X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;fp=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=97bc5a3b7e3a62edff41d05e9a6fdab98591c1cc;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=d651c0bfb7e67dfecbbac0d1161b25998b7b51d6;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index d651c0b..97bc5a3 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -690,8 +690,8 @@ public class ColumnSelection
    * left-most visible column will always be returned.
    * 
    * @param hiddenColumn
-   *          int
-   * @return int
+   *          the column index in the full alignment including hidden columns
+   * @return the position of the column in the visible alignment
    */
   public int findColumnPosition(int hiddenColumn)
   {
@@ -708,15 +708,89 @@ public class ColumnSelection
           result -= region[1] + 1 - region[0];
         }
       } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
-      if (hiddenColumn > region[0] && hiddenColumn < region[1])
-      {
-        return region[0] + hiddenColumn - result;
+
+      if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+       {
+         // Here the hidden column is within a region, so
+         // we want to return the position of region[0]-1, adjusted for any
+         // earlier hidden columns.
+         // Calculate the difference between the actual hidden col position
+         // and region[0]-1, and then subtract from result to convert result from
+         // the adjusted hiddenColumn value to the adjusted region[0]-1 value
+
+        // However, if the region begins at 0 we cannot return region[0]-1
+        // just return 0
+        if (region[0] == 0)
+        {
+          return 0;
+        }
+        else
+        {
+          return result - (hiddenColumn - region[0] + 1);
+        }
       }
     }
     return result; // return the shifted position after removing hidden columns.
   }
 
   /**
+   * Find the visible column which is a given visible number of columns to the
+   * left of another visible column. i.e. for a startColumn x, the column which
+   * is distance 1 away will be column x-1.
+   * 
+   * @param visibleDistance
+   *          the number of visible columns to offset by
+   * @param startColumn
+   *          the column to start from
+   * @return the position of the column in the visible alignment
+   */
+  public int subtractVisibleColumns(int visibleDistance, int startColumn)
+  {
+    int distance = visibleDistance;
+
+    // in case startColumn is in a hidden region, move it to the left
+    int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+
+    // get index of hidden region to left of start
+    int index = getHiddenIndexLeft(start);
+    if (index == -1)
+    {
+      // no hidden regions to left of startColumn
+      return start - distance;
+    }
+
+    // walk backwards through the alignment subtracting the counts of visible
+    // columns from distance
+    int[] region;
+    int gap = 0;
+    int nextstart = start;
+
+    while ((index > -1) && (distance - gap > 0))
+    {
+      // subtract the gap to right of region from distance
+      distance -= gap;
+      start = nextstart;
+
+      // calculate the next gap
+      region = hiddenColumns.get(index);
+      gap = start - region[1];
+
+      // set start to just to left of current region
+      nextstart = region[0] - 1;
+      index--;
+    }
+
+    if (distance - gap > 0)
+    {
+      // fell out of loop because there are no more hidden regions
+      distance -= gap;
+      return nextstart - distance;
+    }
+    return start - distance;
+
+  }
+
+  /**
    * Use this method to determine where the next hiddenRegion starts
    * 
    * @param hiddenRegion
@@ -805,6 +879,35 @@ public class ColumnSelection
 
   }
 
+  /**
+   * This method returns the index of the hidden region to the left of a column
+   * position. If the column is in a hidden region it returns the index of the
+   * region to the left. If there is no hidden region to the left it returns -1.
+   * 
+   * @param pos
+   *          int
+   */
+  private int getHiddenIndexLeft(int pos)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = hiddenColumns.size() - 1;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (pos > region[1])
+        {
+          return index;
+        }
+
+        index--;
+      } while (index > -1);
+    }
+
+    return -1;
+
+  }
+
   public void hideSelectedColumns()
   {
     synchronized (selection)
@@ -866,6 +969,24 @@ public class ColumnSelection
          */
         region[0] = Math.min(region[0], start);
         region[1] = Math.max(region[1], end);
+
+        /*
+         * also update or remove any subsequent ranges 
+         * that are overlapped
+         */
+        while (i < hiddenColumns.size() - 1)
+        {
+          int[] nextRegion = hiddenColumns.get(i + 1);
+          if (nextRegion[0] > end + 1)
+          {
+            /*
+             * gap to next hidden range - no more to update
+             */
+            break;
+          }
+          region[1] = Math.max(nextRegion[1], end);
+          hiddenColumns.remove(i + 1);
+        }
         return;
       }
     }
@@ -1813,4 +1934,55 @@ public class ColumnSelection
     return changed;
   }
 
+  /**
+   * Adjusts column selections, and the given selection group, to match the
+   * range of a stretch (e.g. mouse drag) operation
+   * <p>
+   * Method refactored from ScalePanel.mouseDragged
+   * 
+   * @param res
+   *          current column position, adjusted for hidden columns
+   * @param sg
+   *          current selection group
+   * @param min
+   *          start position of the stretch group
+   * @param max
+   *          end position of the stretch group
+   */
+  public void stretchGroup(int res, SequenceGroup sg, int min, int max)
+  {
+    if (!contains(res))
+    {
+      addElement(res);
+    }
+
+    if (res > sg.getStartRes())
+    {
+      // expand selection group to the right
+      sg.setEndRes(res);
+    }
+    if (res < sg.getStartRes())
+    {
+      // expand selection group to the left
+      sg.setStartRes(res);
+    }
+
+    /*
+     * expand or shrink column selection to match the
+     * range of the drag operation
+     */
+    for (int col = min; col <= max; col++)
+    {
+      if (col < sg.getStartRes() || col > sg.getEndRes())
+      {
+        // shrinking drag - remove from selection
+        removeElement(col);
+      }
+      else
+      {
+        // expanding drag - add to selection
+        addElement(col);
+      }
+    }
+  }
 }