JAL-2388 Unit tests and tidies

[jalview.git] / src / jalview / appletgui / OverviewPanel.java

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 1b6df1d..f0dd524 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SequenceI;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -61,10 +62,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
   private Frame nullFrame;
 
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
     nullFrame = new Frame();
     nullFrame.addNotify();
@@ -75,7 +76,7 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    od = new OverviewDimensions(av);
+    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -123,29 +124,32 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
+    mouseAction(evt);
+  }
+
+  private void mouseAction(MouseEvent evt)
+  {
+    od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av
+            .getPosProps());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 
   /**
-   * DOCUMENT ME!
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -164,8 +168,8 @@ public class OverviewPanel extends Panel implements Runnable,
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
     setSize(new Dimension(od.getWidth(), od.getHeight()));
 
@@ -197,17 +201,14 @@ public class OverviewPanel extends Panel implements Runnable,
 
     Graphics mg = miniMe.getGraphics();
 
-    od.updateScales();
-
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
+    int alheight = av.getAlignment().getAbsoluteHeight();
     float sampleCol = alwidth / (float) od.getWidth();
     float sampleRow = alheight / (float) od.getSequencesHeight();
 
     buildImage(sampleRow, sampleCol, mg);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    if (av.isShowAnnotation())
     {
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
@@ -233,6 +234,9 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
+  /*
+   * Build the overview panel image
+   */
   private void buildImage(float sampleRow, float sampleCol, Graphics mg)
   {
     int lastcol = 0;
@@ -243,8 +247,8 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameRow = 0;
     int sameCol = 0;
 
-    jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
+    SequenceI seq = null;
+
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
 
@@ -253,33 +257,13 @@ public class OverviewPanel extends Panel implements Runnable,
       if ((int) (row * sampleRow) == lastrow)
       {
         sameRow++;
-        continue;
       }
       else
       {
-        // this should largely be a method in Alignment
-        hiddenRow = false;
-        if (hasHiddenRows)
-        {
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
 
         for (int col = 0; col < od.getWidth(); col++)
         {
@@ -314,7 +298,6 @@ public class OverviewPanel extends Panel implements Runnable,
         sameRow = 1;
       }
     }
-
   }
 
   /*
@@ -336,7 +319,7 @@ public class OverviewPanel extends Panel implements Runnable,
     }
     else
     {
-      color = Color.white; // White
+      color = Color.white;
     }
 
     if (hiddenRow
@@ -355,7 +338,8 @@ public class OverviewPanel extends Panel implements Runnable,
    */
   public void setBoxPosition()
   {
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     repaint();
   }