X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=3003c0151c7695466acff015c121a4df9b10ac49;hb=refs%2Fheads%2Ffeatures%2FJAL-2094_colourInterface;hp=9ca3d83f6fdc61dfe69b92cd02e339c513d22307;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 9ca3d83..3003c01 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,40 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.api.ColorI;
+import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 
-/**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
- */
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
+  final static int CHAR_TO_UPPER = 'A' - 'a';
+
   AlignViewport av;
 
   FontMetrics fm;
@@ -78,13 +79,16 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     // If EPS graphics, stringWidth will be a double, not an int
     double dwidth = fm.getStringBounds("M", g).getWidth();
 
-    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
+            .getCharWidth() == dwidth);
 
     this.renderGaps = renderGaps;
   }
 
-  public Color getResidueBoxColour(SequenceI seq, int i)
+  @Override
+  public ColorI getResidueBoxColour(SequenceI seq, int i)
   {
+    // rate limiting step when rendering overview for lots of groups
     allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))
@@ -99,7 +103,32 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
-    return resBoxColour;
+    return new Colour(resBoxColour);
+  }
+
+  /**
+   * Get the residue colour at the given sequence position - as determined by
+   * the sequence group colour (if any), else the colour scheme, possibly
+   * overridden by a feature colour.
+   * 
+   * @param seq
+   * @param position
+   * @param fr
+   * @return
+   */
+  @Override
+  public ColorI getResidueColour(final SequenceI seq, int position,
+          FeatureRenderer fr)
+  {
+    // TODO replace 8 or so code duplications with calls to this method
+    // (refactored as needed)
+    ColorI col = getResidueBoxColour(seq, position);
+
+    if (fr != null)
+    {
+      col = fr.findFeatureColour(col, seq, position);
+    }
+    return col;
   }
 
   /**
@@ -186,12 +215,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           int y1)
   {
     if (seq == null)
+    {
       return; // fix for racecondition
+    }
     int i = start;
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = av.charWidth;
+    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
+            .getCharHeight();
 
     Color tempColour = null;
 
@@ -219,26 +251,25 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       {
         if (tempColour != null)
         {
-          graphics.fillRect(av.charWidth * (curStart - start), y1,
-                  curWidth, av.charHeight);
+          graphics.fillRect(avWidth * (curStart - start), y1, curWidth,
+                  avHeight);
         }
 
         graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = av.charWidth;
+        curWidth = avWidth;
         tempColour = resBoxColour;
       }
       else
       {
-        curWidth += av.charWidth;
+        curWidth += avWidth;
       }
 
       i++;
     }
 
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-            av.charHeight);
+    graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
 
   }
 
@@ -262,7 +293,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    */
   public void drawText(SequenceI seq, int start, int end, int y1)
   {
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
     int charOffset = 0;
     char s;
 
@@ -270,12 +301,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     {
       end = seq.getLength() - 1;
     }
-    graphics.setColor(av.textColour);
+    graphics.setColor(ColorUtils.getColor(av.getTextColour()));
 
-    if (monospacedFont && av.showText && allGroups.length == 0
-            && !av.getColourText() && av.thresholdTextColour == 0)
+    if (monospacedFont && av.getShowText() && allGroups.length == 0
+            && !av.getColourText() && av.getThresholdTextColour() == 0)
     {
-      if (av.renderGaps)
+      if (av.isRenderGaps())
       {
         graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
       }
@@ -288,12 +319,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else
     {
+      boolean srep = av.isDisplayReferenceSeq();
       boolean getboxColour = false;
+      boolean isarep = av.getAlignment().getSeqrep() == seq;
+      boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup
+              .getSeqrep() == seq : false;
+      char sr_c;
       for (int i = start; i <= end; i++)
       {
-        graphics.setColor(av.textColour);
+
+        graphics.setColor(ColorUtils.getColor(av.getTextColour()));
         getboxColour = false;
         s = seq.getCharAt(i);
+
         if (!renderGaps && jalview.util.Comparison.isGap(s))
         {
           continue;
@@ -322,19 +360,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
               if (resBoxColour.getRed() + resBoxColour.getBlue()
                       + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
               {
-                graphics.setColor(currentSequenceGroup.textColour2);
+                graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour2));
               }
             }
           }
           else
           {
-            graphics.setColor(currentSequenceGroup.textColour);
+            graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour));
           }
-          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+          if (!isarep && !isgrep
+                  && currentSequenceGroup.getShowNonconserved()) // todo
+                                                                 // optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
-                    '.');
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
 
           }
 
@@ -361,7 +400,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             }
           }
 
-          if (av.thresholdTextColour > 0)
+          if (av.getThresholdTextColour() > 0)
           {
             if (!getboxColour)
             {
@@ -369,38 +408,64 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
-                    + resBoxColour.getGreen() < av.thresholdTextColour)
+                    + resBoxColour.getGreen() < av.getThresholdTextColour())
             {
-              graphics.setColor(av.textColour2);
+              graphics.setColor(ColorUtils.getColor(av.getTextColour2()));
             }
           }
-          if (av.getShowUnconserved())
+          if (!isarep && av.getShowUnconserved())
           {
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
-                    '.');
+            s = getDisplayChar(srep, i, s, '.', null);
 
           }
 
         }
 
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s), charOffset + av.charWidth
-                * (i - start), y1);
+        charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                charOffset + av.getCharWidth() * (i - start), y1);
 
       }
     }
   }
 
-  private char getDisplayChar(AlignmentAnnotation consensus, int position,
-          char s, char c)
+  /**
+   * Returns 'conservedChar' to represent the given position if the sequence
+   * character at that position is equal to the consensus (ignoring case), else
+   * returns the sequence character
+   * 
+   * @param usesrep
+   * @param position
+   * @param sequenceChar
+   * @param conservedChar
+   * @return
+   */
+  private char getDisplayChar(final boolean usesrep, int position,
+          char sequenceChar, char conservedChar, SequenceGroup currentGroup)
   {
-    char conschar = consensus.annotations[position].displayCharacter
-            .charAt(0);
-    if (conschar != '-' && s == conschar)
+    // TODO - use currentSequenceGroup rather than alignment
+    // currentSequenceGroup.getConsensus()
+    char conschar = (usesrep) ? (currentGroup == null
+            || position < currentGroup.getStartRes()
+            || position > currentGroup.getEndRes() ? av.getAlignment()
+            .getSeqrep().getCharAt(position)
+            : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+                    .getCharAt(position) : av.getAlignment().getSeqrep()
+                    .getCharAt(position)))
+            : (currentGroup != null && currentGroup.getConsensus() != null
+                    && position >= currentGroup.getStartRes()
+                    && position <= currentGroup.getEndRes() && currentGroup
+                    .getConsensus().annotations.length > position) ? currentGroup
+                    .getConsensus().annotations[position].displayCharacter
+                    .charAt(0)
+                    : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                            .charAt(0);
+    if (!jalview.util.Comparison.isGap(conschar)
+            && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
     {
-      s = c;
+      sequenceChar = conservedChar;
     }
-    return s;
+    return sequenceChar;
   }
 
   /**
@@ -453,17 +518,17 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public void drawHighlightedText(SequenceI seq, int start, int end,
           int x1, int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
-            av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1),
+            av.getCharHeight());
     graphics.setColor(Color.white);
 
     char s = '~';
 
     // Need to find the sequence position here.
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       for (int i = start; i <= end; i++)
       {
@@ -472,29 +537,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           s = seq.getCharAt(i);
         }
 
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s), charOffset + x1
-                + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
+        charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (av.getCharWidth() * (i - start)),
+                (y1 + av.getCharHeight()) - pady);
       }
     }
   }
 
   public void drawCursor(SequenceI seq, int res, int x1, int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       graphics.setColor(Color.white);
 
       char s = seq.getCharAt(res);
 
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s), charOffset + x1,
-              (y1 + av.charHeight) - pady);
+              (y1 + av.getCharHeight()) - pady);
     }
 
   }