Less args, faster rendering

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index a9f2329..f542b17 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -100,7 +100,7 @@ public class SeqCanvas extends JComponent
         // NORTH SCALE\r
         for (int i = scalestartx; i < endx; i += 10)\r
         {\r
-            String string = String.valueOf(i);\r
+            String string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));\r
             g.drawString(string, (i - startx - 1) * av.charWidth,\r
                 ypos - (av.charHeight / 2));\r
 \r
@@ -203,7 +203,7 @@ public class SeqCanvas extends JComponent
      */\r
     public void fastPaint(int horizontal, int vertical)\r
     {\r
-        if (fastPaint  || gg == null)\r
+        if (gg == null)\r
         {\r
             return;\r
         }\r
@@ -258,7 +258,7 @@ public class SeqCanvas extends JComponent
         }\r
 \r
         gg.translate(transX, transY);\r
-        drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
+        drawPanel(gg, sr, er, ss, es, 0);\r
         gg.translate(-transX, -transY);\r
 \r
         repaint();\r
@@ -322,8 +322,7 @@ public class SeqCanvas extends JComponent
         }\r
         else\r
         {\r
-            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,\r
-                av.startRes, av.startSeq, 0);\r
+            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
         }\r
 \r
         g.drawImage(img, 0, 0, this);\r
@@ -467,7 +466,7 @@ public class SeqCanvas extends JComponent
             }\r
 \r
 \r
-            drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+            drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
 \r
             if(av.showAnnotation)\r
             {\r
@@ -540,83 +539,94 @@ public class SeqCanvas extends JComponent
     }\r
 \r
 \r
-    void drawPanel(Graphics g1, int x1, int x2, int y1, int y2, int startx, int starty, int offset)\r
+    void drawPanel(Graphics g1, int startRes, int endRes,\r
+                    int startSeq, int endSeq, int offset)\r
     {\r
-      Graphics2D g = (Graphics2D) g1;\r
-      g.setFont(av.getFont());\r
+      if(!av.hasHiddenColumns)\r
+      {\r
+        draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
+      }\r
+      else\r
+      {\r
+        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();\r
 \r
-      SequenceI nextSeq;\r
-     // int aaHeight = av.charHeight;\r
-     // Font  aafont = av.getFont();\r
+        int screenY = 0;\r
+        int blockStart = startRes;\r
+        int blockEnd = endRes;\r
 \r
- /*   dnafont = null, , dna = null, dnaHeight = av.charHeight\r
-   if (av.getShowTranslation())\r
-      {\r
-        aaHeight = (int) (av.getCharHeight() * aaRatio);\r
-        dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));\r
-        java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
-        transform.scale(1f / 3f, 1);\r
-        dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
-                                dnaHeight);\r
-        dnafont = dnafont.deriveFont(transform);\r
-\r
-        aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
-                               aaHeight);\r
-        transform = new java.awt.geom.AffineTransform();\r
-        transform.scale(1 / aaRatio, 1);\r
-        aafont = aafont.deriveFont(transform);\r
+        for (int i = 0; i < regions.size(); i++)\r
+        {\r
+          int[] region = (int[]) regions.elementAt(i);\r
+          int hideStart = region[0];\r
+          int hideEnd = region[1];\r
+\r
+          if (hideStart <= blockStart)\r
+          {\r
+            blockStart += (hideEnd - hideStart) + 1;\r
+            continue;\r
+          }\r
+\r
+          blockEnd = hideStart - 1;\r
+\r
+          g1.translate(screenY * av.charWidth, 0);\r
+\r
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+          g1.setColor(Color.blue);\r
+          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+                      startSeq + offset,\r
+                      (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+                      startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth,\r
+                      startSeq + offset,\r
+                      (blockEnd - blockStart + 1) * av.charWidth,\r
+                      startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+\r
+          g1.translate( -screenY * av.charWidth, 0);\r
+          screenY += blockEnd - blockStart + 1;\r
+          blockStart = hideEnd + 1;\r
+        }\r
+\r
+        if (screenY < (endRes - startRes))\r
+        {\r
+          blockEnd = blockStart + (endRes - startRes) - screenY;\r
+          g1.translate(screenY * av.charWidth, 0);\r
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+          g1.translate( -screenY * av.charWidth, 0);\r
+        }\r
       }\r
-*/\r
 \r
+    }\r
+\r
+\r
+\r
+\r
+    //int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
+    // int x1, int x2, int y1, int y2, int startx, int starty,\r
+    void draw(Graphics g1,\r
+                   int startRes, int endRes,\r
+                   int startSeq, int endSeq,\r
+                   int offset)\r
+   {\r
+      Graphics2D g = (Graphics2D) g1;\r
+      g.setFont(av.getFont());\r
+\r
+      SequenceI nextSeq;\r
 \r
         /// First draw the sequences\r
         /////////////////////////////\r
-        for (int i = y1; i < y2; i++)\r
+        for (int i = startSeq; i < endSeq; i++)\r
         {\r
             nextSeq = av.alignment.getSequenceAt(i);\r
 \r
-         /*   if(av.getShowTranslation())\r
-            {\r
-              dna = nextSeq;\r
-              StringBuffer sb = new StringBuffer();\r
-              for(int r = 0; r<nextSeq.getLength(); r+=3)\r
-              {\r
-                String codon = nextSeq.getSequence(r, r+3);\r
-                codon = codon.replace('U', 'T');\r
-                String res = ResidueProperties.codonTranslate(codon);\r
-                if(res !=null )\r
-                {\r
-                  if (res.equals("STOP"))\r
-                    sb.append("X");\r
-                  else\r
-                    sb.append(res);\r
-                }\r
-              }\r
-              nextSeq = new Sequence("d", sb.toString());\r
-            }*/\r
-\r
             sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
-                            x1, x2, (x1 - startx) * av.charWidth,\r
-                            offset + ( (i - starty) * av.charHeight), av.charWidth,\r
-                            av.charHeight);\r
-\r
-         /*   if(av.getShowTranslation())\r
-            {\r
-              av.setGlobalColourScheme(new NucleotideColourScheme());\r
-              g.setFont(dnafont);\r
-              sr.drawSequence(g, dna, null,\r
-                              x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,\r
-                              offset + ( (i - starty) * av.charHeight) + aaHeight,\r
-                              av.charWidth / 3,\r
-                              dnaHeight);\r
-              av.setGlobalColourScheme(cs);\r
-            }*/\r
+                            startRes, endRes,\r
+                            offset + ( (i - startSeq) * av.charHeight));\r
 \r
             if (av.showSequenceFeatures)\r
             {\r
-                fr.drawSequence(g, nextSeq, x1, x2,\r
-                    (x1 - startx) * av.charWidth,\r
-                    offset + ((i - starty) * av.charHeight), av.charWidth,\r
+                fr.drawSequence(g1, nextSeq, startRes, endRes,\r
+                    offset + ((i - startSeq) * av.charHeight), av.charWidth,\r
                     av.charHeight);\r
             }\r
 \r
@@ -624,14 +634,14 @@ public class SeqCanvas extends JComponent
             //////////////////////////////////////////////////////////\r
             if (searchResults != null)\r
             {\r
-              int[] visibleResults = searchResults.getResults(nextSeq, x1, x2);\r
+              int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);\r
               if (visibleResults != null)\r
                 for (int r = 0; r < visibleResults.length; r += 2)\r
                 {\r
                   sr.drawHighlightedText(nextSeq, visibleResults[r],\r
                                          visibleResults[r + 1],\r
-                                         (visibleResults[r] - startx) * av.charWidth,\r
-                                         offset + ( (i - starty) * av.charHeight),\r
+                                         (visibleResults[r] - startRes) * av.charWidth,\r
+                                         offset + ( (i - startSeq) * av.charHeight),\r
                                          av.charWidth, av.charHeight);\r
                 }\r
             }\r
@@ -664,10 +674,10 @@ public class SeqCanvas extends JComponent
                 int top = -1;\r
                 int bottom = -1;\r
 \r
-                for (i = y1; i < y2; i++)\r
+                for (i = startSeq; i < endSeq; i++)\r
                 {\r
-                    sx = (group.getStartRes() - startx) * av.charWidth;\r
-                    sy = offset + ((i - starty) * av.charHeight);\r
+                    sx = (group.getStartRes() - startRes) * av.charWidth;\r
+                    sy = offset + ((i - startSeq) * av.charHeight);\r
                     ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
                         1;\r
 \r
@@ -676,7 +686,7 @@ public class SeqCanvas extends JComponent
                       continue;\r
                     }\r
 \r
-                    if ( (sx <= (x2-x1)*av.charWidth) &&\r
+                    if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
                             group.sequences.contains(av.alignment.getSequenceAt(\r
                                     i)))\r
                     {\r
@@ -733,8 +743,8 @@ public class SeqCanvas extends JComponent
                         if (sx + ex > imgWidth)\r
                           ex = imgWidth;\r
 \r
-                        else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
-                          ex = (x2 - x1 + 1) * av.charWidth;\r
+                        else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+                          ex = (endRes - startRes + 1) * av.charWidth;\r
 \r
                         if (top != -1)\r
                         {\r
@@ -755,7 +765,7 @@ public class SeqCanvas extends JComponent
 \r
                 if (inGroup)\r
                 {\r
-                  sy = offset + ( (i - starty) * av.charHeight);\r
+                  sy = offset + ( (i - startSeq) * av.charHeight);\r
                   if (sx >= 0 && sx < imgWidth)\r
                     g.drawLine(sx, oldY, sx, sy);\r
 \r
@@ -770,8 +780,8 @@ public class SeqCanvas extends JComponent
 \r
                   if (sx + ex > imgWidth)\r
                     ex = imgWidth;\r
-                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
-                    ex = (x2 - x1 + 1) * av.charWidth;\r
+                  else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+                    ex = (endRes - startRes + 1) * av.charWidth;\r
 \r
                   if (top != -1)\r
                   {\r

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 0c41152..0e4312a 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -40,6 +40,7 @@ public class SequenceRenderer
     Color resBoxColour;\r
     Graphics graphics;\r
     boolean monospacedFont;\r
+    boolean forOverview = false;\r
 \r
     /**\r
      * Creates a new SequenceRenderer object.\r
@@ -95,9 +96,13 @@ public class SequenceRenderer
         {\r
             resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
         }\r
+        else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
+        {\r
+            resBoxColour = Color.lightGray;\r
+        }\r
         else\r
         {\r
-            resBoxColour = Color.white;\r
+          resBoxColour = Color.white;\r
         }\r
     }\r
 \r
@@ -115,19 +120,19 @@ public class SequenceRenderer
      * @param height DOCUMENT ME!\r
      */\r
     public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
-        int start, int end, int x1, int y1, int width, int height)\r
+        int start, int end, int y1)\r
     {\r
         allGroups = sg;\r
 \r
         graphics = g;\r
 \r
-        drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
+        drawBoxes(seq, start, end, y1);\r
 \r
         fm = g.getFontMetrics();\r
 \r
         monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();\r
 \r
-        drawText(seq, start, end, x1, y1, (int) width, height);\r
+        drawText(seq, start, end, y1);\r
     }\r
 \r
     /**\r
@@ -141,14 +146,13 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!\r
      * @param height DOCUMENT ME!\r
      */\r
-    public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
-        int width, int height)\r
+    public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)\r
     {\r
       int i = start;\r
       int length = seq.getLength();\r
 \r
       int curStart = -1;\r
-      int curWidth = width;\r
+      int curWidth = av.charWidth;\r
 \r
       Color tempColour = null;\r
 \r
@@ -176,26 +180,26 @@ public class SequenceRenderer
           {\r
               if (tempColour != null)\r
               {\r
-                  graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
-                      curWidth, height);\r
+                  graphics.fillRect( av.charWidth * (curStart - start), y1,\r
+                      curWidth, av.charHeight);\r
               }\r
 \r
               graphics.setColor(resBoxColour);\r
 \r
               curStart = i;\r
-              curWidth = width;\r
+              curWidth = av.charWidth;\r
               tempColour = resBoxColour;\r
           }\r
           else\r
           {\r
-              curWidth += width;\r
+              curWidth += av.charWidth;\r
           }\r
 \r
           i++;\r
       }\r
 \r
-      graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
-          height);\r
+      graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,\r
+          av.charHeight);\r
 \r
     }\r
 \r
@@ -210,10 +214,9 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!\r
      * @param height DOCUMENT ME!\r
      */\r
-    public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
-                         int width, int height)\r
+    public void drawText(SequenceI seq, int start, int end, int y1)\r
     {\r
-      y1 += height - height / 5; // height/5 replaces pady\r
+      y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady\r
       int charOffset = 0;\r
       char s;\r
 \r
@@ -224,7 +227,7 @@ public class SequenceRenderer
 \r
         if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())\r
         {\r
-          graphics.drawString(seq.getSequence(start, end + 1), x1, y1);\r
+          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);\r
         }\r
         else\r
         {\r
@@ -272,12 +275,15 @@ public class SequenceRenderer
               }\r
             }\r
 \r
-            charOffset = (width - fm.charWidth(s)) / 2;\r
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+\r
+          //  System.out.print(s);\r
             graphics.drawString(String.valueOf(s),\r
-                                charOffset + x1 + width * (i - start),\r
+                                charOffset + av.charWidth * (i - start),\r
                                 y1);\r
 \r
           }\r
+        //  System.out.println("\n");\r
         }\r
     }\r
 \r