JAL-2759 Rename findColumnPosition and adjustForHiddenColumns (yay!)

[jalview.git] / src / jalview / datamodel / HiddenColumns.java

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index ef80b32..f9ee46c 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -735,7 +735,7 @@ public class HiddenColumns
    *          int column index in alignment view (count from zero)
    * @return alignment column index for column
    */
-  public int adjustForHiddenColumns(int column)
+  public int visibleToAbsoluteColumn(int column)
   {
     try
     {
@@ -763,7 +763,7 @@ public class HiddenColumns
    *          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)
+  public int absoluteToVisibleColumn(int hiddenColumn)
   {
     try
     {
@@ -829,7 +829,7 @@ public class HiddenColumns
       int distance = visibleDistance;
 
       // in case startColumn is in a hidden region, move it to the left
-      int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+      int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn));
 
       Iterator<int[]> it = new ReverseRegionsIterator(0, start,
               hiddenColumns);
@@ -1086,7 +1086,7 @@ public class HiddenColumns
 
       if (foundStart)
       {
-        return findColumnPosition(start);
+        return absoluteToVisibleColumn(start);
       }
       // otherwise, sequence was completely hidden
       return visPrev;
@@ -1390,7 +1390,7 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      int adjres = adjustForHiddenColumns(res);
+      int adjres = visibleToAbsoluteColumn(res);
 
       int[] reveal = null;
 
@@ -1471,7 +1471,7 @@ public class HiddenColumns
       LOCK.readLock().lock();
 
       // get absolute position of column in alignment
-      int absoluteStart = adjustForHiddenColumns(start);
+      int absoluteStart = visibleToAbsoluteColumn(start);
 
       // Get cursor position and supply it to the iterator:
       // Since we want visible region start, we look for a cursor for the
@@ -1529,8 +1529,8 @@ public class HiddenColumns
     int adjend = end;
     if (useVisibleCoords)
     {
-      adjstart = adjustForHiddenColumns(start);
-      adjend = adjustForHiddenColumns(end);
+      adjstart = visibleToAbsoluteColumn(start);
+      adjend = visibleToAbsoluteColumn(end);
     }
 
     try