X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=15c15c3d25c0768cd90a6300ae7a09a9a2839703;hb=3bdd4947c87108581abe34d05c878ee110b60f72;hp=f542b17d68effd255169286b4fd82b36e2131255;hpb=3d1120fca6dd9dc2865ee6cde98760f65c2701da;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index f542b17..15c15c3 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -34,8 +34,8 @@ import javax.swing.*;
  */
 public class SeqCanvas extends JComponent
 {
-    FeatureRenderer fr;
-    SequenceRenderer sr;
+    final FeatureRenderer fr;
+    final SequenceRenderer sr;
     BufferedImage img;
     Graphics2D gg;
     int imgWidth;
@@ -46,6 +46,11 @@ public class SeqCanvas extends JComponent
     int LABEL_WEST;
     int LABEL_EAST;
 
+
+    int cursorX = 0;
+    int cursorY = 0;
+
+
     /**
      * Creates a new SeqCanvas object.
      *
@@ -100,8 +105,11 @@ public class SeqCanvas extends JComponent
         // NORTH SCALE
         for (int i = scalestartx; i < endx; i += 10)
         {
-            String string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));
-            g.drawString(string, (i - startx - 1) * av.charWidth,
+            int value = i;
+            if(av.hasHiddenColumns)
+                value = av.getColumnSelection().adjustForHiddenColumns(value);
+
+            g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,
                 ypos - (av.charHeight / 2));
 
             g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
@@ -124,6 +132,9 @@ public class SeqCanvas extends JComponent
         FontMetrics fm = getFontMetrics(av.getFont());
         ypos += av.charHeight;
 
+        if(av.hasHiddenColumns)
+                startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
@@ -166,10 +177,14 @@ public class SeqCanvas extends JComponent
     {
         ypos += av.charHeight;
 
+        if(av.hasHiddenColumns)
+                endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+
+        SequenceI seq;
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-            SequenceI seq = av.alignment.getSequenceAt(i);
+            seq = av.alignment.getSequenceAt(i);
             int index = endx;
             int value = -1;
 
@@ -182,7 +197,7 @@ public class SeqCanvas extends JComponent
                     continue;
                 }
 
-                value = av.alignment.getSequenceAt(i).findPosition(index);
+                value = seq.findPosition(index);
 
                 break;
             }
@@ -208,6 +223,7 @@ public class SeqCanvas extends JComponent
             return;
         }
 
+
         fastPaint = true;
 
         gg.copyArea(horizontal * av.charWidth,
@@ -224,6 +240,7 @@ public class SeqCanvas extends JComponent
         int transX = 0;
         int transY = 0;
 
+
         if (horizontal > 0) // scrollbar pulled right, image to the left
         {
             er ++;
@@ -280,7 +297,7 @@ public class SeqCanvas extends JComponent
     {
         super.paintComponent(g);
 
-        sr.renderGaps(av.renderGaps);
+
 
         if ( img != null && (fastPaint
              || (getVisibleRect().width != g.getClipBounds().width)
@@ -329,7 +346,7 @@ public class SeqCanvas extends JComponent
 
         if (pdbCanvas != null)
         {
-         pdbCanvas.updateSeqColours();
+           pdbCanvas.updateSeqColours();
         }
 
     }
@@ -392,14 +409,12 @@ public class SeqCanvas extends JComponent
 
         FontMetrics fm = getFontMetrics(av.getFont());
 
-        int LABEL_EAST = 0;
 
         if (av.scaleRightWrapped)
         {
             LABEL_EAST = fm.stringWidth(getMask());
         }
 
-        int LABEL_WEST = 0;
 
         if (av.scaleLeftWrapped)
         {
@@ -418,12 +433,18 @@ public class SeqCanvas extends JComponent
         av.endRes = av.startRes + cWidth;
 
 
-        int endx = (startRes + cWidth) - 1;
+        int endx;
         int ypos = hgap;
 
-
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
+          endx = startRes + cWidth -1;
+
+          if (endx > al.getWidth())
+          {
+            endx = al.getWidth();
+          }
+
             g.setFont(av.getFont());
             g.setColor(Color.black);
 
@@ -460,12 +481,6 @@ public class SeqCanvas extends JComponent
                     cWidth * av.charWidth, (int) clip.getBounds().getHeight());
             }
 
-            if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
-            {
-              endx = av.vconsensus.size() - 2;
-            }
-
-
             drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
             if(av.showAnnotation)
@@ -474,7 +489,7 @@ public class SeqCanvas extends JComponent
               if(annotations==null)
                 annotations = new AnnotationPanel(av);
 
-              annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+              annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
               g.translate(0, -cHeight - ypos);
             }
             g.setClip(clip);
@@ -485,12 +500,6 @@ public class SeqCanvas extends JComponent
               ypos -= 3;
 
             startRes += cWidth;
-            endx = (startRes + cWidth) - 1;
-
-            if (endx > al.getWidth())
-            {
-                endx = al.getWidth();
-            }
         }
     }
 
@@ -510,35 +519,12 @@ public class SeqCanvas extends JComponent
      * DOCUMENT ME!
      *
      * @param g1 DOCUMENT ME!
-     * @param x1 DOCUMENT ME!
-     * @param x2 DOCUMENT ME!
-     * @param y1 DOCUMENT ME!
-     * @param y2 DOCUMENT ME!
-     * @param startx DOCUMENT ME!
-     * @param starty DOCUMENT ME!
+     * @param startRes DOCUMENT ME!
+     * @param endRes DOCUMENT ME!
+     * @param startSeq DOCUMENT ME!
+     * @param endSeq DOCUMENT ME!
      * @param offset DOCUMENT ME!
      */
-
-    float aaRatio = 2f/3f;
-    public void increaseAARatio()
-    {
-      aaRatio += .025;
-      if(aaRatio>1)
-        aaRatio = 1;
-
-      repaint();
-    }
-
-    public void decreaseAARation()
-    {
-      aaRatio -= .025;
-      if(aaRatio<0)
-        aaRatio = 0;
-
-      repaint();
-    }
-
-
     void drawPanel(Graphics g1, int startRes, int endRes,
                     int startSeq, int endSeq, int offset)
     {
@@ -587,7 +573,7 @@ public class SeqCanvas extends JComponent
           blockStart = hideEnd + 1;
         }
 
-        if (screenY < (endRes - startRes))
+        if (screenY <= (endRes - startRes))
         {
           blockEnd = blockStart + (endRes - startRes) - screenY;
           g1.translate(screenY * av.charWidth, 0);
@@ -603,13 +589,13 @@ public class SeqCanvas extends JComponent
 
     //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
     // int x1, int x2, int y1, int y2, int startx, int starty,
-    void draw(Graphics g1,
+    void draw(Graphics g,
                    int startRes, int endRes,
                    int startSeq, int endSeq,
                    int offset)
    {
-      Graphics2D g = (Graphics2D) g1;
       g.setFont(av.getFont());
+      sr.prepare(g, av.renderGaps);
 
       SequenceI nextSeq;
 
@@ -619,15 +605,14 @@ public class SeqCanvas extends JComponent
         {
             nextSeq = av.alignment.getSequenceAt(i);
 
-            sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
+            sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
                             startRes, endRes,
                             offset + ( (i - startSeq) * av.charHeight));
 
             if (av.showSequenceFeatures)
             {
-                fr.drawSequence(g1, nextSeq, startRes, endRes,
-                    offset + ((i - startSeq) * av.charHeight), av.charWidth,
-                    av.charHeight);
+                fr.drawSequence(g, nextSeq, startRes, endRes,
+                    offset + ((i - startSeq) * av.charHeight));
             }
 
             /// Highlight search Results once all sequences have been drawn
@@ -641,12 +626,29 @@ public class SeqCanvas extends JComponent
                   sr.drawHighlightedText(nextSeq, visibleResults[r],
                                          visibleResults[r + 1],
                                          (visibleResults[r] - startRes) * av.charWidth,
-                                         offset + ( (i - startSeq) * av.charHeight),
-                                         av.charWidth, av.charHeight);
+                                         offset + ( (i - startSeq) * av.charHeight));
                 }
             }
+
+            if(av.cursorMode && cursorY==i
+               && cursorX>=startRes && cursorX<=endRes)
+            {
+              sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                            offset + ( (i - startSeq) * av.charHeight));
+            }
           }
 
+          if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)
+            drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+
+   }
+
+   void drawGroupsBoundaries(Graphics g1,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+       Graphics2D g = (Graphics2D)g1;
         //
         /////////////////////////////////////
         // Now outline any areas if necessary
@@ -806,9 +808,13 @@ public class SeqCanvas extends JComponent
                 }
 
                 group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+
+                g.setStroke(new BasicStroke());
             }
             while (groupIndex < av.alignment.getGroups().size());
+
         }
+
     }
 
     /**