X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=c844315a41da24e1da5948bf738a93eddf4f5273;hb=d053a3c980cf4318b9a19a255f9fc870e74de989;hp=7e00f2efc632afdef5f4b685d66f81c9576a53e0;hpb=34286266321abbbab6d462c39f500650f9c860c9;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 7e00f2e..c844315 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -83,15 +83,15 @@ public class OverviewPanel extends JPanel implements Runnable
     fr = new FeatureRenderer(ap);
 
     // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth()
-            / (float) av.alignment.getHeight();
+    float initialScale = (float) av.getAlignment().getWidth()
+            / (float) av.getAlignment().getHeight();
 
-    if (av.conservation == null)
+    if (av.getAlignmentConservationAnnotation()== null)
     {
       graphHeight = 0;
     }
 
-    if (av.alignment.getWidth() > av.alignment.getHeight())
+    if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
     {
       // wider
       width = 400;
@@ -178,7 +178,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (boxX > (width - boxWidth))
     {
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         // Try smallest possible box
         boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
@@ -189,7 +189,7 @@ public class OverviewPanel extends JPanel implements Runnable
     int col = (int) (boxX / scalew / av.getCharWidth());
     int row = (int) (boxY / scaleh / av.getCharHeight());
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       if (!av.getColumnSelection().isVisible(col))
       {
@@ -199,9 +199,9 @@ public class OverviewPanel extends JPanel implements Runnable
       col = av.getColumnSelection().findColumnPosition(col);
     }
 
-    if (av.hasHiddenRows)
+    if (av.hasHiddenRows())
     {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+      row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
               row);
     }
 
@@ -251,9 +251,9 @@ public class OverviewPanel extends JPanel implements Runnable
       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
 
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight()
-            + av.alignment.getHiddenSequences().getSize();
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getHeight()
+            + av.getAlignment().getHiddenSequences().getSize();
 
     setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
@@ -294,15 +294,15 @@ public class OverviewPanel extends JPanel implements Runnable
       lastrow = (int) (row * sampleRow);
 
       hiddenRow = false;
-      if (av.hasHiddenRows)
+      if (av.hasHiddenRows())
       {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
         if (seq == null)
         {
-          int index = av.alignment.getHiddenSequences()
+          int index = av.getAlignment().getHiddenSequences()
                   .findIndexWithoutHiddenSeqs(lastrow);
 
-          seq = av.alignment.getSequenceAt(index);
+          seq = av.getAlignment().getSequenceAt(index);
         }
         else
         {
@@ -311,7 +311,7 @@ public class OverviewPanel extends JPanel implements Runnable
       }
       else
       {
-        seq = av.alignment.getSequenceAt(lastrow);
+        seq = av.getAlignment().getSequenceAt(lastrow);
       }
 
       if (seq == null)
@@ -346,7 +346,7 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns && !av.getColumnSelection()
+                || (av.hasHiddenColumns() && !av.getColumnSelection()
                         .isVisible(lastcol)))
         {
           color = new Color(color).darker().darker().getRGB();
@@ -357,7 +357,7 @@ public class OverviewPanel extends JPanel implements Runnable
       }
     }
 
-    if (av.conservation != null)
+    if (av.getAlignmentConservationAnnotation()!= null)
     {
       renderer.updateFromAlignViewport(av); 
       for (col = 0; col < width; col++)
@@ -365,7 +365,7 @@ public class OverviewPanel extends JPanel implements Runnable
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          renderer.drawGraph(mg, av.conservation,
+          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -390,14 +390,14 @@ public class OverviewPanel extends JPanel implements Runnable
    */
   public void setBoxPosition()
   {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight() + av.alignment
+    int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
             .getHiddenSequences().getSize()) * av.getCharHeight();
 
     int startRes = av.getStartRes();
     int endRes = av.getEndRes();
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
       endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
@@ -406,12 +406,12 @@ public class OverviewPanel extends JPanel implements Runnable
     int startSeq = av.startSeq;
     int endSeq = av.endSeq;
 
-    if (av.hasHiddenRows)
+    if (av.hasHiddenRows())
     {
-      startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
+      startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
               startSeq);
 
-      endSeq = av.alignment.getHiddenSequences()
+      endSeq = av.getAlignment().getHiddenSequences()
               .adjustForHiddenSeqs(endSeq);
 
     }
@@ -422,7 +422,7 @@ public class OverviewPanel extends JPanel implements Runnable
     boxX = (int) (startRes * av.getCharWidth() * scalew);
     boxY = (int) (startSeq * av.getCharHeight() * scaleh);
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
     }