X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumnsCursor.java;h=d6b6c10d0059c870af672ea7474d508fca1f7f61;hb=62fb9a3042bdc6daaad8218d47b12cb912907354;hp=9b3854deea45359e0bc174d534e59d2270d2840f;hpb=b913f577205e8df5cdb6342ef161d7fd40ff15a4;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumnsCursor.java b/src/jalview/datamodel/HiddenColumnsCursor.java
index 9b3854d..d6b6c10 100644
--- a/src/jalview/datamodel/HiddenColumnsCursor.java
+++ b/src/jalview/datamodel/HiddenColumnsCursor.java
@@ -66,46 +66,11 @@ public class HiddenColumnsCursor
     if (!hiddenCols.isEmpty())
     {
       firstColumn = hiddenColumns.get(0)[0];
-      cursorPos = new HiddenCursorPosition(index,
-              hiddencount);
+      cursorPos = new HiddenCursorPosition(index, hiddencount);
     }
   }
 
   /**
-   * Delete the region the cursor is currently at. Avoids having to reset the
-   * cursor just because we deleted a region.
-   * 
-   * Calls to updateForDeletedRegion should be made from within a writeLock in
-   * the HiddenColumns class - since changes to the hiddenColumns collection
-   * require a writeLock the lock should already exist.
-   *
-   * @param hiddenCols
-   */
-  protected void updateForDeletedRegion(List<int[]> hiddenCols)
-  {
-
-    if (!hiddenCols.isEmpty())
-    {
-      // if there is a region to the right of the current region,
-      // nothing changes; otherwise
-      // we deleted the last region (index=hiddenCols.size()-1)
-      // or the index was at the end of the alignment (index=hiddenCols.size())
-      HiddenCursorPosition oldpos = cursorPos; // .get();
-
-      int index = oldpos.getRegionIndex();
-      if (index >= hiddenColumns.size() - 1)
-      {
-        // deleted last region, index is now end of alignment
-        index = hiddenCols.size();
-
-        cursorPos = new HiddenCursorPosition(index,
-                oldpos.getHiddenSoFar());
-      }
-    }
-    hiddenColumns = hiddenCols;
-  }
-
-  /**
    * 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
@@ -114,129 +79,134 @@ public class HiddenColumnsCursor
    * If hidden columns is empty returns null.
    * 
    * @param column
-   *          absolute position of a column in the alignment
+   *          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)
+  protected HiddenCursorPosition findRegionForColumn(int column,
+          boolean useVisible)
   {
     if (hiddenColumns.isEmpty())
     {
       return null;
     }
 
-    HiddenCursorPosition oldpos = cursorPos;// .get();
-    int index = oldpos.getRegionIndex();
-    int hiddenCount = oldpos.getHiddenSoFar();
+    // used to add in hiddenColumns offset when working with visible columns
+    int offset = (useVisible ? 1 : 0);
 
-    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;
-    }
+    HiddenCursorPosition pos = cursorPos;
+    int index = pos.getRegionIndex();
+    int hiddenCount = pos.getHiddenSoFar();
 
-    // this if statement excludes case where column is in current region
-    // - no changes needed
     if (column < firstColumn)
     {
-      index = 0;
-      hiddenCount = 0;
+      pos = new HiddenCursorPosition(0, 0);
     }
+
     // column is after current region
-    else if (column > hiddenColumns.get(index)[1])
+    else if ((index < hiddenColumns.size())
+            && (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())
-              && (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;
-      }
+      pos = searchForward(pos, column, useVisible);
     }
 
-    if (index != oldpos.getRegionIndex()
-            || hiddenCount != oldpos.getHiddenSoFar())
+    // column is before current region
+    else
     {
-      cursorPos = new HiddenCursorPosition(index,
-              hiddenCount);
-      return cursorPos;
+      pos = searchBackward(pos, column, useVisible);
     }
-    return oldpos;
+    cursorPos = pos;
+    return pos;
   }
 
   /**
-   * Get the cursor pointing to the hidden region just after a visible column
+   * Search forwards through the hidden columns collection to find the hidden
+   * region immediately before a column
    * 
+   * @param pos
+   *          current position
    * @param column
-   *          index of column in *visible* alignment (therefore by definition
-   *          column is visible)
-   * @return cursor pointing to hidden region to the right of the column
+   *          column to locate
+   * @param useVisible
+   *          whether using visible or absolute coordinates
+   * @return position of region before column
    */
-  protected HiddenCursorPosition findRegionForVisColumn(int column)
+  private HiddenCursorPosition searchForward(HiddenCursorPosition pos,
+          int column, boolean useVisible)
   {
-    if (hiddenColumns.isEmpty())
+    HiddenCursorPosition p = pos;
+    if (useVisible)
     {
-      return null;
-    }
-
-    HiddenCursorPosition oldpos = cursorPos;// .get();
-    int index = oldpos.getRegionIndex();
-    int hiddenCount = oldpos.getHiddenSoFar();
-
-    if (column < firstColumn)
-    {
-      index = 0;
-      hiddenCount = 0;
-    }
-    else if ((index < hiddenColumns.size())
-            && (hiddenColumns.get(index)[0] <= column + hiddenCount))
-    {
-      // iterate from where we are now, if we're lucky we'll be close by
-      // (but still better than iterating from 0)
-      while ((index < hiddenColumns.size())
-              && (hiddenColumns.get(index)[0] <= column + hiddenCount))
+      while ((p.getRegionIndex() < hiddenColumns.size())
+              && hiddenColumns.get(p.getRegionIndex())[0] <= column
+                      + p.getHiddenSoFar())
       {
-        int[] region = hiddenColumns.get(index);
-        hiddenCount += region[1] - region[0] + 1;
-        index++;
+        p = stepForward(p);
       }
     }
     else
     {
-      while ((index > 0)
-              && (hiddenColumns.get(index - 1)[1] >= column + hiddenCount))
+      while ((p.getRegionIndex() < hiddenColumns.size())
+              && hiddenColumns.get(p.getRegionIndex())[1] < column)
       {
-        index--;
-        int[] region = hiddenColumns.get(index);
-        hiddenCount -= region[1] - region[0] + 1;
+        p = stepForward(p);
       }
-
     }
+    return p;
+  }
+
+  /**
+   * Move to the next (rightwards) hidden region after a given cursor position
+   * 
+   * @param p
+   *          current position of cursor
+   * @return new position of cursor at next region
+   */
+  private HiddenCursorPosition stepForward(HiddenCursorPosition p)
+  {
+    int[] region = hiddenColumns.get(p.getRegionIndex());
+
+    // increment the index, and add this region's hidden columns to the hidden
+    // column count
+    return new HiddenCursorPosition(p.getRegionIndex() + 1,
+            p.getHiddenSoFar() + region[1] - region[0] + 1);
+  }
+
+  /**
+   * Search backwards through the hidden columns collection to find the hidden
+   * region immediately before (left of) a given column
+   * 
+   * @param pos
+   *          current position
+   * @param column
+   *          column to locate
+   * @param useVisible
+   *          whether using visible or absolute coordinates
+   * @return position of region immediately to left of column
+   */
+  private HiddenCursorPosition searchBackward(HiddenCursorPosition p,
+          int column, boolean useVisible)
+  {
+    int i = p.getRegionIndex();
+    int h = p.getHiddenSoFar();
+
+    // used to add in hiddenColumns offset when working with visible columns
+    int offset = (useVisible ? 1 : 0);
 
-    if (index != oldpos.getRegionIndex()
-            || hiddenCount != oldpos.getHiddenSoFar())
+    while ((i > 0) && (hiddenColumns.get(i - 1)[1] >= column + offset * h))
     {
-      cursorPos = new HiddenCursorPosition(index,
-              hiddenCount);
-      return cursorPos;
+      i--;
+      int[] region = hiddenColumns.get(i);
+      h -= region[1] - region[0] + 1;
     }
-    return oldpos;
+    return new HiddenCursorPosition(i, h);
   }
+
 }