JAL-2439 Fixes to out-by-one sequence indexing in gui classes

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 024fdc7..cd5aa74 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -21,9 +21,11 @@
 package jalview.appletgui;
 
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
@@ -48,8 +50,6 @@ public class SeqCanvas extends Panel
 
   AlignViewport av;
 
-  SearchResults searchResults = null;
-
   boolean fastPaint = false;
 
   int cursorX = 0;
@@ -90,26 +90,29 @@ public class SeqCanvas extends Panel
 
   private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
-    int scalestartx = startx - startx % 10 + 10;
-
+    updateViewport();
     g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
+    for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+            endx))
     {
-      int value = i;
-      if (av.hasHiddenColumns())
+      int mpos = mark.column; // (i - startx - 1)
+      if (mpos < 0)
       {
-        value = av.getColumnSelection().adjustForHiddenColumns(value);
+        continue;
       }
+      String mstring = mark.text;
 
-      g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
-              ypos - (avcharHeight / 2));
-
-      g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-              (ypos + 2) - (avcharHeight / 2),
-              ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-              ypos - 2);
+      if (mark.major)
+      {
+        if (mstring != null)
+        {
+          g.drawString(mstring, mpos * avcharWidth, ypos
+                  - (avcharHeight / 2));
+        }
+        g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
+                - (avcharHeight / 2), (mpos * avcharWidth)
+                + (avcharWidth / 2), ypos - 2);
+      }
     }
   }
 
@@ -213,12 +216,12 @@ public class SeqCanvas extends Panel
     // Its possible on certain browsers that the call to fastpaint
     // is faster than it can paint, so this check here catches
     // this possibility
-    if (lastsr + horizontal != av.startRes)
+    if (lastsr + horizontal != av.getStartRes())
     {
-      horizontal = av.startRes - lastsr;
+      horizontal = av.getStartRes() - lastsr;
     }
 
-    lastsr = av.startRes;
+    lastsr = av.getStartRes();
 
     fastPaint = true;
     gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
@@ -226,7 +229,8 @@ public class SeqCanvas extends Panel
             imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
             -vertical * avcharHeight);
 
-    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+    int sr = av.getStartRes(), er = av.getEndRes(), ss = av.getStartSeq(), es = av
+            .getEndSeq(), transX = 0, transY = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -241,21 +245,22 @@ public class SeqCanvas extends Panel
     else if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
-        transY = imgHeight - vertical * avcharHeight;
+        transY = imgHeight - ((vertical + 1) * avcharHeight);
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -328,11 +333,12 @@ public class SeqCanvas extends Panel
 
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
+              av.getEndSeq(), 0);
     }
 
     g.drawImage(img, 0, 0, this);
@@ -418,7 +424,7 @@ public class SeqCanvas extends Panel
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.setEndRes(av.getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
@@ -607,7 +613,7 @@ public class SeqCanvas extends Panel
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
 
@@ -627,9 +633,10 @@ public class SeqCanvas extends Panel
 
       // / Highlight search Results once all sequences have been drawn
       // ////////////////////////////////////////////////////////
-      if (searchResults != null)
+      if (av.hasSearchResults())
       {
-        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+        int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+                startRes,
                 endRes);
         if (visibleResults != null)
         {
@@ -690,7 +697,7 @@ public class SeqCanvas extends Panel
         int bottom = -1;
         int alHeight = av.getAlignment().getHeight() - 1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * avcharWidth;
           sy = offset + ((i - startSeq) * avcharHeight);
@@ -838,10 +845,9 @@ public class SeqCanvas extends Panel
     }
   }
 
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
-    searchResults = results;
-
+    av.setSearchResults(results);
     repaint();
   }