JAL-1551 spotless

[jalview.git] / src / jalview / gui / TreeCanvas.java

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 29826f0..3a055ae 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -189,7 +189,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
       BinaryNode lf = leaves.elementAt(i);
 
-      if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
+      if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
       {
         has_placeholders = true;
       }
@@ -285,9 +285,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
-              ? (PLACEHOLDER + node.getName())
-              : node.getName();
+      String name = (markPlaceholders && ((node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())))
+                      ? (PLACEHOLDER + node.getName())
+                      : node.getName();
 
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = font.getSize();
@@ -354,8 +355,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       int ystart = (node.left() == null ? 0
               : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
       int yend = (node.right() == null ? 0
-              : (int) (((BinaryNode) node.right()).ycount * chunk))
-              + offy;
+              : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
@@ -826,14 +826,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     else
     {
       Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
-      if (tp.isColumnWise()) {
-        markColumnsFor(getAssociatedPanels(), leaves, Color.red);
-      } else {
-      for (int i = 0; i < leaves.size(); i++)
+      if (tp.isColumnWise())
       {
-        SequenceI seq = (SequenceI) leaves.elementAt(i).element();
-        treeSelectionChanged(seq);
+        markColumnsFor(getAssociatedPanels(), leaves, Color.red);
       }
+      else
+      {
+        for (int i = 0; i < leaves.size(); i++)
+        {
+          SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+          treeSelectionChanged(seq);
+        }
       }
       av.sendSelection();
     }
@@ -998,7 +1001,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   {
     AlignmentPanel[] aps = getAssociatedPanels();
     List<BitSet> colGroups = new ArrayList<>();
-    Map<BitSet,Color> colors=new HashMap();
+    Map<BitSet, Color> colors = new HashMap();
     for (int i = 0; i < groups.size(); i++)
     {
       Color col = new Color((int) (Math.random() * 255),
@@ -1006,10 +1009,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       setColor(groups.get(i), col.brighter());
 
       Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
-      if (!tp.isColumnWise()) {
+      if (!tp.isColumnWise())
+      {
         createSeqGroupFor(aps, l, col);
-      } else {
-        BitSet gp=createColumnGroupFor(l,col);
+      }
+      else
+      {
+        BitSet gp = createColumnGroupFor(l, col);
 
         colGroups.add(gp);
         colors.put(gp, col);
@@ -1018,12 +1024,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (tp.isColumnWise())
     {
       AlignmentAnnotation aa = tp.getAssocAnnotation();
-      if (aa!=null) {
+      if (aa != null)
+      {
         ContactMatrixI cm = av.getContactMatrix(aa);
-        if (cm!=null)
+        if (cm != null)
         {
           cm.updateGroups(colGroups);
-          for (BitSet gp:colors.keySet())
+          for (BitSet gp : colors.keySet())
           {
             cm.setColorForGroup(gp, colors.get(gp));
           }
@@ -1058,46 +1065,50 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
       return false;
     }
-    if (av==null||av.getAlignment()==null)
+    if (av == null || av.getAlignment() == null)
     {
       // alignment is closed
       return false;
     }
     ColumnSelection cs = av.getColumnSelection();
-    
+
     HiddenColumns hc = av.getAlignment().getHiddenColumns();
     int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
             : colm;
 
     if (!av.hasHiddenColumns())
     {
-      return cs.contains(offp-1);
+      return cs.contains(offp - 1);
     }
-    if (hc.isVisible(offp-1))
+    if (hc.isVisible(offp - 1))
     {
-      return cs.contains(offp-1);
-//      return cs.contains(hc.absoluteToVisibleColumn(offp));
+      return cs.contains(offp - 1);
+      // return cs.contains(hc.absoluteToVisibleColumn(offp));
     }
     return false;
   }
-  
-  private BitSet createColumnGroupFor(Vector<BinaryNode> l,
-          Color col)
+
+  private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
   {
-    BitSet gp=new BitSet();
-    for (BinaryNode bn:l)
+    BitSet gp = new BitSet();
+    for (BinaryNode bn : l)
     {
-      int colm=-1;
-      if (bn.element()!=null && bn.element()instanceof Integer)
-      { colm = (Integer)bn.element();
-      } else {
-        // parse out from nodename
-      try {
-        colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
-      } catch (Exception e)
+      int colm = -1;
+      if (bn.element() != null && bn.element() instanceof Integer)
       {
-        continue;
+        colm = (Integer) bn.element();
       }
+      else
+      {
+        // parse out from nodename
+        try
+        {
+          colm = Integer.parseInt(
+                  bn.getName().substring(bn.getName().indexOf("c") + 1));
+        } catch (Exception e)
+        {
+          continue;
+        }
       }
       gp.set(colm);
     }
@@ -1108,17 +1119,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
           Color col)
   {
     SequenceI rseq = tp.assocAnnotation.sequenceRef;
-    if (av==null||av.getAlignment()==null)
+    if (av == null || av.getAlignment() == null)
     {
       // alignment is closed
       return;
     }
 
-    for (BinaryNode bn:l)
+    for (BinaryNode bn : l)
     {
-      int colm=-1;
-      try {
-        colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
+      int colm = -1;
+      try
+      {
+        colm = Integer.parseInt(
+                bn.getName().substring(bn.getName().indexOf("c") + 1));
       } catch (Exception e)
       {
         continue;
@@ -1126,19 +1139,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       ColumnSelection cs = av.getColumnSelection();
       HiddenColumns hc = av.getAlignment().getHiddenColumns();
       {
-        int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()+colm) : colm;
-        
-        if (!av.hasHiddenColumns() || hc.isVisible(offp-1))
-        { 
-          if (cs.contains(offp-1))
+        int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+                : colm;
+
+        if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+        {
+          if (cs.contains(offp - 1))
           {
-            cs.removeElement(offp-1);
-          } else {
-            cs.addElement(offp-1);
+            cs.removeElement(offp - 1);
+          }
+          else
+          {
+            cs.addElement(offp - 1);
           }
         }
       }
-    } 
+    }
   }
 
   public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,