JAL-2388 Minor refactoring

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 743d217..1b6df1d 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -123,33 +123,23 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    od.setBoxX(evt.getX());
-    od.setBoxY(evt.getY());
-    checkValid();
+    od.setBoxPositionByMouse(evt.getX(), evt.getY());
+    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+    ap.paintAlignment(false);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    od.setBoxX(evt.getX());
-    od.setBoxY(evt.getY());
-    checkValid();
+    od.setBoxPositionByMouse(evt.getX(), evt.getY());
+    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+    ap.paintAlignment(false);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    od.setBoxX(evt.getX());
-    od.setBoxY(evt.getY());
-    checkValid();
-  }
-
-  /**
-   * Check box dimensions and scroll positions and correct if necessary
-   */
-  private void checkValid()
-  {
-    od.checkValid();
+    od.setBoxPositionByMouse(evt.getX(), evt.getY());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
@@ -383,10 +373,7 @@ public class OverviewPanel extends Panel implements Runnable,
     {
       og.drawImage(miniMe, 0, 0, this);
       og.setColor(Color.red);
-      og.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
-              od.getBoxHeight());
-      og.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2,
-              od.getBoxHeight() - 2);
+      od.drawBox(og);
       g.drawImage(offscreen, 0, 0, this);
     }
   }

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index fc3cc4b..d87285c 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -36,7 +36,8 @@ import java.awt.image.BufferedImage;
 import javax.swing.JPanel;
 
 /**
- * DOCUMENT ME!
+ * Panel displaying an overview of the full alignment, with an interactive box
+ * representing the viewport onto the alignment.
  * 
  * @author $author$
  * @version $Revision$
@@ -73,19 +74,19 @@ public class OverviewPanel extends JPanel implements Runnable
   /**
    * Creates a new OverviewPanel object.
    * 
-   * @param ap
+   * @param alPanel
    *          The alignment panel which is shown in the overview panel
    */
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
     sr.forOverview = true;
-    fr = new FeatureRenderer(ap);
+    fr = new FeatureRenderer(alPanel);
 
     od = new OverviewDimensions(av);
 
@@ -111,9 +112,8 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           // TODO: feature: jv2.5 detect shift drag and update selection from
           // it.
-          od.setBoxX(evt.getX());
-          od.setBoxY(evt.getY());
-          checkValid();
+          od.setBoxPositionByMouse(evt.getX(), evt.getY());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -125,9 +125,8 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          od.setBoxX(evt.getX());
-          od.setBoxY(evt.getY());
-          checkValid();
+          od.setBoxPositionByMouse(evt.getX(), evt.getY());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -136,16 +135,6 @@ public class OverviewPanel extends JPanel implements Runnable
   }
 
   /**
-   * Check box dimensions and scroll positions and correct if necessary
-   */
-  private void checkValid()
-  {
-    od.checkValid();
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-
-  }
-
-  /**
    * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
@@ -391,9 +380,6 @@ public class OverviewPanel extends JPanel implements Runnable
     }
     // TODO: render selected regions
     g.setColor(Color.red);
-    g.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
-            od.getBoxHeight());
-    g.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2,
-            od.getBoxHeight() - 2);
+    od.drawBox(g);
   }
 }

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 17f56c9..9b55e55 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -22,6 +22,8 @@ package jalview.viewmodel;
 
 import jalview.api.AlignViewportI;
 
+import java.awt.Graphics;
+
 public class OverviewDimensions
 {
   // Default width and height values
@@ -108,14 +110,15 @@ public class OverviewDimensions
   /**
    * Check box dimensions and scroll positions and correct if necessary
    */
-  public void checkValid()
+  public void setBoxPositionByMouse(int x, int y)
   {
+    boxX = x;
+    boxY = y;
     if (boxY < 0)
     {
       boxY = 0;
     }
-
-    if (boxY > (sequencesHeight - boxHeight))
+    else if (boxY > (sequencesHeight - boxHeight))
     {
       boxY = sequencesHeight - boxHeight + 1;
     }
@@ -124,8 +127,7 @@ public class OverviewDimensions
     {
       boxX = 0;
     }
-
-    if (boxX > (width - boxWidth))
+    else if (boxX > (width - boxWidth))
     {
       if (av.hasHiddenColumns())
       {
@@ -184,21 +186,12 @@ public class OverviewDimensions
 
       endSeq = av.getAlignment().getHiddenSequences()
               .adjustForHiddenSeqs(endSeq);
-
     }
 
     boxX = (int) (startRes * av.getCharWidth() * scalew);
     boxY = (int) (startSeq * av.getCharHeight() * scaleh);
 
-    if (av.hasHiddenColumns())
-    {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-    else
-    {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-
+    boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
     boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
   }
 
@@ -218,6 +211,18 @@ public class OverviewDimensions
     scaleh = (float) sequencesHeight / fullsizeHeight;
   }
 
+  /**
+   * Draw the overview panel's viewport box on a graphics object
+   * 
+   * @param g
+   *          the graphics object to draw on
+   */
+  public void drawBox(Graphics g)
+  {
+    g.drawRect(boxX, boxY, boxWidth, boxHeight);
+    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+  }
+
   // don't like this, scroll vals are separate from setting code
   public int getScrollCol()
   {
@@ -229,11 +234,15 @@ public class OverviewDimensions
     return scrollRow;
   }
 
+  // TODO should be removed, when unit test has mock Graphics object available
+  // to check boxX/boxY
   public int getBoxX()
   {
     return boxX;
   }
 
+  // TODO should be removed, when unit test has mock Graphics object available
+  // to check boxX/boxY
   public int getBoxY()
   {
     return boxY;

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index a9770bd..7c40fe9 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -257,7 +257,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxFromMouseClick()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -347,7 +347,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtStart()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -409,7 +409,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsInMiddle()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -510,7 +510,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtEnd()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -840,7 +840,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtStart()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -884,7 +884,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsInMiddle()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -941,7 +941,7 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtEnd()
   {
-    od.checkValid();
+    od.setBoxPositionByMouse(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -1036,9 +1036,7 @@ public class OverviewDimensionsTest {
    */
   private void mouseClick(OverviewDimensions od, int x, int y)
   {
-    od.setBoxX(x);
-    od.setBoxY(y);
-    od.checkValid();
+    od.setBoxPositionByMouse(x, y);
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally