JAL-2759 Combine findRegionForColumn code in HiddenColumnsCursor

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 9a8669f..fd4a9b5 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -171,7 +171,8 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         // set up cursor reset values
-        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start,
+                false);
         regionindex = cursorPos.getRegionIndex();
 
         if (regionindex > 0)
@@ -356,7 +357,7 @@ public class HiddenColumns
 
       if (!hiddenColumns.isEmpty())
       {
-        int regionIndex = cursor.findRegionForColumn(start)
+        int regionIndex = cursor.findRegionForColumn(start, false)
                 .getRegionIndex();
 
         if (regionIndex != -1 && regionIndex != hiddenColumns.size())
@@ -544,7 +545,8 @@ public class HiddenColumns
 
       if (!hiddenColumns.isEmpty())
       {
-        result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
+        result += cursor.findRegionForColumn(column, true)
+                .getHiddenSoFar();
       }
 
       return result;
@@ -574,7 +576,7 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         HiddenCursorPosition cursorPos = cursor
-                .findRegionForColumn(hiddenColumn);
+                .findRegionForColumn(hiddenColumn, false);
         int index = cursorPos.getRegionIndex();
         int hiddenBeforeCol = cursorPos.getHiddenSoFar();
     
@@ -656,7 +658,8 @@ public class HiddenColumns
       LOCK.readLock().lock();
       if (!hiddenColumns.isEmpty())
       {
-        int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+        int index = cursor.findRegionForColumn(alPos, false)
+                .getRegionIndex();
 
         if (left && index > 0)
         {
@@ -700,7 +703,8 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
 
-      int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+      int regionindex = cursor.findRegionForColumn(column, false)
+              .getRegionIndex();
       if (regionindex > -1 && regionindex < hiddenColumns.size())
       {
         int[] region = hiddenColumns.get(regionindex);
@@ -846,7 +850,7 @@ public class HiddenColumns
       
       if (!hiddenColumns.isEmpty())
       {
-        HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+        HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
         int index = pos.getRegionIndex();
         int startindex = index; // first index in hiddenColumns to remove
 
@@ -863,7 +867,7 @@ public class HiddenColumns
           }
         }
 
-        pos = cursor.findRegionForColumn(end);
+        pos = cursor.findRegionForColumn(end, false);
         index = pos.getRegionIndex();
         int endindex = index - 1; // last index in hiddenColumns to remove
 
@@ -973,7 +977,7 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         // look for a region ending just before adjres
-        int regionindex = cursor.findRegionForColumn(adjres - 1)
+        int regionindex = cursor.findRegionForColumn(adjres - 1, false)
                 .getRegionIndex();
         if (regionindex < hiddenColumns.size()
                 && hiddenColumns.get(regionindex)[1] == adjres - 1)
@@ -1055,7 +1059,7 @@ public class HiddenColumns
       // region we'll get the cursor pointing to the region before, which is
       // what we want
       HiddenCursorPosition pos = cursor
-              .findRegionForColumn(absoluteStart - 1);
+              .findRegionForColumn(absoluteStart - 1, false);
 
       return new BoundedStartRegionIterator(pos, start, end,
               hiddenColumns);

diff --git a/src/jalview/datamodel/HiddenColumnsCursor.java b/src/jalview/datamodel/HiddenColumnsCursor.java
index 3501fce..89c4f99 100644 (file)
--- a/src/jalview/datamodel/HiddenColumnsCursor.java
+++ b/src/jalview/datamodel/HiddenColumnsCursor.java
@@ -118,68 +118,10 @@ public class HiddenColumnsCursor
    * @return cursor pointing to hidden region containing the column (if hidden)
    *         or to the right of the column (if visible)
    */
-  protected HiddenCursorPosition findRegionForColumn(int column)
+  /*protected HiddenCursorPosition findRegionForColumn(int column)
   {
-    if (hiddenColumns.isEmpty())
-    {
-      return null;
-    }
-
-    HiddenCursorPosition oldpos = cursorPos;
-    int index = oldpos.getRegionIndex();
-    int hiddenCount = oldpos.getHiddenSoFar();
-
-    if (index == hiddenColumns.size())
-    {
-      // went past the end of hiddenColumns collection last time
-      index--;
-      int[] region = hiddenColumns.get(index);
-      hiddenCount -= region[1] - region[0] + 1;
-    }
-
-    // this if statement excludes case where column is in current region
-    // - no changes needed
-    if (column < firstColumn)
-    {
-      index = 0;
-      hiddenCount = 0;
-    }
-    // column is after current region
-    else if (column > hiddenColumns.get(index)[1])
-    {
-      // iterate from where we are now, if we're lucky we'll be close by
-      // (but still better than iterating from 0)
-      // stop when we find the region *before* column
-      // i.e. the next region starts after column or if not, ends after column
-      while ((index < hiddenColumns.size())
-              && (column > hiddenColumns.get(index)[1]))
-      {
-        int[] region = hiddenColumns.get(index);
-        hiddenCount += region[1] - region[0] + 1;
-        index++;
-      }
-    }
-    // column is before current region
-    else if (column < hiddenColumns.get(index)[0])
-    {
-      // column is before or in the previous region
-      while ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column))
-      {
-        index--;
-        int[] region = hiddenColumns.get(index);
-        hiddenCount -= region[1] - region[0] + 1;
-      }
-    }
-
-    if (index != oldpos.getRegionIndex()
-            || hiddenCount != oldpos.getHiddenSoFar())
-    {
-      cursorPos = new HiddenCursorPosition(index,
-              hiddenCount);
-      return cursorPos;
-    }
-    return oldpos;
-  }
+    return findRegionForColumn(column, false);
+  }*/
 
   /**
    * Get the cursor pointing to the hidden region just after a visible column
@@ -189,13 +131,37 @@ public class HiddenColumnsCursor
    *          column is visible)
    * @return cursor pointing to hidden region to the right of the column
    */
-  protected HiddenCursorPosition findRegionForVisColumn(int column)
+  /* protected HiddenCursorPosition findRegionForVisColumn(int column)
+  {
+    return findRegionForColumn(column, true);
+  }*/
+
+  /**
+   * Get the cursor pointing to the hidden region that column is within (if
+   * column is hidden) or which is to the right of column (if column is
+   * visible). If no hidden columns are to the right, returns a cursor pointing
+   * to an imaginary hidden region beyond the end of the hidden columns
+   * collection (this ensures the count of previous hidden columns is correct).
+   * If hidden columns is empty returns null.
+   * 
+   * @param column
+   *          index of column in visible or absolute coordinates
+   * @param useVisible
+   *          true if column is in visible coordinates, false if absolute
+   * @return cursor pointing to hidden region containing the column (if hidden)
+   *         or to the right of the column (if visible)
+   */
+  protected HiddenCursorPosition findRegionForColumn(int column,
+          boolean useVisible)
   {
     if (hiddenColumns.isEmpty())
     {
       return null;
     }
 
+    // used to add in hiddenColumns offset when working with visible columns
+    int offset = (useVisible ? 1 : 0);
+
     HiddenCursorPosition oldpos = cursorPos;
     int index = oldpos.getRegionIndex();
     int hiddenCount = oldpos.getHiddenSoFar();
@@ -205,38 +171,47 @@ public class HiddenColumnsCursor
       index = 0;
       hiddenCount = 0;
     }
+
+    // column is after current region
     else if ((index < hiddenColumns.size())
-            && (hiddenColumns.get(index)[0] <= column + hiddenCount))
+            && (hiddenColumns.get(index)[0] <= column
+                    + offset * hiddenCount))
     {
       // iterate from where we are now, if we're lucky we'll be close by
       // (but still better than iterating from 0)
+      // stop when we find the region *before* column
+      // i.e. the next region starts after column or if not, ends after column
       while ((index < hiddenColumns.size())
-              && (hiddenColumns.get(index)[0] <= column + hiddenCount))
+              && (((useVisible && hiddenColumns.get(index)[0] <= column
+                      + offset * hiddenCount))
+                      || (!useVisible
+                              && hiddenColumns.get(index)[1] < column)))
       {
         int[] region = hiddenColumns.get(index);
         hiddenCount += region[1] - region[0] + 1;
         index++;
       }
     }
+
+    // column is before current region
     else
     {
-      while ((index > 0)
-              && (hiddenColumns.get(index - 1)[1] >= column + hiddenCount))
+      // column is before or in the previous region
+      while ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column
+              + offset * hiddenCount))
       {
         index--;
         int[] region = hiddenColumns.get(index);
         hiddenCount -= region[1] - region[0] + 1;
       }
-
     }
 
     if (index != oldpos.getRegionIndex()
             || hiddenCount != oldpos.getHiddenSoFar())
     {
-      cursorPos = new HiddenCursorPosition(index,
-              hiddenCount);
-      return cursorPos;
+      return new HiddenCursorPosition(index, hiddenCount);
     }
     return oldpos;
   }
+
 }

diff --git a/test/jalview/datamodel/HiddenColumnsCursorTest.java b/test/jalview/datamodel/HiddenColumnsCursorTest.java
index 0deed08..3b1bc55 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsCursorTest.java
+++ b/test/jalview/datamodel/HiddenColumnsCursorTest.java
@@ -38,7 +38,7 @@ public class HiddenColumnsCursorTest
   {
     HiddenColumnsCursor cursor = new HiddenColumnsCursor();
     
-    HiddenCursorPosition pos = cursor.findRegionForColumn(20);
+    HiddenCursorPosition pos = cursor.findRegionForColumn(20, false);
     assertNull(pos);
     
     List<int[]> hidden = new ArrayList<>();
@@ -47,44 +47,44 @@ public class HiddenColumnsCursorTest
 
     cursor = new HiddenColumnsCursor(hidden);
 
-    int regionIndex = cursor.findRegionForColumn(126).getRegionIndex();
+    int regionIndex = cursor.findRegionForColumn(126, false).getRegionIndex();
     assertEquals(2, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(125).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(125, false).getRegionIndex();
     assertEquals(1, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(108).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(108, false).getRegionIndex();
     assertEquals(1, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(104).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(104, false).getRegionIndex();
     assertEquals(1, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(103).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(103, false).getRegionIndex();
     assertEquals(1, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(77).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(77, false).getRegionIndex();
     assertEquals(1, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(76).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(76, false).getRegionIndex();
     assertEquals(0, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(53).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(53, false).getRegionIndex();
     assertEquals(0, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(52).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(52, false).getRegionIndex();
     assertEquals(0, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(0).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(0, false).getRegionIndex();
     assertEquals(0, regionIndex);
 
     hidden.add(new int[] { 138, 155 });
 
     cursor = new HiddenColumnsCursor(hidden);
 
-    regionIndex = cursor.findRegionForColumn(160).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(160, false).getRegionIndex();
     assertEquals(3, regionIndex);
 
-    regionIndex = cursor.findRegionForColumn(100).getRegionIndex();
+    regionIndex = cursor.findRegionForColumn(100, false).getRegionIndex();
     assertEquals(1, regionIndex);
   }
 
@@ -96,7 +96,7 @@ public class HiddenColumnsCursorTest
   {
     HiddenColumnsCursor cursor = new HiddenColumnsCursor();
 
-    HiddenCursorPosition pos = cursor.findRegionForVisColumn(20);
+    HiddenCursorPosition pos = cursor.findRegionForColumn(20, true);
     assertNull(pos);
 
     List<int[]> hidden = new ArrayList<>();
@@ -105,23 +105,29 @@ public class HiddenColumnsCursorTest
 
     cursor = new HiddenColumnsCursor(hidden);
 
-    int offset = cursor.findRegionForVisColumn(80).getHiddenSoFar();
+    int offset = cursor.findRegionForColumn(80, true).getHiddenSoFar();
     assertEquals(46, offset);
 
-    offset = cursor.findRegionForVisColumn(79).getHiddenSoFar();
+    offset = cursor.findRegionForColumn(79, true).getHiddenSoFar();
     assertEquals(24, offset);
 
-    offset = cursor.findRegionForVisColumn(53).getHiddenSoFar();
+    offset = cursor.findRegionForColumn(53, true).getHiddenSoFar();
     assertEquals(24, offset);
 
-    offset = cursor.findRegionForVisColumn(52).getHiddenSoFar();
+    offset = cursor.findRegionForColumn(52, true).getHiddenSoFar();
     assertEquals(0, offset);
 
-    offset = cursor.findRegionForVisColumn(10).getHiddenSoFar();
+    offset = cursor.findRegionForColumn(10, true).getHiddenSoFar();
     assertEquals(0, offset);
 
-    offset = cursor.findRegionForVisColumn(0).getHiddenSoFar();
+    offset = cursor.findRegionForColumn(0, true).getHiddenSoFar();
     assertEquals(0, offset);
+
+    offset = cursor.findRegionForColumn(79, true).getHiddenSoFar();
+    assertEquals(24, offset);
+
+    offset = cursor.findRegionForColumn(80, true).getHiddenSoFar();
+    assertEquals(46, offset);
   }
 
 }