Edit and annotate wrapped alignment

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 438d7ad..3202fc4 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -36,7 +36,6 @@ public class SeqCanvas
 \r
   AlignViewport av;\r
 \r
-  boolean showScores = false;\r
   boolean displaySearch = false;\r
   int[] searchResults = null;\r
 \r
@@ -50,7 +49,7 @@ public class SeqCanvas
     this.av = av;\r
     fr = new FeatureRenderer(av);\r
     sr = new SequenceRenderer(av);\r
-    PaintRefresher.Register(this);\r
+    PaintRefresher.Register(this, av.alignment);\r
 \r
   }\r
 \r
@@ -97,7 +96,7 @@ public class SeqCanvas
       }\r
       if (value != -1)\r
       {\r
-        int x = LABEL_WEST - fm.stringWidth(value + "");\r
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
         g.drawString(value + "", x,\r
                      ypos + i * av.charHeight - av.charHeight / 5);\r
       }\r
@@ -126,7 +125,7 @@ public class SeqCanvas
       }\r
       if (value != -1)\r
       {\r
-        g.drawString(value + "", 0,\r
+        g.drawString(value + "", av.charWidth/2,\r
                      ypos + i * av.charHeight - av.charHeight / 5);\r
       }\r
     }\r
@@ -258,24 +257,39 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;\r
   public int getWrappedCanvasWidth(int cwidth)\r
   {\r
-    FontMetrics fm = getFontMetrics(av.getFont());\r
+      FontMetrics fm = getFontMetrics(av.getFont());\r
 \r
-    LABEL_EAST = 0;\r
-    LABEL_WEST = 0;\r
+      LABEL_EAST = 0;\r
+      LABEL_WEST = 0;\r
 \r
-    if (av.scaleRightWrapped)\r
-    {\r
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
-    }\r
+      if (av.scaleRightWrapped)\r
+      {\r
+          LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+      }\r
 \r
-    if (av.scaleLeftWrapped)\r
-    {\r
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
-    }\r
+      if (av.scaleLeftWrapped)\r
+      {\r
+          LABEL_WEST = fm.stringWidth(getMask());\r
+      }\r
 \r
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+      return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
   }\r
 \r
+\r
+  /**\r
+   * Generates a string of zeroes.\r
+   * @return String\r
+   */\r
+  String getMask()\r
+  {\r
+    String mask = "0";\r
+    for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+    {\r
+      mask += "0";\r
+    }\r
+    return mask;\r
+    }\r
+\r
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
                                int startRes)\r
   {\r
@@ -283,15 +297,16 @@ public class SeqCanvas
 \r
     FontMetrics fm = getFontMetrics(av.getFont());\r
 \r
-    int LABEL_EAST = 0;\r
     if (av.scaleRightWrapped)\r
     {\r
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+        LABEL_EAST = fm.stringWidth(getMask()+"0");\r
     }\r
+\r
     int LABEL_WEST = 0;\r
+\r
     if (av.scaleLeftWrapped)\r
     {\r
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+        LABEL_WEST = fm.stringWidth(getMask());\r
     }\r
 \r
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
@@ -313,9 +328,9 @@ public class SeqCanvas
 \r
       if (av.scaleRightWrapped)\r
       {\r
-        g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+        g.translate(canvasWidth - LABEL_EAST, 0);\r
         drawEastScale(g, startRes, endx, ypos);\r
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+        g.translate( - (canvasWidth - LABEL_EAST), 0);\r
       }\r
 \r
       g.translate(LABEL_WEST, 0);\r
@@ -374,7 +389,7 @@ public class SeqCanvas
       sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
                       (x1 - startx) * av.charWidth,\r
                       offset +\r
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+                      (i-starty)*av.charHeight,\r
                       av.charWidth, av.charHeight);\r
 \r
       if (av.showSequenceFeatures)\r
@@ -382,7 +397,7 @@ public class SeqCanvas
         fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
                         (x1 - startx) * av.charWidth,\r
                         offset +\r
-                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+                        (i-starty)*av.charHeight,\r
                         av.charWidth, av.charHeight);\r
       }\r
     }\r
@@ -413,7 +428,7 @@ public class SeqCanvas
         for (i = y1; i < y2; i++)\r
         {\r
           sx = (group.getStartRes() - startx) * av.charWidth;\r
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+          sy = offset + (i-starty)*av.charHeight;\r
           ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;\r
 \r
           if (sx < getSize().width\r
@@ -484,7 +499,7 @@ public class SeqCanvas
             bottom = -1;\r
 \r
           }\r
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+          sy = offset + (i-starty)*av.charHeight;\r
           g.drawLine(sx, oldY, sx, sy);\r
           g.drawLine(sx + ex, oldY, sx + ex, sy);\r
           inGroup = false;\r
@@ -531,9 +546,7 @@ public class SeqCanvas
                                   searchEnd,\r
                                   (searchStart - startx) * av.charWidth,\r
                                   offset +\r
-                                  AlignmentUtil.getPixelHeight(starty,\r
-              searchSeq,\r
-              av.charHeight),\r
+                                  (searchSeq-starty)*av.charHeight,\r
                                   av.charWidth,\r
                                   av.charHeight);\r
         }\r