X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=1ed5e50c31b54b2157dc69ff26bd6eb7b9c7c2d7;hpb=32911e66025ea89c66180d501575cda4d8d4521e;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1ed5e50..42424d9 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -24,6 +24,7 @@ import java.awt.*;
 import java.awt.image.*;
 
 import javax.swing.*;
+import jalview.schemes.*;
 
 
 /**
@@ -43,14 +44,10 @@ public class SeqCanvas extends JComponent
     AlignViewport av;
     boolean displaySearch = false;
     int[] searchResults = null;
-    int chunkHeight;
-    int chunkWidth;
     boolean fastPaint = false;
     int LABEL_WEST;
     int LABEL_EAST;
 
-    boolean isOverview = false;
-
     /**
      * Creates a new SeqCanvas object.
      *
@@ -66,6 +63,28 @@ 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!
      *
@@ -260,18 +279,20 @@ public class SeqCanvas extends JComponent
     // Set this to false to force a full panel paint
     public void paintComponent(Graphics g)
     {
+        super.paintComponent(g);
+
         sr.renderGaps(av.renderGaps);
 
-        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();
@@ -284,7 +305,6 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
@@ -294,11 +314,6 @@ public class SeqCanvas extends JComponent
         gg.setColor(Color.white);
         gg.fillRect(0, 0, imgWidth, imgHeight);
 
-        chunkWidth = getWrappedCanvasWidth(getWidth());
-        chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
-        av.setChunkHeight(chunkHeight);
-        av.setChunkWidth(chunkWidth);
 
         if (av.getWrapAlignment())
         {
@@ -311,6 +326,12 @@ public class SeqCanvas extends JComponent
         }
 
         g.drawImage(img, 0, 0, this);
+
+        if (pdbCanvas != null)
+        {
+         pdbCanvas.updateSeqColours();
+        }
+
     }
 
     /**
@@ -385,16 +406,25 @@ public class SeqCanvas extends JComponent
             LABEL_WEST = fm.stringWidth(getMask());
         }
 
+        int hgap = av.charHeight;
+        if(av.scaleAboveWrapped)
+          hgap += av.charHeight;
+
         int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-        int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+        int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+        av.setWrappedWidth(cWidth);
 
         av.endRes = av.startRes + cWidth;
 
+
         int endx = (startRes + cWidth) - 1;
-        int ypos = 2 * av.charHeight;
+        int ypos = hgap;
+
 
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
+            g.setFont(av.getFont());
             g.setColor(Color.black);
 
             if (av.scaleLeftWrapped)
@@ -437,10 +467,23 @@ public class SeqCanvas extends JComponent
 
 
             drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+
+            if(av.showAnnotation)
+            {
+              g.translate(0, cHeight + ypos + 3);
+              if(annotations==null)
+                annotations = new AnnotationPanel(av);
+
+              annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+              g.translate(0, -cHeight - ypos);
+            }
             g.setClip(clip);
             g.translate(-LABEL_WEST, 0);
 
-            ypos += cHeight;
+            ypos += cHeight+getAnnotationHeight()+hgap;
+            if(av.showAnnotation)
+              ypos -= 3;
+
             startRes += cWidth;
             endx = (startRes + cWidth) - 1;
 
@@ -451,6 +494,18 @@ public class SeqCanvas extends JComponent
         }
     }
 
+    AnnotationPanel annotations;
+    int getAnnotationHeight()
+    {
+      if(!av.showAnnotation)
+        return 0;
+
+      if(annotations==null)
+        annotations = new AnnotationPanel(av);
+
+      return annotations.adjustPanelHeight();
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -463,29 +518,103 @@ public class SeqCanvas extends JComponent
      * @param starty DOCUMENT ME!
      * @param offset DOCUMENT ME!
      */
+
+    float aaRatio = 2f/3f;
+    public void increaseAARatio()
+    {
+      aaRatio += .025;
+      if(aaRatio>1)
+        aaRatio = 1;
+
+      repaint();
+    }
+
+    public void decreaseAARation()
+    {
+      aaRatio -= .025;
+      if(aaRatio<0)
+        aaRatio = 0;
+
+      repaint();
+    }
+
+
     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());
+      Graphics2D g = (Graphics2D) g1;
+      g.setFont(av.getFont());
+
+      SequenceI nextSeq, dna = null;
+      int aaHeight = av.charHeight, dnaHeight = av.charHeight;
+      Font dnafont = null, aafont = av.getFont();
+
+ /*     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);
+      }
+*/
 
-        SequenceI nextSeq;
+      ColourSchemeI cs = av.getGlobalColourScheme();
 
         /// First draw the sequences
         /////////////////////////////
         for (int i = y1; i < y2; i++)
         {
             nextSeq = av.alignment.getSequenceAt(i);
+            g.setFont(aafont);
+         /*   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);
+                            x1, x2, (x1 - startx) * av.charWidth,
+                            offset + ( (i - starty) * av.charHeight), av.charWidth,
+                            aaHeight);
+
+         /*   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);
+            }*/
 
             if (av.showSequenceFeatures)
             {
-                fr.drawSequence(g, nextSeq,
-                    av.alignment.findAllGroups(nextSeq), x1, x2,
+                fr.drawSequence(g, nextSeq, x1, x2,
                     (x1 - startx) * av.charWidth,
                     offset + ((i - starty) * av.charHeight), av.charWidth,
                     av.charHeight);
@@ -497,21 +626,19 @@ public class SeqCanvas extends JComponent
         // 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
             {
@@ -647,14 +774,14 @@ public class SeqCanvas extends JComponent
 
                 groupIndex++;
 
-                if (groupIndex >= groups.size())
+                if (groupIndex >= av.alignment.getGroups().size())
                 {
                     break;
                 }
 
-                group = (SequenceGroup) groups.elementAt(groupIndex);
+                group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
             }
-            while (groupIndex < groups.size());
+            while (groupIndex < av.alignment.getGroups().size());
         }
 
         /// Highlight search Results once all sequences have been drawn