JAL-653 JAL-1780 minimise call rate now av.hasHiddenRows is dynamic

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 7f9eba9..5204094 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -56,7 +56,8 @@ public class IdCanvas extends Panel
     PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
-  public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
+  public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+          int i, int starty,
           int ypos)
   {
     int charHeight = av.getCharHeight();
@@ -88,7 +89,7 @@ public class IdCanvas extends Panel
             ((i - starty) * charHeight) + ypos + charHeight
                     - (charHeight / 5));
 
-    if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+    if (hiddenRows)
     {
       drawMarker(i, starty, ypos);
     }
@@ -199,6 +200,10 @@ public class IdCanvas extends Panel
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
+    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+            && av.getShowHiddenMarkers();
+
     if (av.getWrapAlignment())
     {
       int maxwidth = av.getAlignment().getWidth();
@@ -227,7 +232,6 @@ public class IdCanvas extends Panel
       int cHeight = alheight * avcharHeight + hgap + annotationHeight;
 
       int rowSize = av.getEndRes() - av.getStartRes();
-
       // Draw the rest of the panels
       for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
               && (row < maxwidth); ypos += cHeight, row += rowSize)
@@ -237,11 +241,11 @@ public class IdCanvas extends Panel
 
           SequenceI s = av.getAlignment().getSequenceAt(i);
           gg.setFont(italic);
-          if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+          if (doHiddenCheck)
           {
             setHiddenFont(s);
           }
-          drawIdString(gg, s, i, 0, ypos);
+          drawIdString(gg, hiddenRows, s, i, 0, ypos);
         }
 
         if (labels != null)
@@ -267,7 +271,7 @@ public class IdCanvas extends Panel
         }
         gg.setFont(italic);
         // boolean isrep=false;
-        if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+        if (doHiddenCheck)
         {
           // isrep =
           setHiddenFont(seq);
@@ -302,7 +306,7 @@ public class IdCanvas extends Panel
                 (((i - starty) * avcharHeight) + avcharHeight)
                         - (avcharHeight / 5));
 
-        if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+        if (hiddenRows)
         {
           drawMarker(i, starty, 0);
         }

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 1749e23..f09bda5 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -298,6 +298,8 @@ public class OverviewPanel extends Panel implements Runnable,
     Color color = Color.yellow;
     int row, col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI seq;
+    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+            .hasHiddenColumns();
     boolean hiddenRow = false;
     AlignmentI alignment = av.getAlignment();
     for (row = 0; row <= sequencesHeight; row++)
@@ -309,7 +311,7 @@ public class OverviewPanel extends Panel implements Runnable,
       }
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
         seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
         if (seq == null)
@@ -355,7 +357,7 @@ public class OverviewPanel extends Panel implements Runnable,
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns() && !av.getColumnSelection()
+                || (hasHiddenCols && !av.getColumnSelection()
                         .isVisible(lastcol)))
         {
           color = color.darker().darker();

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index a7a4e34..fe42e1e 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -86,6 +86,8 @@ public class IdCanvas extends JPanel
    * 
    * @param gg
    *          DOCUMENT ME!
+   * @param hiddenRows
+   *          true - check and display hidden row marker if need be
    * @param s
    *          DOCUMENT ME!
    * @param i
@@ -95,7 +97,8 @@ public class IdCanvas extends JPanel
    * @param ypos
    *          DOCUMENT ME!
    */
-  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+  public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+          int i, int starty,
           int ypos)
   {
     int xPos = 0;
@@ -134,7 +137,7 @@ public class IdCanvas extends JPanel
     gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
             (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-    if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+    if (hiddenRows)
     {
       drawMarker(i, starty, ypos);
     }
@@ -274,6 +277,9 @@ public class IdCanvas extends JPanel
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
+    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
     if (av.getWrapAlignment())
     {
       int maxwidth = av.getAlignment().getWidth();
@@ -317,7 +323,7 @@ public class IdCanvas extends JPanel
         for (int i = starty; i < alheight; i++)
         {
           SequenceI s = av.getAlignment().getSequenceAt(i);
-          if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+          if (doHiddenCheck)
           {
             setHiddenFont(s);
           }
@@ -326,7 +332,7 @@ public class IdCanvas extends JPanel
             gg.setFont(getIdfont());
           }
 
-          drawIdString(gg, s, i, 0, ypos);
+          drawIdString(gg, hiddenRows, s, i, 0, ypos);
         }
 
         if (labels != null && av.isShowAnnotation())
@@ -357,7 +363,7 @@ public class IdCanvas extends JPanel
           continue;
         }
 
-        if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+        if (doHiddenCheck)
         {
           setHiddenFont(sequence);
         }
@@ -399,7 +405,7 @@ public class IdCanvas extends JPanel
                 (((i - starty) * av.getCharHeight()) + av.getCharHeight())
                         - (av.getCharHeight() / 5));
 
-        if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+        if (hiddenRows)
         {
           drawMarker(i, starty, 0);
         }

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 39a232a..609e010 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -292,6 +292,8 @@ public class OverviewPanel extends JPanel implements Runnable
     int color = Color.white.getRGB();
     int row, col;
     jalview.datamodel.SequenceI seq;
+    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+            .hasHiddenColumns();
     boolean hiddenRow = false;
     for (row = 0; row < sequencesHeight; row++)
     {
@@ -309,7 +311,7 @@ public class OverviewPanel extends JPanel implements Runnable
       lastrow = (int) (row * sampleRow);
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
         seq = av.getAlignment().getHiddenSequences()
                 .getHiddenSequence(lastrow);
@@ -362,7 +364,7 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns() && !av.getColumnSelection()
+                || (hasHiddenCols && !av.getColumnSelection()
                         .isVisible(lastcol)))
         {
           color = new Color(color).darker().darker().getRGB();