X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=8c4ead82acfd5011b37a51746463066c85e2e758;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=f2eae2a110e45f590f1f68702e32248082cb8eea;hpb=8f050c10c0bd044493b7537b6c6d119c7c29c986;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index f2eae2a..8c4ead8 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,26 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 java.awt.*;
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
 
 /**
  * DOCUMENT ME!
@@ -30,6 +37,8 @@ import jalview.schemes.*;
  */
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
+  final static int CHAR_TO_UPPER = 'A' - 'a';
+
   AlignViewport av;
 
   FontMetrics fm;
@@ -73,14 +82,16 @@ 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;
   }
 
+  @Override
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    allGroups = av.alignment.findAllGroups(seq);
+    allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))
     {
@@ -91,13 +102,38 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
     }
 
     return 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 Color getResidueColour(final SequenceI seq, int position,
+          FeatureRenderer fr)
+  {
+    // TODO replace 8 or so code duplications with calls to this method
+    // (refactored as needed)
+    Color col = getResidueBoxColour(seq, position);
+
+    if (fr != null)
+    {
+      col = fr.findFeatureColour(col, seq, position);
+    }
+    return col;
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param cs
@@ -111,7 +147,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -125,25 +161,35 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   }
 
   /**
-   * draw coloured sequence to the current graphics cursor
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *          DOCUMENT ME!
    * @param seq
+   *          DOCUMENT ME!
    * @param sg
+   *          DOCUMENT ME!
    * @param start
+   *          DOCUMENT ME!
    * @param end
+   *          DOCUMENT ME!
+   * @param x1
+   *          DOCUMENT ME!
    * @param y1
-   * @param drawBox - draw background
-   * @param drawText - draw text (if shading style permits)
+   *          DOCUMENT ME!
+   * @param width
+   *          DOCUMENT ME!
+   * @param height
+   *          DOCUMENT ME!
    */
   public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
-          int end, int y1, boolean drawBox, boolean drawText)
+          int end, int y1)
   {
     allGroups = sg;
 
-    if (drawBox) {
-      drawBoxes(seq, start, end, y1);
-    }
+    drawBoxes(seq, start, end, y1);
 
-    if (av.validCharWidth && drawText)
+    if (av.validCharWidth)
     {
       drawText(seq, start, end, y1);
     }
@@ -171,12 +217,15 @@ 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;
 
@@ -195,7 +244,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.globalColourScheme, seq, i);
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
 
       }
@@ -204,26 +253,25 @@ 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);
 
   }
 
@@ -247,7 +295,7 @@ 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;
 
@@ -255,12 +303,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     {
       end = seq.getLength() - 1;
     }
-    graphics.setColor(av.textColour);
+    graphics.setColor(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);
       }
@@ -273,12 +321,19 @@ 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(av.getTextColour());
         getboxColour = false;
         s = seq.getCharAt(i);
+
         if (!renderGaps && jalview.util.Comparison.isGap(s))
         {
           continue;
@@ -315,10 +370,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
-          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+          if (!isarep && !isgrep
+                  && currentSequenceGroup.getShowNonconserved()) // todo
+                                                                 // optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.consensus, i, s, '.');
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
 
           }
 
@@ -333,7 +390,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.globalColourScheme, seq, i);
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -345,45 +402,67 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             }
           }
 
-          if (av.thresholdTextColour > 0)
+          if (av.getThresholdTextColour() > 0)
           {
             if (!getboxColour)
             {
-              getBoxColour(av.globalColourScheme, seq, i);
+              getBoxColour(av.getGlobalColourScheme(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
-                    + resBoxColour.getGreen() < av.thresholdTextColour)
+                    + resBoxColour.getGreen() < av.getThresholdTextColour())
             {
-              graphics.setColor(av.textColour2);
+              graphics.setColor(av.getTextColour2());
             }
           }
-          if (av.showUnconserved)
+          if (!isarep && av.getShowUnconserved())
           {
-            s = getDisplayChar(av.consensus, i, s, '.');
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
 
           }
 
         }
 
-        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 ? av.getAlignment()
+            .getSeqrep().getCharAt(position)
+            : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+                    .getCharAt(position) : av.getAlignment().getSeqrep()
+                    .getCharAt(position)))
+            : (currentGroup != null && currentGroup.getConsensus() != null) ? 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;
   }
 
   /**
@@ -436,17 +515,17 @@ 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++)
       {
@@ -455,29 +534,30 @@ 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);
     }
 
   }