JAL-2759 First pass instantiate hiddenColumns collection in constructor

diff --git a/src/jalview/datamodel/HiddenColsIterator.java b/src/jalview/datamodel/HiddenColsIterator.java
index 610445c..55a3d8b 100644 (file)
--- a/src/jalview/datamodel/HiddenColsIterator.java
+++ b/src/jalview/datamodel/HiddenColsIterator.java
@@ -25,7 +25,7 @@ public class HiddenColsIterator implements Iterator<int[]>
    */
   HiddenColsIterator(List<int[]> hiddenColumns)
   {
-    if (hiddenColumns != null)
+    if (!hiddenColumns.isEmpty())
     {
       int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
       init(0, last, hiddenColumns);

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 83b1e36..718f64e 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -69,7 +69,7 @@ public class HiddenColumns
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
    */
-  private List<int[]> hiddenColumns;
+  private List<int[]> hiddenColumns = new ArrayList<>();
 
   /**
    * Constructor
@@ -119,7 +119,6 @@ public class HiddenColumns
       LOCK.writeLock().lock();
       if (copy != null)
       {
-        hiddenColumns = new ArrayList<>();
         numColumns = 0;
         Iterator<int[]> it = copy.getBoundedIterator(start, end);
         while (it.hasNext())
@@ -170,11 +169,7 @@ public class HiddenColumns
       int previndex = 0;
       int prevHiddenCount = 0;
       int regionindex = 0;
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList<>();
-      }
-      else
+      if (!hiddenColumns.isEmpty())
       {
         // set up cursor reset values
         HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
@@ -329,21 +324,20 @@ public class HiddenColumns
     try
     {
       LOCK.writeLock().lock();
-      if (hiddenColumns != null)
+
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
       {
-        Iterator<int[]> it = hiddenColumns.iterator();
-        while (it.hasNext())
+        int[] region = it.next();
+        for (int j = region[0]; j < region[1] + 1; j++)
         {
-          int[] region = it.next();
-          for (int j = region[0]; j < region[1] + 1; j++)
-          {
-            sel.addElement(j);
-          }
+          sel.addElement(j);
         }
-        hiddenColumns = null;
-        cursor.resetCursor(hiddenColumns);
-        numColumns = 0;
       }
+      hiddenColumns.clear();
+      cursor.resetCursor(hiddenColumns);
+      numColumns = 0;
+
     } finally
     {
       LOCK.writeLock().unlock();
@@ -365,7 +359,7 @@ public class HiddenColumns
     {
       LOCK.writeLock().lock();
 
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
         int regionIndex = cursor.findRegionForColumn(start)
                 .getRegionIndex();
@@ -386,7 +380,7 @@ public class HiddenColumns
 
             if (hiddenColumns.isEmpty())
             {
-              hiddenColumns = null;
+              hiddenColumns.clear();
               numColumns = 0;
             }
             else
@@ -459,7 +453,7 @@ public class HiddenColumns
       BitSet hidden = new BitSet();
       markHiddenRegions(hidden);
       hidden.andNot(gaps);
-      hiddenColumns = null;
+      hiddenColumns.clear();
       this.hideColumns(hidden);
 
       // for each sequence in the alignment, except the profile sequence,
@@ -585,20 +579,19 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
       StringBuilder regionBuilder = new StringBuilder();
-      if (hiddenColumns != null)
+
+      Iterator<int[]> it = hiddenColumns.iterator();
+      while (it.hasNext())
       {
-        Iterator<int[]> it = hiddenColumns.iterator();
-        while (it.hasNext())
+        int[] range = it.next();
+        regionBuilder.append(delimiter).append(range[0]).append(between)
+                .append(range[1]);
+        if (!it.hasNext())
         {
-          int[] range = it.next();
-          regionBuilder.append(delimiter).append(range[0]).append(between)
-                  .append(range[1]);
-          if (!it.hasNext())
-          {
-            regionBuilder.deleteCharAt(0);
-          }
+          regionBuilder.deleteCharAt(0);
         }
       }
+
       return regionBuilder.toString();
     } finally
     {
@@ -617,7 +610,7 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
 
-      if (numColumns == 0 && hiddenColumns != null)
+      if (numColumns == 0)
       {
         // numColumns is out of date, so recalculate
         int size = 0;
@@ -677,12 +670,8 @@ public class HiddenColumns
       /*
        * check hidden columns are either both null, or match
        */
-      if (this.hiddenColumns == null)
-      {
-        return (that.hiddenColumns == null);
-      }
-      if (that.hiddenColumns == null
-              || that.hiddenColumns.size() != this.hiddenColumns.size())
+
+      if (that.hiddenColumns.size() != this.hiddenColumns.size())
       {
         return false;
       }
@@ -719,7 +708,7 @@ public class HiddenColumns
       LOCK.readLock().lock();
       int result = column;
 
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
         result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
       }
@@ -748,7 +737,7 @@ public class HiddenColumns
       LOCK.readLock().lock();
       int result = hiddenColumn;
 
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
         HiddenCursorPosition cursorPos = cursor
                 .findRegionForColumn(hiddenColumn);
@@ -854,7 +843,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
         int index = cursor.findRegionForColumn(alPos).getRegionIndex();
         if (index < hiddenColumns.size())
@@ -895,7 +884,7 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
 
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
         int index = cursor.findRegionForColumn(alPos).getRegionIndex();
 
@@ -964,7 +953,7 @@ public class HiddenColumns
       LOCK.readLock().lock();
       int iSize = seqs.length;
       String[] selections = new String[iSize];
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
+      if (!hiddenColumns.isEmpty())
       {
         for (int i = 0; i < iSize; i++)
         {
@@ -1021,7 +1010,7 @@ public class HiddenColumns
       LOCK.readLock().lock();
       int start = 0;
 
-      if (hiddenColumns == null || hiddenColumns.size() == 0)
+      if (hiddenColumns.isEmpty())
       {
         return seq.findIndex(seq.getStart()) - 1;
       }
@@ -1114,7 +1103,7 @@ public class HiddenColumns
       if (alignmentAnnotation != null
               && alignmentAnnotation.annotations != null)
       {
-        if (hiddenColumns != null && hiddenColumns.size() > 0)
+        if (!hiddenColumns.isEmpty())
         {
           removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
         }
@@ -1200,7 +1189,7 @@ public class HiddenColumns
 
       // we don't use getSize()>0 here because it has to iterate over
       // the full hiddenColumns collection and so will be much slower
-      return hiddenColumns != null && hiddenColumns.size() > 0;
+      return (!hiddenColumns.isEmpty());
     } finally
     {
       LOCK.readLock().unlock();
@@ -1216,7 +1205,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      return hiddenColumns != null && hiddenColumns.size() > 1;
+      return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1;
     } finally
     {
       LOCK.readLock().unlock();
@@ -1284,10 +1273,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      if (hiddenColumns == null)
-      {
-        return;
-      }
+
       Iterator<int[]> it = hiddenColumns.iterator();
       while (it.hasNext())
       {
@@ -1319,7 +1305,7 @@ public class HiddenColumns
       int[] lowestRange = new int[] { -1, -1 };
       int[] higestRange = new int[] { -1, -1 };
 
-      if (hiddenColumns == null)
+      if (hiddenColumns.isEmpty())
       {
         return new int[] { startPos, endPos };
       }
@@ -1373,7 +1359,7 @@ public class HiddenColumns
 
       int[] reveal = null;
 
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
         // look for a region ending just before adjres
         int regionindex = cursor.findRegionForColumn(adjres - 1)

diff --git a/src/jalview/datamodel/HiddenColumnsCursor.java b/src/jalview/datamodel/HiddenColumnsCursor.java
index 0fef622..a875f87 100644 (file)
--- a/src/jalview/datamodel/HiddenColumnsCursor.java
+++ b/src/jalview/datamodel/HiddenColumnsCursor.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicReference;
 
@@ -28,7 +29,7 @@ public class HiddenColumnsCursor
   // absolute position of first hidden column
   private int firstColumn;
 
-  private List<int[]> hiddenColumns;
+  private List<int[]> hiddenColumns = new ArrayList<>();
 
   // AtomicReference to hold the current region index and hidden column count
   // Could be done with synchronisation but benchmarking shows this way is 2x
@@ -70,7 +71,7 @@ public class HiddenColumnsCursor
           int hiddencount)
   {
     hiddenColumns = hiddenCols;
-    if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
+    if (!hiddenCols.isEmpty())
     {
       firstColumn = hiddenColumns.get(0)[0];
       HiddenCursorPosition oldpos = cursorPos.get();
@@ -93,7 +94,7 @@ public class HiddenColumnsCursor
   protected void updateForDeletedRegion(List<int[]> hiddenCols)
   {
 
-    if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
+    if (!hiddenCols.isEmpty())
     {
       // if there is a region to the right of the current region,
       // nothing changes; otherwise
@@ -130,7 +131,7 @@ public class HiddenColumnsCursor
    */
   protected HiddenCursorPosition findRegionForColumn(int column)
   {
-    if (hiddenColumns == null)
+    if (hiddenColumns.isEmpty())
     {
       return null;
     }
@@ -202,7 +203,7 @@ public class HiddenColumnsCursor
    */
   protected HiddenCursorPosition findRegionForVisColumn(int column)
   {
-    if (hiddenColumns == null)
+    if (hiddenColumns.isEmpty())
     {
       return null;
     }