JAL-2388 Removing AlignmentPanel dependency (mostly)

diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
index dea8ddc..51819cd 100644 (file)
--- a/src/jalview/appletgui/OverviewCanvas.java
+++ b/src/jalview/appletgui/OverviewCanvas.java
@@ -48,8 +48,6 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewport av;
 
-  private AlignmentPanel ap;
-
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   private SequenceRenderer sr;
@@ -59,11 +57,10 @@ public class OverviewCanvas extends JComponent
   private Frame nullFrame;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
-          AlignViewport alignvp, AlignmentPanel alignp)
+          AlignViewport alignvp)
   {
     od = overviewDims;
-    av = alignp.av;
-    ap = alignp;
+    av = alignvp;
 
     nullFrame = new Frame();
     nullFrame.addNotify();
@@ -95,7 +92,8 @@ public class OverviewCanvas extends JComponent
     }
   }
 
-  public void draw(boolean showSequenceFeatures, boolean showAnnotation)
+  public void draw(boolean showSequenceFeatures, boolean showAnnotation,
+          AlignmentPanel ap)
   {
     miniMe = null;
 
@@ -137,7 +135,7 @@ public class OverviewCanvas extends JComponent
     if (restart)
     {
       restart = false;
-      draw(showSequenceFeatures, showAnnotation);
+      draw(showSequenceFeatures, showAnnotation, ap);
     }
     else
     {

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 8962bdc..d64c72f 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -53,7 +53,7 @@ public class OverviewPanel extends Panel implements Runnable,
     od = new OverviewDimensions(av.getRanges(),
             (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
-    oviewCanvas = new OverviewCanvas(od, av, ap);
+    oviewCanvas = new OverviewCanvas(od, av);
     setLayout(new BorderLayout());
     add(oviewCanvas, BorderLayout.CENTER);
 
@@ -157,7 +157,7 @@ public class OverviewPanel extends Panel implements Runnable,
   {
     oviewCanvas.draw(av.isShowSequenceFeatures(),
             (av.isShowAnnotation() && av
-                    .getAlignmentConservationAnnotation() != null));
+                    .getAlignmentConservationAnnotation() != null), ap);
     setBoxPosition();
   }
 
@@ -172,8 +172,4 @@ public class OverviewPanel extends Panel implements Runnable,
             .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }
-
-
-
- 
 }

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 8c02423..3ced9ee 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -48,8 +48,6 @@ public class OverviewCanvas extends JComponent
 
   private BufferedImage lastMiniMe = null;
 
-
-
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   private SequenceRenderer sr;
@@ -60,21 +58,18 @@ public class OverviewCanvas extends JComponent
 
   OverviewDimensions od;
 
-  AlignViewport av;
-
-  AlignmentPanel ap;
+  AlignViewportI av;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
-          AlignViewportI alignvp, AlignmentPanel alignp)
+          AlignViewportI alignvp)
   {
     od = overviewDims;
-    av = alignp.av;
-    ap = alignp;
+    av = alignvp;
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
     sr.forOverview = true;
-    fr = new FeatureRenderer(ap);
+    fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
   }
 
   /*
@@ -97,13 +92,14 @@ public class OverviewCanvas extends JComponent
     }
   }
 
-  public void draw(boolean showSequenceFeatures, boolean showAnnotation)
+  public void draw(boolean showSequenceFeatures, boolean showAnnotation,
+          FeatureRenderer transferRenderer)
   {
     miniMe = null;
 
     if (showSequenceFeatures)
     {
-      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+      fr.transferSettings(transferRenderer);
     }
 
     // why do we need to set preferred size again? was set in
@@ -152,7 +148,7 @@ public class OverviewCanvas extends JComponent
     if (restart)
     {
       restart = false;
-      draw(showSequenceFeatures, showAnnotation);
+      draw(showSequenceFeatures, showAnnotation, transferRenderer);
     }
     else
     {

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index faa94e9..68b4dc5 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -64,7 +64,7 @@ public class OverviewPanel extends JPanel implements Runnable
             (av.isShowAnnotation() && av
                     .getAlignmentConservationAnnotation() != null));
 
-    oviewCanvas = new OverviewCanvas(od, av, ap);
+    oviewCanvas = new OverviewCanvas(od, av);
     setLayout(new BorderLayout());
     add(oviewCanvas, BorderLayout.CENTER);
 
@@ -143,7 +143,8 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     oviewCanvas.draw(av.isShowSequenceFeatures(),
             (av.isShowAnnotation() && av
-                    .getAlignmentConservationAnnotation() != null));
+                    .getAlignmentConservationAnnotation() != null), ap
+                    .getSeqPanel().seqCanvas.getFeatureRenderer());
     setBoxPosition();
   }
 

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 1c0420d..2a2a0cf 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
@@ -34,7 +35,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   final static int CHAR_TO_UPPER = 'A' - 'a';
 
-  AlignViewport av;
+  AlignViewportI av;
 
   FontMetrics fm;
 
@@ -57,7 +58,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * 
    * @param viewport
    */
-  public SequenceRenderer(AlignViewport viewport)
+  public SequenceRenderer(AlignViewportI viewport)
   {
     this.av = viewport;
   }
@@ -181,7 +182,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
     drawBoxes(seq, start, end, y1);
 
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       drawText(seq, start, end, y1);
     }