JAL-4259 construct a new SequenceRenderer when rendering an MSA to an exporter

diff --git a/src/jalview/api/SequenceRenderer.java b/src/jalview/api/SequenceRenderer.java
index 54f7fb6..d5d07ef 100644 (file)
--- a/src/jalview/api/SequenceRenderer.java
+++ b/src/jalview/api/SequenceRenderer.java
@@ -20,10 +20,12 @@
  */
 package jalview.api;
 
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
+import java.awt.Graphics;
 
 public interface SequenceRenderer
 {
@@ -31,4 +33,19 @@ public interface SequenceRenderer
   Color getResidueColour(SequenceI seq, int position,
           FeatureColourFinder finder);
 
+  /**
+   * Configure the Graphics canvas and render options for the renderer
+   * @param g - the canvas to render to
+   * @param renderGaps - when true, gap characters will be included when rendered
+   *          
+   */
+  void prepare(Graphics g, boolean renderGaps);
+
+  void drawSequence(SequenceI nextSeq, SequenceGroup[] findAllGroups,
+          int startRes, int endRes, int i);
+
+  void drawHighlightedText(SequenceI nextSeq, int i, int j, int k, int l);
+
+  void drawCursor(Graphics g, char s, int i, int j);
+
 }

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 3b79f12..735046e 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -644,7 +644,9 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       if (av.cursorMode && cursorY == i && cursorX >= startRes
               && cursorX <= endRes)
       {
-        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
+        char s = nextSeq.getCharAt(cursorX);
+
+        sr.drawCursor(g,s, (cursorX - startRes) * avcharWidth,
                 offset + ((i - startSeq) * avcharHeight));
       }
     }

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index eab6e39..34ad217 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -353,7 +353,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
   }
 
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  public void drawCursor(Graphics graphics, char s, int x1, int y1)
   {
     int pady = av.getCharHeight() / 5;
     int charOffset = 0;
@@ -363,7 +363,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
     graphics.setColor(Color.white);
 
-    char s = seq.getCharAt(res);
     if (av.validCharWidth)
     {
 

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 39039eb..537af58 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -35,6 +35,7 @@ import java.util.List;
 
 import javax.swing.JPanel;
 
+import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
@@ -107,7 +108,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
   {
     this.av = ap.av;
     fr = new FeatureRenderer(ap);
-    seqRdr = new SequenceRenderer(av);
+    seqRdr = new jalview.gui.SequenceRenderer(av);
     setLayout(new BorderLayout());
     PaintRefresher.Register(this, av.getSequenceSetId());
     setBackground(Color.white);
@@ -355,7 +356,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       /** @j2sNative xxi = this.img */
 
       gg.translate(transX, transY);
-      drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
+      drawPanel(seqRdr, gg, startRes, endRes, startSeq, endSeq, 0);
       gg.translate(-transX, -transY);
       gg.dispose();
 
@@ -455,11 +456,11 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
 
       if (av.getWrapAlignment())
       {
-        drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+        drawWrappedPanel(seqRdr, gg, getWidth(), getHeight(), ranges.getStartRes());
       }
       else
       {
-        drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
+        drawPanel(seqRdr,gg, startRes, endRes, startSeq, endSeq, 0);
       }
 
       drawSelectionGroup(gg, startRes, endRes, startSeq, endSeq);
@@ -491,7 +492,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
   public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
           int startSeq, int endSeq)
   {
-    drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+    SequenceRenderer localSeqR = new jalview.gui.SequenceRenderer(av);
+    drawPanel(localSeqR,g1, startRes, endRes, startSeq, endSeq, 0);
 
     drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq);
   }
@@ -511,7 +513,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
   public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
           int canvasHeight, int startRes)
   {
-    drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+    SequenceRenderer localSeqR = new jalview.gui.SequenceRenderer(av);
+    drawWrappedPanel(localSeqR, g, canvasWidth, canvasHeight, startRes);
 
     SequenceGroup group = av.getSelectionGroup();
     if (group != null)
@@ -608,7 +611,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    * @param startColumn
    *          the first column (0...) of the alignment to draw
    */
-  public void drawWrappedPanel(Graphics g, int canvasWidth,
+  public void drawWrappedPanel(SequenceRenderer seqRdr, Graphics g, int canvasWidth,
           int canvasHeight, final int startColumn)
   {
     int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth,
@@ -637,7 +640,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     {
       int endColumn = Math.min(maxWidth,
               start + wrappedWidthInResidues - 1);
-      drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
+      drawWrappedWidth(seqRdr, g, ypos, start, endColumn, canvasHeight);
       ypos += wrappedRepeatHeightPx;
       start += wrappedWidthInResidues;
       currentWidth++;
@@ -730,7 +733,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    * @param endColumn
    * @param canvasHeight
    */
-  protected void drawWrappedWidth(Graphics g, final int ypos,
+  protected void drawWrappedWidth(SequenceRenderer seqRdr, Graphics g, final int ypos,
           final int startColumn, final int endColumn,
           final int canvasHeight)
   {
@@ -759,7 +762,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
             wrappedRepeatHeightPx);
 
-    drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
+    drawPanel(seqRdr, g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
             ypos);
 
     int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
@@ -963,6 +966,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    * are hidden column markers in the visible region, then each sub-region
    * between the markers is drawn separately, followed by the hidden column
    * marker.
+   * @param localSeqR - sequence renderer implementation - when null, uses the one used for rendering interactive GUI
    * 
    * @param g1
    *          the graphics context, positioned at the first residue to be drawn
@@ -977,15 +981,19 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    * @param yOffset
    *          vertical offset at which to draw (for wrapped alignments)
    */
-  public void drawPanel(Graphics g1, final int startRes, final int endRes,
+  public void drawPanel(SequenceRenderer localSeqR, Graphics g1, final int startRes, final int endRes,
           final int startSeq, final int endSeq, final int yOffset)
   {
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
 
+    if (localSeqR==null)
+    {
+      localSeqR = seqRdr;
+    }
     if (!av.hasHiddenColumns())
     {
-      draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
+      draw(localSeqR, g1, startRes, endRes, startSeq, endSeq, yOffset);
     }
     else
     {
@@ -1009,7 +1017,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
          */
         g1.translate(screenY * charWidth, 0);
 
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
+        draw(localSeqR, g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
 
         /*
          * draw the downline of the hidden column marker (ScalePanel draws the
@@ -1034,6 +1042,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
 
   /**
    * Draws a region of the visible alignment
+   * @param seqRdr 
    * 
    * @param g1
    * @param startRes
@@ -1047,7 +1056,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    * @param yOffset
    *          vertical offset at which to draw (for wrapped alignments)
    */
-  private void draw(Graphics g, int startRes, int endRes, int startSeq,
+  private void draw(SequenceRenderer seqRdr, Graphics g, int startRes, int endRes, int startSeq,
           int endSeq, int offset)
   {
     int charHeight = av.getCharHeight();
@@ -1667,7 +1676,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
       Graphics gg = img.getGraphics();
       gg.translate(transX, transY);
-      drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
+      drawPanel(seqRdr, gg, firstCol, lastCol, firstSeq, lastSeq, 0);
       gg.translate(-transX, -transY);
       gg.dispose();
     }
@@ -1819,7 +1828,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       if (scrollX < 0)
       {
         int startRes = ranges.getStartRes();
-        drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes,
+        drawWrappedWidth(seqRdr,gg, wrappedSpaceAboveAlignment, startRes,
                 startRes - scrollX - 1, getHeight());
       }
       else
@@ -1893,7 +1902,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
               wrappedRepeatHeightPx);
       gg.translate(-xOffset, 0);
 
-      drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
+      drawWrappedWidth(seqRdr, gg, ypos, startRes, endRes, canvasHeight);
 
     }
 
@@ -1926,7 +1935,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
 
     if (startRes < ranges.getVisibleAlignmentWidth())
     {
-      drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
+      drawWrappedWidth(seqRdr, gg, ypos, startRes, endRes, canvasHeight);
     }
 
     /*
@@ -2147,7 +2156,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
               {
                 matchFound = true;
                 gg.translate(transX, transY);
-                drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
+                drawPanel(seqRdr,gg, displayColumn, displayColumn, seqNo, seqNo,
                         yOffset);
                 gg.translate(-transX, -transY);
               }

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 43fef15..fedcc37 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -70,6 +70,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * @param b
    *          DOCUMENT ME!
    */
+  @Override
   public void prepare(Graphics g, boolean renderGaps)
   {
     graphics = g;