(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index fc4fb8c..4b646c3 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -17,6 +17,8 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.AlignmentI;
+
 import java.awt.*;
 import java.awt.event.*;
 
@@ -65,17 +67,17 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
     fr.overview = true;
-
+    
     // 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.hconsensus == null)
+    if (av.getSequenceConsensusHash() == null)
     {
       graphHeight = 0;
     }
 
-    if (av.alignment.getWidth() > av.alignment.getHeight())
+    if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
     {
       // wider
       width = 400;
@@ -174,7 +176,7 @@ public class OverviewPanel extends Panel 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);
@@ -185,7 +187,7 @@ public class OverviewPanel extends Panel 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))
       {
@@ -195,9 +197,9 @@ public class OverviewPanel extends Panel implements Runnable,
       col = av.getColumnSelection().findColumnPosition(col);
     }
 
-    if (av.hasHiddenRows)
+    if (av.hasHiddenRows())
     {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+      row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
               row);
     }
 
@@ -243,8 +245,8 @@ public class OverviewPanel extends Panel implements Runnable,
   public void run()
   {
     miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getHeight();
 
     if (av.showSequenceFeatures)
     {
@@ -278,6 +280,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int row, col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI seq;
     boolean hiddenRow = false;
+    AlignmentI alignment=av.getAlignment();
     for (row = 0; row <= sequencesHeight; row++)
     {
       if ((int) (row * sampleRow) == lastrow)
@@ -287,15 +290,15 @@ public class OverviewPanel extends Panel implements Runnable,
       }
 
       hiddenRow = false;
-      if (av.hasHiddenRows)
+      if (av.hasHiddenRows())
       {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
         if (seq == null)
         {
-          int index = av.alignment.getHiddenSequences()
+          int index = alignment.getHiddenSequences()
                   .findIndexWithoutHiddenSeqs(lastrow);
 
-          seq = av.alignment.getSequenceAt(index);
+          seq = alignment.getSequenceAt(index);
         }
         else
         {
@@ -304,7 +307,7 @@ public class OverviewPanel extends Panel implements Runnable,
       }
       else
       {
-        seq = av.alignment.getSequenceAt(lastrow);
+        seq = alignment.getSequenceAt(lastrow);
       }
 
       for (col = 0; col < width; col++)
@@ -333,7 +336,7 @@ public class OverviewPanel extends Panel implements Runnable,
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns && !av.getColumnSelection()
+                || (av.hasHiddenColumns() && !av.getColumnSelection()
                         .isVisible(lastcol)))
         {
           color = color.darker().darker();
@@ -357,14 +360,14 @@ public class OverviewPanel extends Panel implements Runnable,
       sameRow = 1;
     }
 
-    if (av.conservation != null)
+    if (av.getAlignmentConservationAnnotation()!= null)
     {
       for (col = 0; col < width; col++)
       {
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          ap.annotationPanel.renderer.drawGraph(mg, av.conservation,
+          ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -386,14 +389,14 @@ public class OverviewPanel extends Panel 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);
@@ -402,12 +405,12 @@ public class OverviewPanel extends Panel 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);
 
     }
@@ -418,7 +421,7 @@ public class OverviewPanel extends Panel 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);
     }