X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=571b593d29e70577322ac61d19e8c4f1f327a207;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=d5b81f133f9677ccd851641dc71bae7b255f788d;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d5b81f1..571b593 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,23 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.image.*;
-import javax.swing.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.JComponent;
 
 /**
  * DOCUMENT ME!
@@ -69,6 +81,7 @@ public class SeqCanvas extends JComponent
   public SeqCanvas(AlignmentPanel ap)
   {
     this.av = ap.av;
+    updateViewport();
     fr = new FeatureRenderer(ap);
     sr = new SequenceRenderer(av);
     setLayout(new BorderLayout());
@@ -86,6 +99,14 @@ public class SeqCanvas extends JComponent
     return fr;
   }
 
+  int charHeight = 0, charWidth = 0;
+
+  private void updateViewport()
+  {
+    charHeight = av.getCharHeight();
+    charWidth = av.getCharWidth();
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -98,12 +119,12 @@ public class SeqCanvas extends JComponent
    * @param ypos
    *          DOCUMENT ME!
    */
-  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
+    updateViewport();
     int scalestartx = startx - (startx % 10) + 10;
 
     g.setColor(Color.black);
-
     // NORTH SCALE
     for (int i = scalestartx; i < endx; i += 10)
     {
@@ -113,13 +134,12 @@ public class SeqCanvas extends JComponent
         value = av.getColumnSelection().adjustForHiddenColumns(value);
       }
 
-      g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
-              ypos - (av.charHeight / 2));
+      g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
+              ypos - (charHeight / 2));
 
-      g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
-              (ypos + 2) - (av.charHeight / 2),
-              ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
-              ypos - 2);
+      g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
+              (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
+                      + (charWidth / 2), ypos - 2);
     }
   }
 
@@ -138,7 +158,7 @@ public class SeqCanvas extends JComponent
   void drawWestScale(Graphics g, int startx, int endx, int ypos)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
-    ypos += av.charHeight;
+    ypos += charHeight;
 
     if (av.hasHiddenColumns())
     {
@@ -176,9 +196,9 @@ public class SeqCanvas extends JComponent
       if (value != -1)
       {
         int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
-                - av.charWidth / 2;
-        g.drawString(value + "", x, (ypos + (i * av.charHeight))
-                - (av.charHeight / 5));
+                - charWidth / 2;
+        g.drawString(value + "", x, (ypos + (i * charHeight))
+                - (charHeight / 5));
       }
     }
   }
@@ -197,7 +217,7 @@ public class SeqCanvas extends JComponent
    */
   void drawEastScale(Graphics g, int startx, int endx, int ypos)
   {
-    ypos += av.charHeight;
+    ypos += charHeight;
 
     if (av.hasHiddenColumns())
     {
@@ -228,8 +248,8 @@ public class SeqCanvas extends JComponent
 
       if (value != -1)
       {
-        g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
-                - (av.charHeight / 5));
+        g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
+                - (charHeight / 5));
       }
     }
   }
@@ -247,21 +267,15 @@ public class SeqCanvas extends JComponent
    */
   public void fastPaint(int horizontal, int vertical)
   {
-    if (fastpainting)
+    if (fastpainting || gg == null)
     {
       return;
     }
     fastpainting = true;
-    if (gg == null)
-    {
-      return;
-    }
-
     fastPaint = true;
-
-    gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
-            imgWidth, imgHeight, -horizontal * av.charWidth, -vertical
-                    * av.charHeight);
+    updateViewport();
+    gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+            imgHeight, -horizontal * charWidth, -vertical * charHeight);
 
     int sr = av.startRes;
     int er = av.endRes;
@@ -273,7 +287,7 @@ public class SeqCanvas extends JComponent
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
       er++;
-      transX = (er - sr - horizontal) * av.charWidth;
+      transX = (er - sr - horizontal) * charWidth;
       sr = er - horizontal;
     }
     else if (horizontal < 0)
@@ -290,7 +304,7 @@ public class SeqCanvas extends JComponent
       }
       else
       {
-        transY = imgHeight - (vertical * av.charHeight);
+        transY = imgHeight - (vertical * charHeight);
       }
     }
     else if (vertical < 0)
@@ -323,6 +337,7 @@ public class SeqCanvas extends JComponent
   // Set this to false to force a full panel paint
   public void paintComponent(Graphics g)
   {
+    updateViewport();
     BufferedImage lcimg = img; // take reference since other threads may null
     // img and call later.
     super.paintComponent(g);
@@ -341,8 +356,8 @@ public class SeqCanvas extends JComponent
     imgWidth = getWidth();
     imgHeight = getHeight();
 
-    imgWidth -= (imgWidth % av.charWidth);
-    imgHeight -= (imgHeight % av.charHeight);
+    imgWidth -= (imgWidth % charWidth);
+    imgHeight -= (imgHeight % charHeight);
 
     if ((imgWidth < 1) || (imgHeight < 1))
     {
@@ -405,17 +420,17 @@ public class SeqCanvas extends JComponent
     LABEL_EAST = 0;
     LABEL_WEST = 0;
 
-    if (av.scaleRightWrapped)
+    if (av.getScaleRightWrapped())
     {
       LABEL_EAST = fm.stringWidth(getMask());
     }
 
-    if (av.scaleLeftWrapped)
+    if (av.getScaleLeftWrapped())
     {
       LABEL_WEST = fm.stringWidth(getMask());
     }
 
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
   }
 
   /**
@@ -459,28 +474,29 @@ public class SeqCanvas extends JComponent
   public void drawWrappedPanel(Graphics g, int canvasWidth,
           int canvasHeight, int startRes)
   {
+    updateViewport();
     AlignmentI al = av.getAlignment();
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    if (av.scaleRightWrapped)
+    if (av.getScaleRightWrapped())
     {
       LABEL_EAST = fm.stringWidth(getMask());
     }
 
-    if (av.scaleLeftWrapped)
+    if (av.getScaleLeftWrapped())
     {
       LABEL_WEST = fm.stringWidth(getMask());
     }
 
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
+    int hgap = charHeight;
+    if (av.getScaleAboveWrapped())
     {
-      hgap += av.charHeight;
+      hgap += charHeight;
     }
 
-    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+    int cHeight = av.getAlignment().getHeight() * charHeight;
 
     av.setWrappedWidth(cWidth);
 
@@ -507,12 +523,12 @@ public class SeqCanvas extends JComponent
       g.setFont(av.getFont());
       g.setColor(Color.black);
 
-      if (av.scaleLeftWrapped)
+      if (av.getScaleLeftWrapped())
       {
         drawWestScale(g, startRes, endx, ypos);
       }
 
-      if (av.scaleRightWrapped)
+      if (av.getScaleRightWrapped())
       {
         g.translate(canvasWidth - LABEL_EAST, 0);
         drawEastScale(g, startRes, endx, ypos);
@@ -521,12 +537,12 @@ public class SeqCanvas extends JComponent
 
       g.translate(LABEL_WEST, 0);
 
-      if (av.scaleAboveWrapped)
+      if (av.getScaleAboveWrapped())
       {
         drawNorthScale(g, startRes, endx, ypos);
       }
 
-      if (av.hasHiddenColumns() && av.showHiddenMarkers)
+      if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
       {
         g.setColor(Color.blue);
         int res;
@@ -541,12 +557,12 @@ public class SeqCanvas extends JComponent
             continue;
           }
 
-          gg.fillPolygon(new int[]
-          { res * av.charWidth - av.charHeight / 4,
-              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
-                  new int[]
-                  { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
-                      ypos - (av.charHeight / 2) + 8 }, 3);
+          gg.fillPolygon(
+                  new int[] { res * charWidth - charHeight / 4,
+                      res * charWidth + charHeight / 4, res * charWidth },
+                  new int[] { ypos - (charHeight / 2),
+                      ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+                  3);
 
         }
       }
@@ -557,17 +573,17 @@ public class SeqCanvas extends JComponent
 
       if (clip == null)
       {
-        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+        g.setClip(0, 0, cWidth * charWidth, canvasHeight);
       }
       else
       {
-        g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth,
+        g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
                 (int) clip.getBounds().getHeight());
       }
 
       drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         g.translate(0, cHeight + ypos + 3);
         if (annotations == null)
@@ -575,8 +591,8 @@ public class SeqCanvas extends JComponent
           annotations = new AnnotationPanel(av);
         }
 
-        annotations.renderer.drawComponent(annotations, av, (Graphics2D) g,
-                -1, startRes, endx + 1);
+        annotations.renderer.drawComponent(annotations, av, g, -1,
+                startRes, endx + 1);
         g.translate(0, -cHeight - ypos - 3);
       }
       g.setClip(clip);
@@ -592,7 +608,7 @@ public class SeqCanvas extends JComponent
 
   int getAnnotationHeight()
   {
-    if (!av.showAnnotation)
+    if (!av.isShowAnnotation())
     {
       return 0;
     }
@@ -621,24 +637,24 @@ public class SeqCanvas extends JComponent
    * @param offset
    *          DOCUMENT ME!
    */
-  void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
-          int endSeq, int offset)
+  public void drawPanel(Graphics g1, int startRes, int endRes,
+          int startSeq, int endSeq, int offset)
   {
+    updateViewport();
     if (!av.hasHiddenColumns())
     {
       draw(g1, startRes, endRes, startSeq, endSeq, offset);
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+      List<int[]> regions = av.getColumnSelection().getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
       int blockEnd = endRes;
 
-      for (int i = 0; regions != null && i < regions.size(); i++)
+      for (int[] region : regions)
       {
-        int[] region = (int[]) regions.elementAt(i);
         int hideStart = region[0];
         int hideEnd = region[1];
 
@@ -650,7 +666,7 @@ public class SeqCanvas extends JComponent
 
         blockEnd = hideStart - 1;
 
-        g1.translate(screenY * av.charWidth, 0);
+        g1.translate(screenY * charWidth, 0);
 
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
@@ -658,12 +674,12 @@ public class SeqCanvas extends JComponent
         {
           g1.setColor(Color.blue);
 
-          g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
-                  0 + offset, (blockEnd - blockStart + 1) * av.charWidth
-                          - 1, (endSeq - startSeq) * av.charHeight + offset);
+          g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+                  0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+                  (endSeq - startSeq) * charHeight + offset);
         }
 
-        g1.translate(-screenY * av.charWidth, 0);
+        g1.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
         blockStart = hideEnd + 1;
       }
@@ -671,10 +687,10 @@ public class SeqCanvas extends JComponent
       if (screenY <= (endRes - startRes))
       {
         blockEnd = blockStart + (endRes - startRes) - screenY;
-        g1.translate(screenY * av.charWidth, 0);
+        g1.translate(screenY * charWidth, 0);
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-        g1.translate(-screenY * av.charWidth, 0);
+        g1.translate(-screenY * charWidth, 0);
       }
     }
 
@@ -682,11 +698,11 @@ public class SeqCanvas extends JComponent
 
   // 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 g, int startRes, int endRes, int startSeq, int endSeq,
-          int offset)
+  private void draw(Graphics g, int startRes, int endRes, int startSeq,
+          int endSeq, int offset)
   {
     g.setFont(av.getFont());
-    sr.prepare(g, av.renderGaps);
+    sr.prepare(g, av.isRenderGaps());
 
     SequenceI nextSeq;
 
@@ -702,12 +718,12 @@ public class SeqCanvas extends JComponent
         continue;
       }
       sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
-              startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+              startRes, endRes, offset + ((i - startSeq) * charHeight));
 
-      if (av.showSequenceFeatures)
+      if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
-                + ((i - startSeq) * av.charHeight));
+                + ((i - startSeq) * charHeight));
       }
 
       // / Highlight search Results once all sequences have been drawn
@@ -722,8 +738,8 @@ public class SeqCanvas extends JComponent
           {
             sr.drawHighlightedText(nextSeq, visibleResults[r],
                     visibleResults[r + 1], (visibleResults[r] - startRes)
-                            * av.charWidth, offset
-                            + ((i - startSeq) * av.charHeight));
+                            * charWidth, offset
+                            + ((i - startSeq) * charHeight));
           }
         }
       }
@@ -731,9 +747,8 @@ public class SeqCanvas extends JComponent
       if (av.cursorMode && cursorY == i && cursorX >= startRes
               && cursorX <= endRes)
       {
-        sr.drawCursor(nextSeq, cursorX,
-                (cursorX - startRes) * av.charWidth, offset
-                        + ((i - startSeq) * av.charHeight));
+        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+                offset + ((i - startSeq) * charHeight));
       }
     }
 
@@ -759,11 +774,11 @@ public class SeqCanvas extends JComponent
     int sy = -1;
     int ex = -1;
     int groupIndex = -1;
-    int visWidth = (endRes - startRes + 1) * av.charWidth;
+    int visWidth = (endRes - startRes + 1) * charWidth;
 
     if ((group == null) && (av.getAlignment().getGroups().size() > 0))
     {
-      group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+      group = av.getAlignment().getGroups().get(0);
       groupIndex = 0;
     }
 
@@ -779,16 +794,16 @@ public class SeqCanvas extends JComponent
 
         for (i = startSeq; i < endSeq; i++)
         {
-          sx = (group.getStartRes() - startRes) * av.charWidth;
-          sy = offset + ((i - startSeq) * av.charHeight);
-          ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+          sx = (group.getStartRes() - startRes) * charWidth;
+          sy = offset + ((i - startSeq) * charHeight);
+          ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
 
           if (sx + ex < 0 || sx > visWidth)
           {
             continue;
           }
 
-          if ((sx <= (endRes - startRes) * av.charWidth)
+          if ((sx <= (endRes - startRes) * charWidth)
                   && group.getSequences(null).contains(
                           av.getAlignment().getSequenceAt(i)))
           {
@@ -796,7 +811,7 @@ public class SeqCanvas extends JComponent
                     && !group.getSequences(null).contains(
                             av.getAlignment().getSequenceAt(i + 1)))
             {
-              bottom = sy + av.charHeight;
+              bottom = sy + charHeight;
             }
 
             if (!inGroup)
@@ -814,8 +829,8 @@ public class SeqCanvas extends JComponent
               if (group == av.getSelectionGroup())
               {
                 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
-                        BasicStroke.JOIN_ROUND, 3f, new float[]
-                        { 5f, 3f }, 0f));
+                        BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+                        0f));
                 g.setColor(Color.RED);
               }
               else
@@ -850,9 +865,9 @@ public class SeqCanvas extends JComponent
                 ex = visWidth;
               }
 
-              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+              else if (sx + ex >= (endRes - startRes + 1) * charWidth)
               {
-                ex = (endRes - startRes + 1) * av.charWidth;
+                ex = (endRes - startRes + 1) * charWidth;
               }
 
               if (top != -1)
@@ -874,7 +889,7 @@ public class SeqCanvas extends JComponent
 
         if (inGroup)
         {
-          sy = offset + ((i - startSeq) * av.charHeight);
+          sy = offset + ((i - startSeq) * charHeight);
           if (sx >= 0 && sx < visWidth)
           {
             g.drawLine(sx, oldY, sx, sy);
@@ -895,9 +910,9 @@ public class SeqCanvas extends JComponent
           {
             ex = visWidth;
           }
-          else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+          else if (sx + ex >= (endRes - startRes + 1) * charWidth)
           {
-            ex = (endRes - startRes + 1) * av.charWidth;
+            ex = (endRes - startRes + 1) * charWidth;
           }
 
           if (top != -1)
@@ -924,8 +939,7 @@ public class SeqCanvas extends JComponent
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups()
-                .get(groupIndex);
+        group = av.getAlignment().getGroups().get(groupIndex);
 
       } while (groupIndex < av.getAlignment().getGroups().size());