X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=99447a4b1aabbafd3c6fcb04635474a9b774b3b7;hb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;hp=42c52d3c4e7404977607db821d3539b677b95214;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 42c52d3..99447a4 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -34,20 +34,22 @@ import javax.swing.*;
  */
 public class SeqCanvas extends JComponent
 {
-    FeatureRenderer fr;
-    SequenceRenderer sr;
+    final FeatureRenderer fr;
+    final SequenceRenderer sr;
     BufferedImage img;
     Graphics2D gg;
     int imgWidth;
     int imgHeight;
     AlignViewport av;
-    boolean displaySearch = false;
-    int[] searchResults = null;
+    SearchResults searchResults = null;
     boolean fastPaint = false;
     int LABEL_WEST;
     int LABEL_EAST;
 
-    boolean isOverview = false;
+
+    int cursorX = 0;
+    int cursorY = 0;
+
 
     /**
      * Creates a new SeqCanvas object.
@@ -64,6 +66,28 @@ public class SeqCanvas extends JComponent
         setBackground(Color.white);
     }
 
+    MCview.PDBCanvas pdbCanvas;
+    public SequenceRenderer getSequenceRenderer()
+    {
+      return sr;
+    }
+
+    public FeatureRenderer getFeatureRenderer()
+    {
+      return fr;
+    }
+
+    public void setPDBCanvas(MCview.PDBCanvas pc)
+    {
+      pdbCanvas = pc;
+    }
+
+    public AlignViewport getViewport()
+    {
+      return av;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -81,8 +105,11 @@ 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),
@@ -105,6 +132,9 @@ 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++)
         {
@@ -147,6 +177,9 @@ 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++)
         {
@@ -154,6 +187,8 @@ public class SeqCanvas extends JComponent
             int index = endx;
             int value = -1;
 
+
+
             while (index > startx)
             {
                 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
@@ -170,7 +205,7 @@ public class SeqCanvas extends JComponent
 
             if (value != -1)
             {
-                g.drawString(String.valueOf(value), av.charWidth/2,
+                g.drawString(String.valueOf(value), 0,
                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
             }
         }
@@ -189,6 +224,9 @@ public class SeqCanvas extends JComponent
             return;
         }
 
+
+        fastPaint = true;
+
         gg.copyArea(horizontal * av.charWidth,
                     vertical * av.charHeight,
                     imgWidth,
@@ -203,6 +241,7 @@ public class SeqCanvas extends JComponent
         int transX = 0;
         int transY = 0;
 
+
         if (horizontal > 0) // scrollbar pulled right, image to the left
         {
             er ++;
@@ -237,10 +276,9 @@ 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);
 
-        fastPaint = true;
         repaint();
     }
 
@@ -258,18 +296,20 @@ public class SeqCanvas extends JComponent
     // Set this to false to force a full panel paint
     public void paintComponent(Graphics g)
     {
-        sr.renderGaps(av.renderGaps);
+        super.paintComponent(g);
 
-        if ((img != null) &&
-                (fastPaint || (getWidth() != g.getClipBounds().width) ||
-                (getHeight() != g.getClipBounds().height)))
+
+
+        if ( img != null && (fastPaint
+             || (getVisibleRect().width != g.getClipBounds().width)
+             || (getVisibleRect().height != g.getClipBounds().height)))
         {
             g.drawImage(img, 0, 0, this);
             fastPaint = false;
-
             return;
         }
 
+
         // this draws the whole of the alignment
         imgWidth = getWidth();
         imgHeight = getHeight();
@@ -282,12 +322,13 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
-        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-          RenderingHints.VALUE_ANTIALIAS_ON);
+
+        if (av.antiAlias)
+          gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                              RenderingHints.VALUE_ANTIALIAS_ON);
 
         gg.setColor(Color.white);
         gg.fillRect(0, 0, imgWidth, imgHeight);
@@ -299,11 +340,16 @@ 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);
+
+        if (pdbCanvas != null)
+        {
+           pdbCanvas.updateSeqColours();
+        }
+
     }
 
     /**
@@ -322,7 +368,7 @@ public class SeqCanvas extends JComponent
 
         if (av.scaleRightWrapped)
         {
-            LABEL_EAST = fm.stringWidth(getMask()+"0");
+            LABEL_EAST = fm.stringWidth(getMask());
         }
 
         if (av.scaleLeftWrapped)
@@ -340,7 +386,7 @@ public class SeqCanvas extends JComponent
      */
     String getMask()
     {
-      String mask = "0";
+      String mask = "00";
       for (int i = av.alignment.getWidth(); i > 0; i /= 10)
       {
         mask += "0";
@@ -368,7 +414,7 @@ public class SeqCanvas extends JComponent
 
         if (av.scaleRightWrapped)
         {
-            LABEL_EAST = fm.stringWidth(getMask()+"0");
+            LABEL_EAST = fm.stringWidth(getMask());
         }
 
         int LABEL_WEST = 0;
@@ -390,12 +436,18 @@ public class SeqCanvas extends JComponent
         av.endRes = av.startRes + cWidth;
 
 
-        int endx = (startRes + cWidth) - 1;
+        int endx;
         int ypos = hgap;
 
-
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
+          endx = startRes + cWidth;
+
+          if (endx > al.getWidth())
+          {
+            endx = al.getWidth();
+          }
+
             g.setFont(av.getFont());
             g.setColor(Color.black);
 
@@ -432,13 +484,7 @@ public class SeqCanvas extends JComponent
                     cWidth * av.charWidth, (int) clip.getBounds().getHeight());
             }
 
-            if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
-            {
-              endx = av.vconsensus.size() - 2;
-            }
-
-
-            drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+            drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
             if(av.showAnnotation)
             {
@@ -446,7 +492,7 @@ public class SeqCanvas extends JComponent
               if(annotations==null)
                 annotations = new AnnotationPanel(av);
 
-              annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+              annotations.drawComponent( (Graphics2D) g, startRes, endx);
               g.translate(0, -cHeight - ypos);
             }
             g.setClip(clip);
@@ -457,12 +503,6 @@ public class SeqCanvas extends JComponent
               ypos -= 3;
 
             startRes += cWidth;
-            endx = (startRes + cWidth) - 1;
-
-            if (endx > al.getWidth())
-            {
-                endx = al.getWidth();
-            }
         }
     }
 
@@ -482,123 +522,146 @@ public class SeqCanvas extends JComponent
      * DOCUMENT ME!
      *
      * @param g1 DOCUMENT ME!
-     * @param x1 DOCUMENT ME!
-     * @param x2 DOCUMENT ME!
-     * @param y1 DOCUMENT ME!
-     * @param y2 DOCUMENT ME!
-     * @param startx DOCUMENT ME!
-     * @param starty DOCUMENT ME!
+     * @param startRes DOCUMENT ME!
+     * @param endRes DOCUMENT ME!
+     * @param startSeq DOCUMENT ME!
+     * @param endSeq DOCUMENT ME!
      * @param offset DOCUMENT ME!
      */
-
-    float aaRatio = 2f/3f;
-    public void increaseAARatio()
+    void drawPanel(Graphics g1, int startRes, int endRes,
+                    int startSeq, int endSeq, int offset)
     {
-      aaRatio += .025;
-      if(aaRatio>1)
-        aaRatio = 1;
+      if(!av.hasHiddenColumns)
+      {
+        draw(g1, startRes, endRes, startSeq, endSeq, offset);
+      }
+      else
+      {
+        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
 
-      repaint();
-    }
+        int screenY = 0;
+        int blockStart = startRes;
+        int blockEnd = endRes;
 
-    public void decreaseAARation()
-    {
-      aaRatio -= .025;
-      if(aaRatio<0)
-        aaRatio = 0;
+        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;
+        }
 
-      repaint();
-    }
+        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);
+        }
+      }
 
-    synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
-        int y2, int startx, int starty, int offset)
-    {
-        Graphics2D g = (Graphics2D) g1;
-        g.setFont(av.getFont());
+    }
 
 
-  SequenceI nextSeq;
 
-  SequenceI dna = null;
 
-  int aaHeight = (int)(av.getCharHeight()*aaRatio);
-  int dnaHeight =(int)(av.getCharHeight() * (1-aaRatio));
+    //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)
+   {
 
 
-  java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();
-  transform.scale(1f/3f , 1);
-  Font dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                              dnaHeight);
-  dnafont = dnafont.deriveFont(transform);
+      Graphics2D g = (Graphics2D) g1;
+      g.setFont(av.getFont());
+      sr.prepare(g, av.renderGaps);
 
-  Font 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);
+      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);
-            g.setFont(aafont);
-/*
-            StringBuffer dnasb = new StringBuffer();
-            for (int j = 0; j < nextSeq.getLength(); j++)
-            {
-              java.util.Vector codons = jalview.schemes.ResidueProperties.getCodons(nextSeq.getSequence(j,
-                  j + 1));
-              if (codons != null && codons.size() > 0)
-                dnasb.append(codons.elementAt(0).toString());
-            }
-
-            dna = new Sequence("dna", dnasb.toString());*/
-
 
-            sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
-                            x1, x2, (x1 - startx) * av.charWidth,
-                            offset + ( (i - starty) * av.charHeight), av.charWidth,
-                            aaHeight);
+            sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                            startRes, endRes,
+                            offset + ( (i - startSeq) * av.charHeight));
 
+            if (av.showSequenceFeatures)
+            {
+                fr.drawSequence(g1, nextSeq, startRes, endRes,
+                    offset + ((i - startSeq) * av.charHeight));
+            }
 
-         /*   g.setFont(dnafont);
-
-            sr.drawSequence(g, dna, null,
-                            x1, x2 * 3 +2, ( (x1 - startx) * av.charWidth) / 3,
-                            offset + ( (i - starty) * av.charHeight) + aaHeight, av.charWidth / 3,
-                            dnaHeight);*/
+            /// Highlight search Results once all sequences have been drawn
+            //////////////////////////////////////////////////////////
+            if (searchResults != null)
+            {
+              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] - startRes) * av.charWidth,
+                                         offset + ( (i - startSeq) * av.charHeight));
+                }
+            }
 
-            if (av.showSequenceFeatures)
+            if(av.cursorMode && cursorY==i
+               && cursorX>=startRes && cursorX<=endRes)
             {
-                fr.drawSequence(g, nextSeq,
-                    av.alignment.findAllGroups(nextSeq), x1, x2,
-                    (x1 - startx) * av.charWidth,
-                    offset + ((i - starty) * av.charHeight), av.charWidth,
-                    av.charHeight);
+              sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                            offset + ( (i - startSeq) * av.charHeight));
             }
-        }
+          }
 
         //
         /////////////////////////////////////
         // Now outline any areas if necessary
         /////////////////////////////////////
         SequenceGroup group = av.getSelectionGroup();
-        java.util.Vector groups = av.alignment.getGroups();
 
         int sx = -1;
         int sy = -1;
         int ex = -1;
         int groupIndex = -1;
 
-        if ((group == null) && (groups.size() > 0))
+        if ((group == null) && (av.alignment.getGroups().size() > 0))
         {
-            group = (SequenceGroup) groups.elementAt(0);
+            group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
             groupIndex = 0;
         }
 
-
-        if (group != null && !isOverview)
+        if (group != null)
         {
             do
             {
@@ -608,10 +671,10 @@ 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;
 
@@ -620,7 +683,7 @@ 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)))
                     {
@@ -677,8 +740,8 @@ 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)
                         {
@@ -699,7 +762,7 @@ 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);
 
@@ -714,8 +777,8 @@ 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)
                   {
@@ -734,49 +797,14 @@ public class SeqCanvas extends JComponent
 
                 groupIndex++;
 
-                if (groupIndex >= groups.size())
+                if (groupIndex >= av.alignment.getGroups().size())
                 {
                     break;
                 }
 
-                group = (SequenceGroup) groups.elementAt(groupIndex);
-            }
-            while (groupIndex < groups.size());
-        }
-
-        /// Highlight search Results once all sequences have been drawn
-        //////////////////////////////////////////////////////////
-        if (displaySearch)
-        {
-            for (int r = 0; r < searchResults.length; r += 3)
-            {
-                int searchSeq = searchResults[r];
-
-                if ((searchSeq >= y1) && (searchSeq < y2))
-                {
-                    SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
-
-                    int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
-                    int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
-
-                    SequenceRenderer ssr = (SequenceRenderer) sr;
-
-                    if (searchStart < x1)
-                    {
-                        searchStart = x1;
-                    }
-
-                    if (searchEnd > x2)
-                    {
-                        searchEnd = x2;
-                    }
-
-                    ssr.drawHighlightedText(seq, searchStart, searchEnd,
-                        (searchStart - startx) * av.charWidth,
-                        offset + ((searchSeq - starty) * av.charHeight),
-                        av.charWidth, av.charHeight);
-                }
+                group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
             }
+            while (groupIndex < av.alignment.getGroups().size());
         }
     }
 
@@ -785,17 +813,9 @@ public class SeqCanvas extends JComponent
      *
      * @param results DOCUMENT ME!
      */
-    public void highlightSearchResults(int[] results)
+    public void highlightSearchResults(SearchResults results)
     {
-        // results are in the order sequence, startRes, endRes
-        if (results == null)
-        {
-            displaySearch = false;
-        }
-        else
-        {
-            displaySearch = true;
-        }
+        img = null;
 
         searchResults = results;