X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=2b5995c7e3b72b74580c9bfda4e3f6aadb3a2985;hb=4263dac5b885f760215fa599eb453e1221767d04;hp=a9f2329ea34bb3bc2e6dcdc38d33182ebc42a2aa;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index a9f2329..2b5995c 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -100,8 +100,11 @@ public class SeqCanvas extends JComponent
         // NORTH SCALE
         for (int i = scalestartx; i < endx; i += 10)
         {
-            String string = String.valueOf(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 +127,9 @@ 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++)
         {
@@ -166,6 +172,9 @@ public class SeqCanvas extends JComponent
     {
         ypos += av.charHeight;
 
+        if(av.hasHiddenColumns)
+                endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
@@ -173,6 +182,8 @@ public class SeqCanvas extends JComponent
             int index = endx;
             int value = -1;
 
+
+
             while (index > startx)
             {
                 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
@@ -203,11 +214,12 @@ public class SeqCanvas extends JComponent
      */
     public void fastPaint(int horizontal, int vertical)
     {
-        if (fastPaint  || gg == null)
+        if (gg == null)
         {
             return;
         }
 
+
         fastPaint = true;
 
         gg.copyArea(horizontal * av.charWidth,
@@ -224,6 +236,7 @@ public class SeqCanvas extends JComponent
         int transX = 0;
         int transY = 0;
 
+
         if (horizontal > 0) // scrollbar pulled right, image to the left
         {
             er ++;
@@ -258,7 +271,7 @@ public class SeqCanvas extends JComponent
         }
 
         gg.translate(transX, transY);
-        drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+        drawPanel(gg, sr, er, ss, es, 0);
         gg.translate(-transX, -transY);
 
         repaint();
@@ -280,7 +293,7 @@ public class SeqCanvas extends JComponent
     {
         super.paintComponent(g);
 
-        sr.renderGaps(av.renderGaps);
+
 
         if ( img != null && (fastPaint
              || (getVisibleRect().width != g.getClipBounds().width)
@@ -322,8 +335,7 @@ public class SeqCanvas extends JComponent
         }
         else
         {
-            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
-                av.startRes, av.startSeq, 0);
+            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
         }
 
         g.drawImage(img, 0, 0, this);
@@ -422,7 +434,6 @@ public class SeqCanvas extends JComponent
         int endx = (startRes + cWidth) - 1;
         int ypos = hgap;
 
-
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
             g.setFont(av.getFont());
@@ -467,7 +478,7 @@ public class SeqCanvas extends JComponent
             }
 
 
-            drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+            drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
             if(av.showAnnotation)
             {
@@ -540,83 +551,96 @@ public class SeqCanvas extends JComponent
     }
 
 
-    void drawPanel(Graphics g1, int x1, int x2, int y1, int y2, int startx, int starty, int offset)
+    void drawPanel(Graphics g1, int startRes, int endRes,
+                    int startSeq, int endSeq, int offset)
     {
-      Graphics2D g = (Graphics2D) g1;
-      g.setFont(av.getFont());
+      if(!av.hasHiddenColumns)
+      {
+        draw(g1, startRes, endRes, startSeq, endSeq, offset);
+      }
+      else
+      {
+        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
 
-      SequenceI nextSeq;
-     // int aaHeight = av.charHeight;
-     // Font  aafont = av.getFont();
+        int screenY = 0;
+        int blockStart = startRes;
+        int blockEnd = endRes;
 
- /*   dnafont = null, , dna = null, dnaHeight = av.charHeight
-   if (av.getShowTranslation())
-      {
-        aaHeight = (int) (av.getCharHeight() * aaRatio);
-        dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));
-        java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();
-        transform.scale(1f / 3f, 1);
-        dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                                dnaHeight);
-        dnafont = dnafont.deriveFont(transform);
-
-        aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                               aaHeight);
-        transform = new java.awt.geom.AffineTransform();
-        transform.scale(1 / aaRatio, 1);
-        aafont = aafont.deriveFont(transform);
+        for (int i = 0; i < regions.size(); i++)
+        {
+          int[] region = (int[]) regions.elementAt(i);
+          int hideStart = region[0];
+          int hideEnd = region[1];
+
+          if (hideStart <= blockStart)
+          {
+            blockStart += (hideEnd - hideStart) + 1;
+            continue;
+          }
+
+          blockEnd = hideStart - 1;
+
+          g1.translate(screenY * av.charWidth, 0);
+
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+          g1.setColor(Color.blue);
+          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
+                      startSeq + offset,
+                      (blockEnd - blockStart + 1) * av.charWidth - 1,
+                      startSeq + (endSeq - startSeq) * av.charHeight + offset);
+          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth,
+                      startSeq + offset,
+                      (blockEnd - blockStart + 1) * av.charWidth,
+                      startSeq + (endSeq - startSeq) * av.charHeight + offset);
+
+          g1.translate( -screenY * av.charWidth, 0);
+          screenY += blockEnd - blockStart + 1;
+          blockStart = hideEnd + 1;
+        }
+
+        if (screenY <= (endRes - startRes))
+        {
+          blockEnd = blockStart + (endRes - startRes) - screenY;
+          g1.translate(screenY * av.charWidth, 0);
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+          g1.translate( -screenY * av.charWidth, 0);
+        }
       }
-*/
 
+    }
+
+
+
+
+    //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,
+                   int startRes, int endRes,
+                   int startSeq, int endSeq,
+                   int offset)
+   {
+
+      sr.renderGaps(av.renderGaps);
+      Graphics2D g = (Graphics2D) g1;
+      g.setFont(av.getFont());
+
+      SequenceI nextSeq;
 
         /// First draw the sequences
         /////////////////////////////
-        for (int i = y1; i < y2; i++)
+        for (int i = startSeq; i < endSeq; i++)
         {
             nextSeq = av.alignment.getSequenceAt(i);
 
-         /*   if(av.getShowTranslation())
-            {
-              dna = nextSeq;
-              StringBuffer sb = new StringBuffer();
-              for(int r = 0; r<nextSeq.getLength(); r+=3)
-              {
-                String codon = nextSeq.getSequence(r, r+3);
-                codon = codon.replace('U', 'T');
-                String res = ResidueProperties.codonTranslate(codon);
-                if(res !=null )
-                {
-                  if (res.equals("STOP"))
-                    sb.append("X");
-                  else
-                    sb.append(res);
-                }
-              }
-              nextSeq = new Sequence("d", sb.toString());
-            }*/
-
             sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
-                            x1, x2, (x1 - startx) * av.charWidth,
-                            offset + ( (i - starty) * av.charHeight), av.charWidth,
-                            av.charHeight);
-
-         /*   if(av.getShowTranslation())
-            {
-              av.setGlobalColourScheme(new NucleotideColourScheme());
-              g.setFont(dnafont);
-              sr.drawSequence(g, dna, null,
-                              x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,
-                              offset + ( (i - starty) * av.charHeight) + aaHeight,
-                              av.charWidth / 3,
-                              dnaHeight);
-              av.setGlobalColourScheme(cs);
-            }*/
+                            startRes, endRes,
+                            offset + ( (i - startSeq) * av.charHeight));
 
             if (av.showSequenceFeatures)
             {
-                fr.drawSequence(g, nextSeq, x1, x2,
-                    (x1 - startx) * av.charWidth,
-                    offset + ((i - starty) * av.charHeight), av.charWidth,
+                fr.drawSequence(g1, nextSeq, startRes, endRes,
+                    offset + ((i - startSeq) * av.charHeight), av.charWidth,
                     av.charHeight);
             }
 
@@ -624,14 +648,14 @@ public class SeqCanvas extends JComponent
             //////////////////////////////////////////////////////////
             if (searchResults != null)
             {
-              int[] visibleResults = searchResults.getResults(nextSeq, x1, x2);
+              int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);
               if (visibleResults != null)
                 for (int r = 0; r < visibleResults.length; r += 2)
                 {
                   sr.drawHighlightedText(nextSeq, visibleResults[r],
                                          visibleResults[r + 1],
-                                         (visibleResults[r] - startx) * av.charWidth,
-                                         offset + ( (i - starty) * av.charHeight),
+                                         (visibleResults[r] - startRes) * av.charWidth,
+                                         offset + ( (i - startSeq) * av.charHeight),
                                          av.charWidth, av.charHeight);
                 }
             }
@@ -664,10 +688,10 @@ public class SeqCanvas extends JComponent
                 int top = -1;
                 int bottom = -1;
 
-                for (i = y1; i < y2; i++)
+                for (i = startSeq; i < endSeq; i++)
                 {
-                    sx = (group.getStartRes() - startx) * av.charWidth;
-                    sy = offset + ((i - starty) * av.charHeight);
+                    sx = (group.getStartRes() - startRes) * av.charWidth;
+                    sy = offset + ((i - startSeq) * av.charHeight);
                     ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
                         1;
 
@@ -676,7 +700,7 @@ public class SeqCanvas extends JComponent
                       continue;
                     }
 
-                    if ( (sx <= (x2-x1)*av.charWidth) &&
+                    if ( (sx <= (endRes-startRes)*av.charWidth) &&
                             group.sequences.contains(av.alignment.getSequenceAt(
                                     i)))
                     {
@@ -733,8 +757,8 @@ public class SeqCanvas extends JComponent
                         if (sx + ex > imgWidth)
                           ex = imgWidth;
 
-                        else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                          ex = (x2 - x1 + 1) * av.charWidth;
+                        else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                          ex = (endRes - startRes + 1) * av.charWidth;
 
                         if (top != -1)
                         {
@@ -755,7 +779,7 @@ public class SeqCanvas extends JComponent
 
                 if (inGroup)
                 {
-                  sy = offset + ( (i - starty) * av.charHeight);
+                  sy = offset + ( (i - startSeq) * av.charHeight);
                   if (sx >= 0 && sx < imgWidth)
                     g.drawLine(sx, oldY, sx, sy);
 
@@ -770,8 +794,8 @@ public class SeqCanvas extends JComponent
 
                   if (sx + ex > imgWidth)
                     ex = imgWidth;
-                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                    ex = (x2 - x1 + 1) * av.charWidth;
+                  else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                    ex = (endRes - startRes + 1) * av.charWidth;
 
                   if (top != -1)
                   {