToggleAdjustBranchLengths;
 	QAction * actionToggleShowInsertions;
 	QAction * actionToggleShowDeletions;
 	QAction * actionToggleSynteny;

diff --git a/src/PhylogenyTreeStatusBar.cpp b/src/PhylogenyTreeStatusBar.cpp
@@ -10,6 +10,8 @@
 PhylogenyTreeStatusBar::PhylogenyTreeStatusBar()
 : QWidget()
 {
+	mult = 1;
+
 	labelName = new StatusLabel();
 	labelDistance = new StatusLabel();
 	labelBootstrap = new StatusLabel();
@@ -73,7 +75,7 @@ void PhylogenyTreeStatusBar::setPhylogenyTreeNode(const PhylogenyTreeNode * phyl
 	}
 	else
 	{
-		labelDistance->setText(QString("%1").arg(node->getDistance()));
+		labelDistance->setText(QString("%1").arg(node->getDistance() * mult));
 		labelBootstrap->setText(QString("%1").arg(node->getBootstrap()));
 
 		if ( node->getBootstrap() > .5 || node->getBootstrap() == 0 )

diff --git a/src/PhylogenyTreeStatusBar.h b/src/PhylogenyTreeStatusBar.h
@@ -17,6 +17,7 @@ class PhylogenyTreeStatusBar : public QWidget
 
 	PhylogenyTreeStatusBar();
 
+	void setMultiplier(double multNew);
 	void setName(const QString & name);
 	void setPhylogenyTreeNode(const PhylogenyTreeNode * PhylogenyTreeNode, const QString & name, int leaf = -1);
 
@@ -26,6 +27,9 @@ class PhylogenyTreeStatusBar : public QWidget
 	StatusLabel * labelName;
 	StatusLabel * labelDistance;
 	StatusLabel * labelBootstrap;
+	double mult;
 };
 
+inline void PhylogenyTreeStatusBar::setMultiplier(double multNew) { mult = multNew; }
+
 #endif /* defined(__gavqt__PhylogenyTreeStatusBar__) */