From 3ac211a6636821af226745459dcd3d5128ef0eaa Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 6 Mar 2017 16:23:53 +0000
Subject: [PATCH] JAL-2388 Dependency tidy

---
 src/jalview/gui/AlignViewport.java               |    2 +-
 src/jalview/viewmodel/ViewportPositionProps.java |   66 +---------------------
 2 files changed, 2 insertions(+), 66 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5c264c0..b64d98e 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -310,7 +310,7 @@ public class AlignViewport extends AlignmentViewport implements
       residueShading.setConsensus(hconsensus);
     }
 
-    posProps = new ViewportPositionProps(this.alignment, this);
+    posProps = new ViewportPositionProps(this.alignment);
   }
 
   /**
diff --git a/src/jalview/viewmodel/ViewportPositionProps.java b/src/jalview/viewmodel/ViewportPositionProps.java
index 176da8a..69a60f5 100644
--- a/src/jalview/viewmodel/ViewportPositionProps.java
+++ b/src/jalview/viewmodel/ViewportPositionProps.java
@@ -20,7 +20,6 @@
  */
 package jalview.viewmodel;
 
-import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentI;
 
 /**
@@ -44,15 +43,11 @@ public class ViewportPositionProps extends ViewportProperties
   // alignment
   private AlignmentI al;
 
-  // viewport
-  private AlignViewportI av; // this is a bad dependency, viewmodel should not
-                             // depend on api
-
   /**
    * Constructor
    * @param alignment TODO
    */
-  public ViewportPositionProps(AlignmentI alignment, AlignViewportI viewport)
+  public ViewportPositionProps(AlignmentI alignment)
   {
     // initial values of viewport settings
     this.startRes = 0;
@@ -60,7 +55,6 @@ public class ViewportPositionProps extends ViewportProperties
     this.startSeq = 0;
     this.endSeq = alignment.getHeight() - 1;
     this.al = alignment;
-    this.av = viewport;
   }
 
   // ways to update values
@@ -168,62 +162,4 @@ public class ViewportPositionProps extends ViewportProperties
   {
     return endSeq;
   }
-
-  /**
-   * Get absolute start residue of viewport
-   */
-  public int getAbsoluteStartRes()
-  {
-    int start = startRes;
-
-    if (av.hasHiddenColumns())
-    {
-      start = av.getColumnSelection().adjustForHiddenColumns(start);
-    }
-    return start;
-  }
-
-  /**
-   * Get absolute start residue of viewport
-   */
-  public int getAbsoluteEndRes()
-  {
-    int end = endRes;
-
-    if (av.hasHiddenColumns())
-    {
-      end = av.getColumnSelection().adjustForHiddenColumns(end);
-    }
-    return end;
-  }
-
-  /**
-   * Get absolute start sequence of viewport
-   */
-  public int getAbsoluteStartSeq()
-  {
-    int start = startSeq;
-
-    if (av.hasHiddenRows())
-    {
-      start = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(start);
-    }
-    return start;
-  }
-
-  /**
-   * Get absolute end sequence of viewport
-   */
-  public int getAbsoluteEndSeq()
-  {
-    int end = endSeq;
-
-    if (av.hasHiddenRows())
-    {
-      end = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(end);
-    }
-    return end;
-  }
-
 }
-- 
1.7.10.2