X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=fd8330977705d18b7b81a13e6639bdb5c23941c2;hb=8878681ec11f85c050248236a96ffbcaf2f0497b;hp=5aa5d663d84574664fbce7267aa40320dee8bebf;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5aa5d66..fd83309 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;
 
@@ -45,6 +43,8 @@ public class SeqCanvas
 
   boolean fastPaint = false;
 
+  boolean isOverview = false;
+
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
@@ -97,7 +97,7 @@ 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 +126,7 @@ public class SeqCanvas
       }
       if (value != -1)
       {
-        g.drawString(value + "", 0,
+        g.drawString(value + "", av.charWidth/2,
                      ypos + i * av.charHeight - av.charHeight / 5);
       }
     }
@@ -135,7 +135,7 @@ public class SeqCanvas
 
   public void fastPaint(int horizontal, int vertical)
   {
-    if (horizontal == 0 && vertical == 0 || gg == null)
+    if (gg == null)
     {
       return;
     }
@@ -205,6 +205,8 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
+    sr.renderGaps(av.renderGaps);
+
     if (fastPaint)
     {
       g.drawImage(img, 0, 0, this);
@@ -243,7 +245,7 @@ public class SeqCanvas
 
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
     }
     else
     {
@@ -258,24 +260,39 @@ 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 +300,16 @@ 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 +331,9 @@ 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 +342,16 @@ 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 +384,7 @@ 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 +392,7 @@ 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);
       }
     }
@@ -402,101 +412,143 @@ public class SeqCanvas
       groupIndex = 0;
     }
 
-    if (group != null)
+    if (group != null && !isOverview)
     {
       do
       {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1, bottom = -1;
-        for (i = y1; i < y2; i++)
-        {
-          sx = (group.getStartRes() - startx) * av.charWidth;
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;
+          int oldY = -1;
+          int i = 0;
+          boolean inGroup = false;
+          int top = -1;
+          int bottom = -1;
 
-          if (sx < getSize().width
-              && ex > 0
-              && group.sequences.contains(av.alignment.getSequenceAt(i)))
+          for (i = y1; i < y2; i++)
           {
-            if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||
-                                 !group.sequences.contains(av.alignment.
-                getSequenceAt(i + 1))))
-            {
-              bottom = sy + av.charHeight;
-            }
+              sx = (group.getStartRes() - startx) * av.charWidth;
+              sy = offset + ((i - starty) * av.charHeight);
+              ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
+                  1;
 
-            if (!inGroup)
-            {
-              if (top == -1 && i == 0 ||
-                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
+              if(sx+ex<0 || sx>imgWidth)
               {
-                top = sy;
+                continue;
               }
 
-              oldY = sy;
-              inGroup = true;
-              if (group == av.getSelectionGroup())
+              if ( (sx <= (x2-x1)*av.charWidth) &&
+                      group.sequences.contains(av.alignment.getSequenceAt(
+                              i)))
               {
-                g.setColor(new Color(255, 0, 0));
+                  if ((bottom == -1) &&
+                          !group.sequences.contains(
+                              av.alignment.getSequenceAt(i + 1)))
+                  {
+                      bottom = sy + av.charHeight;
+                  }
+
+                  if (!inGroup)
+                  {
+                      if (((top == -1) && (i == 0)) ||
+                              !group.sequences.contains(
+                                  av.alignment.getSequenceAt(i - 1)))
+                      {
+                          top = sy;
+                      }
+
+                      oldY = sy;
+                      inGroup = true;
+
+                      if (group == av.getSelectionGroup())
+                      {
+                          g.setColor(Color.red);
+                      }
+                      else
+                      {
+                          g.setColor(group.getOutlineColour());
+                      }
+                  }
               }
               else
               {
-                g.setColor(group.getOutlineColour());
+                if (inGroup)
+                {
+                  if (sx >= 0 && sx < imgWidth)
+                    g.drawLine(sx, oldY, sx, sy);
+
+                  if (sx + ex < imgWidth)
+                    g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+                  if (sx < 0)
+                  {
+                    ex += sx;
+                    sx = 0;
+                  }
+
+                  if (sx + ex > imgWidth)
+                    ex = imgWidth;
+
+                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
+                    ex = (x2 - x1 + 1) * av.charWidth;
+
+                  if (top != -1)
+                  {
+                    g.drawLine(sx, top, sx + ex, top);
+                    top = -1;
+                  }
+
+                  if (bottom != -1)
+                  {
+                    g.drawLine(sx, bottom, sx + ex, bottom);
+                    bottom = -1;
+                  }
+
+                  inGroup = false;
+                  }
               }
-            }
           }
-          else
+
+          if (inGroup)
           {
-            if (inGroup)
-            {
+            sy = offset + ( (i - starty) * av.charHeight);
+            if (sx >= 0 && sx < imgWidth)
               g.drawLine(sx, oldY, sx, sy);
+
+            if (sx + ex < imgWidth)
               g.drawLine(sx + ex, oldY, sx + ex, sy);
 
-              if (top != -1)
-              {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
-              }
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom, sx + ex, bottom);
-                bottom = -1;
-              }
+            if (sx < 0)
+            {
+              ex += sx;
+              sx = 0;
+            }
 
-              inGroup = false;
+            if (sx + ex > imgWidth)
+              ex = imgWidth;
+            else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
+              ex = (x2 - x1 + 1) * av.charWidth;
+
+            if (top != -1)
+            {
+              g.drawLine(sx, top, sx + ex, top);
+              top = -1;
             }
-          }
-        }
 
-        if (inGroup)
-        {
+            if (bottom != -1)
+            {
+              g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+              bottom = -1;
+            }
 
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + ex, top);
-            top = -1;
+              inGroup = false;
           }
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-            bottom = -1;
 
-          }
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          g.drawLine(sx, oldY, sx, sy);
-          g.drawLine(sx + ex, oldY, sx + ex, sy);
-          inGroup = false;
-        }
-        groupIndex++;
-        if (groupIndex >= groups.size())
-        {
-          break;
-        }
+          groupIndex++;
 
-        group = (SequenceGroup) groups.elementAt(groupIndex);
+          if (groupIndex >= groups.size())
+          {
+              break;
+          }
 
+          group = (SequenceGroup) groups.elementAt(groupIndex);
       }
       while (groupIndex < groups.size());
     }
@@ -531,9 +583,7 @@ public class SeqCanvas
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty,
-              searchSeq,
-              av.charHeight),
+                                  (searchSeq-starty)*av.charHeight,
                                   av.charWidth,
                                   av.charHeight);
         }