JAL-2054 Renamed getStartEnd in AlignFrame to getVisibleStartAndEndIndex, and refacto...

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d1ea70d..a9b0d53 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1793,4 +1793,40 @@ public class Alignment implements AlignmentI
     }
     return null;
   }
+
+  @Override
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+  {
+    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+    int startPos = alignmentStartEnd[0];
+    int endPos = alignmentStartEnd[1];
+
+    int[] lowestRange = new int[] { -1, -1 };
+    int[] higestRange = new int[] { -1, -1 };
+
+    for (int[] hiddenCol : hiddenCols)
+    {
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+
+    if (lowestRange[0] == -1 && lowestRange[1] == -1)
+    {
+      startPos = alignmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == -1 && higestRange[1] == -1)
+    {
+      endPos = alignmentStartEnd[1];
+    }
+    else
+    {
+      endPos = higestRange[0] - 1;
+    }
+    return new int[] { startPos, endPos };
+  }
 }