X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7d953989280b719458107acbddd20ed0802e899d;hb=refs%2Fheads%2Ffeatures%2FJAL-653_JAL-1766_htslib_refseqsupport;hp=5706fe76c9c7f7f6ac01db1c891cb5e8299123c8;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 5706fe7..7d95398 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -21,9 +21,12 @@
 package jalview.gui;
 
 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.ViewportRanges;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -60,8 +63,6 @@ public class SeqCanvas extends JComponent
 
   AlignViewport av;
 
-  SearchResults searchResults = null;
-
   boolean fastPaint = false;
 
   int LABEL_WEST;
@@ -122,24 +123,26 @@ public class SeqCanvas extends JComponent
   private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     updateViewport();
-    int scalestartx = startx - (startx % 10) + 10;
-
-    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) * charWidth,
-              ypos - (charHeight / 2));
-
-      g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
-              (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
-                      + (charWidth / 2), ypos - 2);
+      if (mark.major)
+      {
+        if (mstring != null)
+        {
+          g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+        }
+        g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
+                - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
+                ypos - 2);
+      }
     }
   }
 
@@ -277,10 +280,11 @@ public class SeqCanvas extends JComponent
     gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
             imgHeight, -horizontal * charWidth, -vertical * charHeight);
 
-    int sr = av.startRes;
-    int er = av.endRes;
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    ViewportRanges ranges = av.getRanges();
+    int sr = ranges.getStartRes();
+    int er = ranges.getEndRes();
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transX = 0;
     int transY = 0;
 
@@ -298,22 +302,22 @@ public class SeqCanvas extends JComponent
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - (vertical * charHeight);
+        transY = imgHeight - ((vertical + 1) * charHeight);
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -335,6 +339,7 @@ public class SeqCanvas extends JComponent
    */
 
   // Set this to false to force a full panel paint
+  @Override
   public void paintComponent(Graphics g)
   {
     updateViewport();
@@ -392,13 +397,15 @@ public class SeqCanvas extends JComponent
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
+    ViewportRanges ranges = av.getRanges();
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
     }
 
     g.drawImage(lcimg, 0, 0, this);
@@ -500,7 +507,7 @@ public class SeqCanvas extends JComponent
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
@@ -682,10 +689,17 @@ public class SeqCanvas extends JComponent
         g1.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
         blockStart = hideEnd + 1;
+
+        if (screenY > (endRes - startRes))
+        {
+          // already rendered last block
+          return;
+        }
       }
 
       if (screenY <= (endRes - startRes))
       {
+        // remaining visible region to render
         blockEnd = blockStart + (endRes - startRes) - screenY;
         g1.translate(screenY * charWidth, 0);
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
@@ -708,7 +722,7 @@ public class SeqCanvas extends JComponent
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
       if (nextSeq == null)
@@ -722,16 +736,17 @@ public class SeqCanvas extends JComponent
 
       if (av.isShowSequenceFeatures())
       {
-        fr.drawSequence(g, nextSeq, startRes, endRes, offset
+        fr.drawSequence(g, nextSeq, startRes,
+                endRes, offset
                 + ((i - startSeq) * charHeight));
       }
 
       // / Highlight search Results once all sequences have been drawn
       // ////////////////////////////////////////////////////////
-      if (searchResults != null)
+      if (av.hasSearchResults())
       {
-        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
-                endRes);
+        int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+                startRes, endRes);
         if (visibleResults != null)
         {
           for (int r = 0; r < visibleResults.length; r += 2)
@@ -792,7 +807,7 @@ public class SeqCanvas extends JComponent
         int top = -1;
         int bottom = -1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * charWidth;
           sy = offset + ((i - startSeq) * charHeight);
@@ -953,11 +968,11 @@ public class SeqCanvas extends JComponent
    * @param results
    *          DOCUMENT ME!
    */
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
     img = null;
 
-    searchResults = results;
+    av.setSearchResults(results);
 
     repaint();
   }