X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=5313b413969ca7815e62e5d3e70d3953f52b5e84;hb=52298f6987c5807b9f672e33f416dee9e14e1952;hp=58a4af155c9926991dd989e459e6de139a347e8d;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 58a4af1..5313b41 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,27 +1,38 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.beans.PropertyChangeEvent;
+import java.util.List;
 
-public class IdCanvas extends Panel
+public class IdCanvas extends Panel implements ViewportListenerI
 {
   protected AlignViewport av;
 
@@ -39,17 +50,18 @@ public class IdCanvas extends Panel
 
   boolean fastPaint = false;
 
-  java.util.Vector searchResults;
+  List<SequenceI> searchResults;
 
   public IdCanvas(AlignViewport av)
   {
     setLayout(null);
     this.av = av;
     PaintRefresher.Register(this, av.getSequenceSetId());
+    av.getRanges().addPropertyChangeListener(this);
   }
 
-  public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
-          int ypos)
+  public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+          int i, int starty, int ypos)
   {
     int charHeight = av.getCharHeight();
 
@@ -80,7 +92,7 @@ public class IdCanvas extends Panel
             ((i - starty) * charHeight) + ypos + charHeight
                     - (charHeight / 5));
 
-    if (av.hasHiddenRows && av.showHiddenMarkers)
+    if (hiddenRows)
     {
       drawMarker(i, starty, ypos);
     }
@@ -95,28 +107,32 @@ public class IdCanvas extends Panel
       return;
     }
 
-    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical
-            * av.charHeight);
+    ViewportRanges ranges = av.getRanges();
+
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+            -vertical * av.getCharHeight());
 
-    int ss = av.startSeq, es = av.endSeq, transY = 0;
+    int ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transY = 0;
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+                                     // at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - vertical * av.charHeight;
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -130,11 +146,13 @@ public class IdCanvas extends Panel
     repaint();
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     if (getSize().height < 0 || getSize().width < 0)
@@ -149,7 +167,7 @@ public class IdCanvas extends Panel
     }
 
     imgHeight = getSize().height;
-    imgHeight -= imgHeight % av.charHeight;
+    imgHeight -= imgHeight % av.getCharHeight();
 
     if (imgHeight < 1)
     {
@@ -170,71 +188,83 @@ public class IdCanvas extends Panel
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.startSeq, av.endSeq);
+    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
     g.drawImage(image, 0, 0, this);
   }
 
+  /**
+   * local copy of av.getCharHeight set at top of drawIds
+   */
+  private int avcharHeight;
+
   void drawIds(int starty, int endy)
   {
+    // hardwired italic IDs in applet currently
     Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
             .getFont().getSize());
+    // temp variable for speed
+    avcharHeight = av.getCharHeight();
 
     gg.setFont(italic);
 
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
+    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+            && av.getShowHiddenMarkers();
+
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.alignment.getWidth();
-      int alheight = av.alignment.getHeight();
+      int maxwidth = av.getAlignment().getWidth();
+      int alheight = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
       }
 
       int annotationHeight = 0;
       AnnotationLabels labels = null;
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         AnnotationPanel ap = new AnnotationPanel(av);
         annotationHeight = ap.adjustPanelHeight();
         labels = new AnnotationLabels(av);
       }
-
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = avcharHeight;
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += avcharHeight;
       }
 
-      int cHeight = alheight * av.charHeight + hgap + annotationHeight;
-
-      int rowSize = av.getEndRes() - av.getStartRes();
+      int cHeight = alheight * avcharHeight + hgap + annotationHeight;
 
+      int rowSize = av.getRanges().getEndRes()
+              - av.getRanges().getStartRes();
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+      for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getSize().height)
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
         {
 
-          SequenceI s = av.alignment.getSequenceAt(i);
+          SequenceI s = av.getAlignment().getSequenceAt(i);
           gg.setFont(italic);
-          if (av.hasHiddenRows)
+          if (doHiddenCheck)
           {
             setHiddenFont(s);
           }
-          drawIdString(gg, s, i, 0, ypos);
+          drawIdString(gg, hiddenRows, s, i, 0, ypos);
         }
 
         if (labels != null)
         {
-          gg.translate(0, ypos + (alheight * av.charHeight));
+          gg.translate(0, ypos + (alheight * avcharHeight));
           labels.drawComponent(gg, getSize().width);
-          gg.translate(0, -ypos - (alheight * av.charHeight));
+          gg.translate(0, -ypos - (alheight * avcharHeight));
         }
 
       }
@@ -243,17 +273,17 @@ public class IdCanvas extends Panel
     {
       // Now draw the id strings
       SequenceI seq;
-      for (int i = starty; i < endy; i++)
+      for (int i = starty; i <= endy; i++)
       {
 
-        seq = av.alignment.getSequenceAt(i);
+        seq = av.getAlignment().getSequenceAt(i);
         if (seq == null)
         {
           continue;
         }
         gg.setFont(italic);
         // boolean isrep=false;
-        if (av.hasHiddenRows)
+        if (doHiddenCheck)
         {
           // isrep =
           setHiddenFont(seq);
@@ -280,15 +310,15 @@ public class IdCanvas extends Panel
         gg.setColor(currentColor);
         // TODO: isrep could be used to highlight the representative in a
         // different way
-        gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
-                av.charHeight);
+        gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+                avcharHeight);
         gg.setColor(currentTextColor);
 
         gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
-                (((i - starty) * av.charHeight) + av.charHeight)
-                        - (av.charHeight / 5));
+                (((i - starty) * avcharHeight) + avcharHeight)
+                        - (avcharHeight / 5));
 
-        if (av.hasHiddenRows && av.showHiddenMarkers)
+        if (hiddenRows)
         {
           drawMarker(i, starty, 0);
         }
@@ -296,15 +326,15 @@ public class IdCanvas extends Panel
     }
   }
 
-  public void setHighlighted(java.util.Vector found)
+  public void setHighlighted(List<SequenceI> list)
   {
-    searchResults = found;
+    searchResults = list;
     repaint();
   }
 
   void drawMarker(int i, int starty, int yoffset)
   {
-    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
     // Use this method here instead of calling hiddenSeq adjust
     // 3 times.
     int hSize = hseqs.length;
@@ -338,21 +368,19 @@ public class IdCanvas extends Panel
     gg.setColor(Color.blue);
     if (below)
     {
-      gg.fillPolygon(new int[]
-      { getSize().width - av.charHeight, getSize().width - av.charHeight,
-          getSize().width }, new int[]
-      { (i - starty) * av.charHeight + yoffset,
-          (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
-          (i - starty) * av.charHeight + yoffset }, 3);
+      gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+          getSize().width - avcharHeight, getSize().width }, new int[] {
+          (i - starty) * avcharHeight + yoffset,
+          (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+          (i - starty) * avcharHeight + yoffset }, 3);
     }
     if (above)
     {
-      gg.fillPolygon(new int[]
-      { getSize().width - av.charHeight, getSize().width - av.charHeight,
-          getSize().width }, new int[]
-      { (i - starty + 1) * av.charHeight + yoffset,
-          (i - starty + 1) * av.charHeight + yoffset - av.charHeight / 4,
-          (i - starty + 1) * av.charHeight + yoffset }, 3);
+      gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+          getSize().width - avcharHeight, getSize().width }, new int[] {
+          (i - starty + 1) * avcharHeight + yoffset,
+          (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+          (i - starty + 1) * avcharHeight + yoffset }, 3);
 
     }
   }
@@ -362,12 +390,26 @@ public class IdCanvas extends Panel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.hiddenRepSequences != null
-            && av.hiddenRepSequences.containsKey(seq))
+    if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
       return true;
     }
     return false;
   }
+
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport range changes (e.g. alignment panel was scrolled)
+    // Both scrolling and resizing change viewport ranges: scrolling changes
+    // both start and end points, but resize only changes end values.
+    // Here we only want to fastpaint on a scroll, with resize using a normal
+    // paint, so scroll events are identified as changes to the horizontal or
+    // vertical start value.
+    if (evt.getPropertyName().equals(ViewportRanges.STARTSEQ))
+    {
+      fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+  }
 }