X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=8ffad089b1ce96cf2dfdb16a1dec38fef46c8935;hb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;hp=5aa5d663d84574664fbce7267aa40320dee8bebf;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5aa5d66..8ffad08 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -21,7 +21,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 
 public class SeqCanvas
@@ -36,7 +35,6 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean showScores = false;
   boolean displaySearch = false;
   int[] searchResults = null;
 
@@ -97,7 +95,7 @@ public class SeqCanvas
       }
       if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(value + "");
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
         g.drawString(value + "", x,
                      ypos + i * av.charHeight - av.charHeight / 5);
       }
@@ -126,7 +124,7 @@ public class SeqCanvas
       }
       if (value != -1)
       {
-        g.drawString(value + "", 0,
+        g.drawString(value + "", av.charWidth/2,
                      ypos + i * av.charHeight - av.charHeight / 5);
       }
     }
@@ -243,7 +241,7 @@ public class SeqCanvas
 
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
     }
     else
     {
@@ -258,24 +256,39 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
-    FontMetrics fm = getFontMetrics(av.getFont());
+      FontMetrics fm = getFontMetrics(av.getFont());
 
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
+      LABEL_EAST = 0;
+      LABEL_WEST = 0;
 
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
-    }
+      if (av.scaleRightWrapped)
+      {
+          LABEL_EAST = fm.stringWidth(getMask()+"0");
+      }
 
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
-    }
+      if (av.scaleLeftWrapped)
+      {
+          LABEL_WEST = fm.stringWidth(getMask());
+      }
 
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+      return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
+
+  /**
+   * Generates a string of zeroes.
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "0";
+    for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+    {
+      mask += "0";
+    }
+    return mask;
+    }
+
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
   {
@@ -283,15 +296,16 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
     if (av.scaleRightWrapped)
     {
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+        LABEL_EAST = fm.stringWidth(getMask()+"0");
     }
+
     int LABEL_WEST = 0;
+
     if (av.scaleLeftWrapped)
     {
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+        LABEL_WEST = fm.stringWidth(getMask());
     }
 
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
@@ -313,9 +327,9 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);
+        g.translate(canvasWidth - LABEL_EAST, 0);
         drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);
+        g.translate( - (canvasWidth - LABEL_EAST), 0);
       }
 
       g.translate(LABEL_WEST, 0);
@@ -324,24 +338,16 @@ public class SeqCanvas
         drawNorthScale(g, startRes, endx, ypos);
       }
 
-      // When printing we have an extra clipped region,
-      // the Printable page which we need to account for here
-      Shape clip = g.getClip();
-      if (clip == null)
-      {
-        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
-      }
-      else
-      {
-        g.setClip(0,
-                  (int) clip.getBounds().y,
-                  cWidth * av.charWidth,
-                  (int) clip.getBounds().height
-            );
-      }
 
-      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(clip);
+     if(g.getClip()==null)
+       g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+
+     if (av.alignment.getWidth() >= av.vconsensus.size())
+     {
+       endx = av.vconsensus.size() - 2;
+     }
+     drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+      g.setClip(null);
       g.translate( -LABEL_WEST, 0);
 
       ypos += cHeight;
@@ -374,7 +380,7 @@ public class SeqCanvas
       sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
                       (x1 - startx) * av.charWidth,
                       offset +
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                      (i-starty)*av.charHeight,
                       av.charWidth, av.charHeight);
 
       if (av.showSequenceFeatures)
@@ -382,7 +388,7 @@ public class SeqCanvas
         fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
                         (x1 - startx) * av.charWidth,
                         offset +
-                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                        (i-starty)*av.charHeight,
                         av.charWidth, av.charHeight);
       }
     }
@@ -413,7 +419,7 @@ public class SeqCanvas
         for (i = y1; i < y2; i++)
         {
           sx = (group.getStartRes() - startx) * av.charWidth;
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          sy = offset + (i-starty)*av.charHeight;
           ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;
 
           if (sx < getSize().width
@@ -484,7 +490,7 @@ public class SeqCanvas
             bottom = -1;
 
           }
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          sy = offset + (i-starty)*av.charHeight;
           g.drawLine(sx, oldY, sx, sy);
           g.drawLine(sx + ex, oldY, sx + ex, sy);
           inGroup = false;
@@ -531,9 +537,7 @@ public class SeqCanvas
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty,
-              searchSeq,
-              av.charHeight),
+                                  (searchSeq-starty)*av.charHeight,
                                   av.charWidth,
                                   av.charHeight);
         }