From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 1 Jun 2012 19:28:57 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8bf432f4963f5cbadb6a194192b682b1b7bda40f;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 233952e..5bca398 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -626,7 +626,7 @@ final class ControlPanel extends JPanel implements ActionListener {
 
     void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
         if ( ( _mainpanel != null )
-                && ( _mainpanel.getCurrentPhylogeny() != null && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
+                && ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
             if ( getOptions().isShowOverview() ) {
                 _mainpanel.getCurrentTreePanel().updateOvSizes();
             }
@@ -1713,7 +1713,7 @@ final class ControlPanel extends JPanel implements ActionListener {
      * Fit entire tree into window.
      */
     void showWhole() {
-        if ( _mainpanel.getCurrentScrollPane() == null || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
+        if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
             return;
         }
         getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 096c8d5..5bd03f3 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -3670,7 +3670,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                final int graphics_file_height,
                                final int graphics_file_x,
                                final int graphics_file_y ) {
-        if ( _phylogeny == null || _phylogeny.isEmpty() ) {
+        if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return;
         }
         if ( _control_panel.isShowSequenceRelations() ) {
diff --git a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
index a6d814b..766f212 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java
@@ -99,7 +99,7 @@ public class TaxonomyDataObtainer extends RunnableProcess {
         finally {
             end( _mf );
         }
-        if ( _phy == null || _phy.isEmpty() ) {
+        if ( ( _phy == null ) || _phy.isEmpty() ) {
             try {
                 JOptionPane.showMessageDialog( _mf,
                                                "None of the external node taxonomies could be resolved",