JAL-2388 Remove OverviewDimensions dependency on gui classes

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 0bb9392..8f91835 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -83,7 +83,7 @@ public class OverviewPanel extends Panel implements Runnable,
       showAnnotation = true;
     }
 
-    od = new OverviewDimensions(av, showAnnotation);
+    od = new OverviewDimensions(av.getPosProps(), showAnnotation);
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -148,7 +148,9 @@ public class OverviewPanel extends Panel implements Runnable,
 
   private void mouseAction(MouseEvent evt)
   {
-    od.updateViewportFromMouse(evt.getX(), evt.getY());
+    od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av
+            .getPosProps());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
@@ -343,7 +345,8 @@ public class OverviewPanel extends Panel implements Runnable,
    */
   public void setBoxPosition()
   {
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     repaint();
   }
 

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d15ec40..e399bc1 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -95,7 +95,7 @@ public class OverviewPanel extends JPanel implements Runnable
     {
       showAnnotation = true;
     }
-    od = new OverviewDimensions(av, showAnnotation);
+    od = new OverviewDimensions(av.getPosProps(), showAnnotation);
 
     addComponentListener(new ComponentAdapter()
     {
@@ -119,7 +119,9 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           // TODO: feature: jv2.5 detect shift drag and update selection from
           // it.
-          od.updateViewportFromMouse(evt.getX(), evt.getY());
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getPosProps());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -132,7 +134,9 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          od.updateViewportFromMouse(evt.getX(), evt.getY());
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getPosProps());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -331,7 +335,8 @@ public class OverviewPanel extends JPanel implements Runnable
    */
   public void setBoxPosition()
   {
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     repaint();
   }
 

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index ed9a155..34b7aff 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -20,7 +20,6 @@
  */
 package jalview.viewmodel;
 
-import jalview.api.AlignViewportI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
 
@@ -39,10 +38,6 @@ public class OverviewDimensions
 
   private static final int MAX_SEQ_HEIGHT = 300;
 
-  private AlignViewportI av;
-
-  private ViewportPositionProps posProps;
-
   // width of the overview panel
   private int width;
 
@@ -65,26 +60,34 @@ public class OverviewDimensions
   // height of box
   private int boxHeight = -1;
 
+  // scroll position in viewport corresponding to boxX
   private int scrollCol = -1;
 
+  // scroll position in viewport corresponding to boxY
   private int scrollRow = -1;
 
-  public OverviewDimensions(AlignViewportI avi, boolean showAnnotationPanel)
+  /**
+   * Create an OverviewDimensions object
+   * 
+   * @param props
+   *          positional properties of the viewport
+   * @param showAnnotationPanel
+   *          true if the annotation panel is to be shown, false otherwise
+   */
+  public OverviewDimensions(ViewportPositionProps props,
+          boolean showAnnotationPanel)
   {
-    this.av = avi;
-    this.posProps = av.getPosProps();
-
     // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) posProps.getAlignmentWidthInCols()
-            / (float) posProps.getAlignmentHeightInRows();
+    float initialScale = (float) props.getAbsoluteAlignmentWidth()
+            / (float) props.getAbsoluteAlignmentHeight();
 
     if (!showAnnotationPanel)
     {
       graphHeight = 0;
     }
 
-    if (posProps.getAlignmentWidthInCols() > posProps
-            .getAlignmentHeightInRows())
+    if (props.getAbsoluteAlignmentWidth() > props
+            .getAbsoluteAlignmentHeight())
     {
       // wider
       width = MAX_WIDTH;
@@ -109,14 +112,27 @@ public class OverviewDimensions
 
   /**
    * Check box dimensions and scroll positions and correct if necessary
+   * 
+   * @param mousex
+   *          x position in overview panel
+   * @param mousey
+   *          y position in overview panel
+   * @param hiddenSeqs
+   *          hidden sequences
+   * @param hiddenCols
+   *          hidden columns
+   * @param props
+   *          viewport position properties
    */
-  public void updateViewportFromMouse(int x, int y)
+  public void updateViewportFromMouse(int mousex, int mousey,
+          HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
+          ViewportPositionProps props)
   {
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getAbsoluteHeight();
+    int x = mousex;
+    int y = mousey;
 
-    HiddenSequences hiddenSeqs = av.getAlignment().getHiddenSequences();
-    ColumnSelection hiddenCols = av.getColumnSelection();
+    int alwidth = props.getAbsoluteAlignmentWidth();
+    int alheight = props.getAbsoluteAlignmentHeight();
 
     if (x < 0)
     {
@@ -148,8 +164,7 @@ public class OverviewDimensions
     int xAsRes = Math.round((float) x * alwidth / width);
 
     // get viewport width in residues
-    int vpwidth = av.getPosProps().getEndRes()
-            - av.getPosProps().getStartRes() + 1;
+    int vpwidth = props.getEndRes() - props.getStartRes() + 1;
 
     // get where x should be when accounting for hidden cols
     // if x is in a hidden col region, shift to left - but we still need
@@ -178,8 +193,7 @@ public class OverviewDimensions
     int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
 
     // get viewport height in sequences
-    int vpheight = av.getPosProps().getEndSeq()
-            - av.getPosProps().getStartSeq();
+    int vpheight = props.getEndSeq() - props.getStartSeq();
 
     // get where y should be when accounting for hidden rows
     // if y is in a hidden row region, shift up - but we still need absolute
@@ -210,23 +224,35 @@ public class OverviewDimensions
    * Update the overview panel box when the associated alignment panel is
    * changed
    * 
+   * @param hiddenSeqs
+   *          hidden sequences
+   * @param hiddenCols
+   *          hidden columns
+   * @param props
+   *          viewport position properties
    */
-  public void setBoxPosition()
+  public void setBoxPosition(HiddenSequences hiddenSeqs,
+          ColumnSelection hiddenCols, ViewportPositionProps props)
   {
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getAbsoluteHeight();
+    int alwidth = props.getAbsoluteAlignmentWidth();
+    int alheight = props.getAbsoluteAlignmentHeight();
 
-    int startRes = av.getPosProps().getAbsoluteStartRes();
-    int endRes = av.getPosProps().getAbsoluteEndRes();
+    // work with absolute values of startRes and endRes
+    int startRes = hiddenCols.adjustForHiddenColumns(props.getStartRes());
+    int endRes = hiddenCols.adjustForHiddenColumns(props.getEndRes());
 
-    int startSeq = av.getPosProps().getAbsoluteStartSeq();
-    int endSeq = av.getPosProps().getAbsoluteEndSeq();
+    // work with absolute values of startSeq and endSeq
+    int startSeq = hiddenSeqs.adjustForHiddenSeqs(props.getStartSeq());
+    int endSeq = hiddenSeqs.adjustForHiddenSeqs(props.getEndSeq());
 
+    // boxX, boxY is the x,y location equivalent to startRes, startSeq
     boxX = Math.round((float) startRes * width / alwidth);
     boxY = Math.round((float) startSeq * sequencesHeight / alheight);
 
+    // boxWidth is the width in residues translated to pixels
     boxWidth = Math
             .round((float) (endRes - startRes + 1) * width / alwidth);
+    // boxHeight is the height in sequences translated to pixels
     boxHeight = Math.round((float) (endSeq - startSeq) * sequencesHeight
             / alheight);
   }
@@ -280,16 +306,6 @@ public class OverviewDimensions
     return boxHeight;
   }
 
-  public void setBoxX(int x)
-  {
-    boxX = x;
-  }
-
-  public void setBoxY(int y)
-  {
-    boxY = y;
-  }
-
   public void setWidth(int w)
   {
     width = w;

diff --git a/src/jalview/viewmodel/ViewportPositionProps.java b/src/jalview/viewmodel/ViewportPositionProps.java
index 2789d77..176da8a 100644 (file)
--- a/src/jalview/viewmodel/ViewportPositionProps.java
+++ b/src/jalview/viewmodel/ViewportPositionProps.java
@@ -70,19 +70,19 @@ public class ViewportPositionProps extends ViewportProperties
   // ways to supply positional information
 
   /**
-   * Get alignment width
+   * Get alignment width in cols, including hidden cols
    */
-  public int getAlignmentWidthInCols()
+  public int getAbsoluteAlignmentWidth()
   {
     return al.getWidth();
   }
 
   /**
-   * Get alignment height
+   * Get alignment height in rows, including hidden rows
    */
-  public int getAlignmentHeightInRows()
+  public int getAbsoluteAlignmentHeight()
   {
-    return al.getHeight();
+    return al.getHeight() + al.getHiddenSequences().getSize();
   }
 
   public void setStartRes(int res)

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index d470c35..be8154c 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -121,7 +121,7 @@ public class OverviewDimensionsTest {
     
     av = af.getViewport();
 
-    od = new OverviewDimensions(av, true);
+    od = new OverviewDimensions(av.getPosProps(), true);
 
     while (av.isCalcInProgress())
     {
@@ -135,7 +135,8 @@ public class OverviewDimensionsTest {
     }
 
     // Initial box sizing - default path through code
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
 
     init();
   }
@@ -167,6 +168,7 @@ public class OverviewDimensionsTest {
     viewWidth = av.getEndRes() - av.getStartRes();
 
     // wait for gui to get set up
+    // this does actually appear to be necessary
     while (viewHeight != 17 || viewWidth != 62)
     {
       try
@@ -232,7 +234,7 @@ public class OverviewDimensionsTest {
     al1.setDataset(null);
     AlignViewport av1 = new AlignViewport(al1);
 
-    OverviewDimensions od = new OverviewDimensions(av1, true);
+    OverviewDimensions od = new OverviewDimensions(av1.getPosProps(), true);
     int scaledHeight = 266;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), scaledHeight);
@@ -245,7 +247,7 @@ public class OverviewDimensionsTest {
     al2.setDataset(null);
     AlignViewport av2 = new AlignViewport(al2);
 
-    od = new OverviewDimensions(av2, true);
+    od = new OverviewDimensions(av2.getPosProps(), true);
     int scaledWidth = 300;
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
@@ -259,7 +261,7 @@ public class OverviewDimensionsTest {
     al3.setDataset(null);
     AlignViewport av3 = new AlignViewport(al3);
 
-    od = new OverviewDimensions(av3, true);
+    od = new OverviewDimensions(av3.getPosProps(), true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), minSeqHeight);
     assertEquals(od.getWidth(), maxWidth);
@@ -272,7 +274,7 @@ public class OverviewDimensionsTest {
     al4.setDataset(null);
     AlignViewport av4 = new AlignViewport(al4);
 
-    od = new OverviewDimensions(av4, true);
+    od = new OverviewDimensions(av4.getPosProps(), true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
@@ -282,7 +284,7 @@ public class OverviewDimensionsTest {
     al5.setDataset(null);
     AlignViewport av5 = new AlignViewport(al5);
 
-    od = new OverviewDimensions(av5, false);
+    od = new OverviewDimensions(av5.getPosProps(), false);
     assertEquals(od.getGraphHeight(), 0);
     assertEquals(od.getSequencesHeight(), maxSeqHeight);
     assertEquals(od.getWidth(), minWidth);
@@ -302,7 +304,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testSetBoxFromMouseClick()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -396,7 +400,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtStart()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -408,7 +414,8 @@ public class OverviewDimensionsTest {
     int lastHiddenCol = 30;
     hideColumns(0, lastHiddenCol);
 
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(),
             Math.round((float) (lastHiddenCol + 1) * od.getWidth()
                     / alwidth));
@@ -460,7 +467,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsInMiddle()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -472,7 +481,8 @@ public class OverviewDimensionsTest {
     int lastHidden = 73;
     hideColumns(firstHidden, lastHidden);
 
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -565,7 +575,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenColsAtEnd()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -576,7 +588,8 @@ public class OverviewDimensionsTest {
     int firstHidden = 140;
     int lastHidden = 157;
     hideColumns(firstHidden, lastHidden);
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -909,7 +922,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtStart()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -922,7 +937,8 @@ public class OverviewDimensionsTest {
     int lastHiddenRow = 30;
     hideSequences(0, lastHiddenRow + 1, lastHiddenRow + 1);
 
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
             Math.round((float) (lastHiddenRow + 1)
@@ -955,7 +971,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsInMiddle()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -970,7 +988,8 @@ public class OverviewDimensionsTest {
     int lastHiddenRow = 60;
     hideSequences(firstHiddenRow, lastHiddenRow + 1, lastHiddenRow + 1);
 
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -1015,7 +1034,9 @@ public class OverviewDimensionsTest {
   @Test(groups = { "Functional" })
   public void testFromMouseWithHiddenRowsAtEnd()
   {
-    od.updateViewportFromMouse(0, 0);
+    od.updateViewportFromMouse(0, 0,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -1029,7 +1050,8 @@ public class OverviewDimensionsTest {
     int lastHidden = 524;
     hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);
 
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -1079,7 +1101,8 @@ public class OverviewDimensionsTest {
   {
     av.setStartRes(startRes);
     av.setEndRes(startRes + viewWidth);
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
   }
 
   /*
@@ -1089,7 +1112,8 @@ public class OverviewDimensionsTest {
   {
     av.setStartSeq(startSeq);
     av.setEndSeq(startSeq + viewHeight);
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
   }
 
   /*
@@ -1101,7 +1125,8 @@ public class OverviewDimensionsTest {
     av.setEndRes(startRes + viewWidth);
     av.setStartSeq(startSeq);
     av.setEndSeq(startSeq + viewHeight);
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
   }
 
   /*
@@ -1109,7 +1134,9 @@ public class OverviewDimensionsTest {
    */
   private void mouseClick(OverviewDimensions od, int x, int y)
   {
-    od.updateViewportFromMouse(x, y);
+    od.updateViewportFromMouse(x, y,
+            av.getAlignment().getHiddenSequences(),
+            av.getColumnSelection(), av.getPosProps());
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally
@@ -1119,7 +1146,8 @@ public class OverviewDimensionsTest {
     av.setEndRes(od.getScrollCol() + viewWidth);
     av.setStartSeq(od.getScrollRow());
     av.setEndSeq(od.getScrollRow() + viewHeight);
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
   }
   
   private void testBoxIsAtClickPoint(int xpos, int ypos)