X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=e55f2a529b458f14e5ede202cc835dbcbeeaf35e;hb=e04bcd38992def511190a30f98cb3db3a720e0fc;hp=510b32fe7ef3f94a46dbbdd9ff7aa4403d85c7de;hpb=e6879a932d0144d64a5ab703ae311aed0eeb83e5;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 510b32f..e55f2a5 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,325 +1,378 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class SequenceRenderer
-{
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-  boolean forOverview = false;
-
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void prepare(Graphics g, boolean renderGaps)
-  {
-      graphics = g;
-      fm = g.getFontMetrics();
-
-      this.renderGaps = renderGaps;
-    }
-
-  public Color getResidueBoxColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-
-    if (inCurrentSequenceGroup(i))
-    {
-      if (currentSequenceGroup.getDisplayBoxes())
-      {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
-      }
-    }
-    else if (av.getShowBoxes())
-    {
-        getBoxColour(av.globalColourScheme, seq, i);
-    }
-
-    return resBoxColour;
-    }
-
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
-    {
-      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
-    }
-    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
-    {
-        resBoxColour = Color.lightGray;
-    }
-    else
-    {
-      resBoxColour = Color.white;
-    }
-
-  }
-
-  public Color findSequenceColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i,i, 0);
-    return resBoxColour;
-  }
-
-  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end,  int y1)
-  {
-    allGroups = sg;
-
-    drawBoxes(seq, start, end,  y1);
-
-    if(av.validCharWidth)
-    {
-      drawText(seq, start, end, y1);
-    }
-  }
-
-  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
-  {
-    int i = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = av.charWidth;
-
-    Color tempColour = null;
-    while (i <= end)
-    {
-      resBoxColour = Color.white;
-      if(i < length)
-      {
-        if (inCurrentSequenceGroup(i))
-        {
-          if (currentSequenceGroup.getDisplayBoxes())
-          {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-          }
-        }
-        else if (av.getShowBoxes())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-        }
-      }
-
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                            av.charHeight);
-        }
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = av.charWidth;
-        tempColour = resBoxColour;
-
-      }
-      else
-      {
-        curWidth += av.charWidth;
-      }
-
-      i++;
-    }
-
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
-  }
-
-  public void drawText(SequenceI seq, int start, int end, int y1)
-  {
-   Font boldFont = null;
-   boolean bold = false;
-   if(av.upperCasebold)
-   {
-     boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
-
-     graphics.setFont(av.getFont());
-   }
-
-    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
-
-    int charOffset = 0;
-
-    // Need to find the sequence position here.
-    if(end+1>=seq.getLength())
-          end = seq.getLength()-1;
-
-    char s = ' ';
-
-    for (int i = start; i <= end; i++)
-    {
-      graphics.setColor(Color.black);
-
-      s = seq.getCharAt(i);
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
-      {
-        continue;
-      }
-
-      if (inCurrentSequenceGroup(i))
-      {
-        if (!currentSequenceGroup.getDisplayText())
-        {
-          continue;
-        }
-
-        if (currentSequenceGroup.getColourText())
-        {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
-          graphics.setColor(resBoxColour.darker());
-        }
-      }
-      else
-      {
-        if (!av.getShowText())
-        {
-          continue;
-        }
-
-        if (av.getColourText())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-          if (av.getShowBoxes())
-          {
-            graphics.setColor(resBoxColour.darker());
-          }
-          else
-          {
-            graphics.setColor(resBoxColour);
-          }
-        }
-      }
-
-      if (av.upperCasebold)
-      {
-        fm = graphics.getFontMetrics();
-        if ('A' <= s && s <= 'Z')
-        {
-          if(!bold)
-          {
-
-            graphics.setFont(boldFont);
-          }
-          bold = true;
-        }
-        else if(bold)
-        {
-          graphics.setFont(av.font);
-          bold = false;
-        }
-
-      }
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                         charOffset + av.charWidth * (i - start),
-                        y1 );
-    }
-
-  }
-
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
-    }
-
-    for (int i = 0; i < allGroups.length; i++)
-    {
-      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
-      {
-        currentSequenceGroup = allGroups[i];
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
-    graphics.setColor(Color.white);
-
-    char s = '~';
-    // Need to find the sequence position here.
-    if(av.validCharWidth)
-    {
-      for (int i = start; i <= end; i++)
-      {
-        if (i < seq.getLength())
-        {
-          s = seq.getSequence().charAt(i);
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + x1 + av.charWidth * (i - start),
-                            y1 + av.charHeight - pady);
-      }
-    }
-  }
-
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-    graphics.setColor(Color.white);
-
-    graphics.setColor(Color.white);
-
-    char s = seq.getCharAt(res);
-    if (av.validCharWidth)
-    {
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1,
-                          (y1 + av.charHeight) - pady);
-    }
-    }
-
-}
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueColourFinder;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+
+public class SequenceRenderer implements jalview.api.SequenceRenderer
+{
+  final static int CHAR_TO_UPPER = 'A' - 'a';
+
+  AlignViewport av;
+
+  FontMetrics fm;
+
+  boolean renderGaps = true;
+
+  SequenceGroup[] allGroups = null;
+
+  Color resBoxColour;
+
+  Graphics graphics;
+
+  ResidueColourFinder resColourFinder;
+
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+    resColourFinder = new ResidueColourFinder();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
+  {
+    graphics = g;
+    fm = g.getFontMetrics();
+
+    this.renderGaps = renderGaps;
+  }
+
+  /**
+   * 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 finder
+   * @return
+   */
+  @Override
+  public Color getResidueColour(final SequenceI seq, int position,
+          FeatureColourFinder finder)
+  {
+    // TODO replace 8 or so code duplications with calls to this method
+    // (refactored as needed)
+    return resColourFinder.getResidueColour(av.getShowBoxes(),
+            av.getResidueShading(),
+            allGroups, seq, position, finder);
+  }
+
+  public Color findSequenceColour(SequenceI seq, int i)
+  {
+    allGroups = av.getAlignment().findAllGroups(seq);
+    drawBoxes(seq, i, i, 0);
+    return resBoxColour;
+  }
+
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
+          int end, int y1)
+  {
+    if (seq == null)
+    {
+      return;
+    }
+
+    allGroups = sg;
+
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
+    {
+      drawText(seq, start, end, y1);
+    }
+  }
+
+  public void drawBoxes(SequenceI seq, int start, int end, int y1)
+  {
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(),
+            avCharHeight = av.getCharHeight();
+
+    Color resBoxColour = Color.white;
+    Color tempColour = null;
+    while (i <= end)
+    {
+      resBoxColour = Color.white;
+      if (i < length)
+      {
+        SequenceGroup currentSequenceGroup = resColourFinder
+                .getCurrentSequenceGroup(allGroups, i);
+        if (currentSequenceGroup != null)
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            resBoxColour = resColourFinder.getBoxColour(
+                    currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          resBoxColour = resColourFinder
+                  .getBoxColour(av.getResidueShading(), seq, i);
+        }
+      }
+
+      if (resBoxColour != tempColour)
+      {
+        if (tempColour != null)
+        {
+          graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+                  avCharHeight);
+        }
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = avCharWidth;
+        tempColour = resBoxColour;
+
+      }
+      else
+      {
+        curWidth += avCharWidth;
+      }
+
+      i++;
+    }
+
+    graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+            avCharHeight);
+  }
+
+  public void drawText(SequenceI seq, int start, int end, int y1)
+  {
+    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+    Font boldFont = null;
+    boolean bold = false;
+    if (av.isUpperCasebold())
+    {
+      boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
+
+      graphics.setFont(av.getFont());
+    }
+
+    y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
+
+    int charOffset = 0;
+
+    // Need to find the sequence position here.
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+
+    char s = ' ';
+    boolean srep = av.isDisplayReferenceSeq();
+    for (int i = start; i <= end; i++)
+    {
+      graphics.setColor(Color.black);
+
+      s = seq.getCharAt(i);
+      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      {
+        continue;
+      }
+
+      SequenceGroup currentSequenceGroup = resColourFinder
+              .getCurrentSequenceGroup(allGroups, i);
+      if (currentSequenceGroup != null)
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
+
+        if (currentSequenceGroup.getColourText())
+        {
+          resBoxColour = resColourFinder.getBoxColour(
+                  currentSequenceGroup.getGroupColourScheme(), seq, i);
+          graphics.setColor(resBoxColour.darker());
+        }
+        if (currentSequenceGroup.getShowNonconserved())
+        {
+          s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+        }
+      }
+      else
+      {
+        if (!av.getShowText())
+        {
+          continue;
+        }
+
+        if (av.getColourText())
+        {
+          resBoxColour = resColourFinder
+                  .getBoxColour(av.getResidueShading(), seq, i);
+          if (av.getShowBoxes())
+          {
+            graphics.setColor(resBoxColour.darker());
+          }
+          else
+          {
+            graphics.setColor(resBoxColour);
+          }
+        }
+        if (av.getShowUnconserved())
+        {
+          s = getDisplayChar(srep, i, s, '.', null);
+
+        }
+      }
+
+      if (av.isUpperCasebold())
+      {
+        fm = graphics.getFontMetrics();
+        if ('A' <= s && s <= 'Z')
+        {
+          if (!bold)
+          {
+
+            graphics.setFont(boldFont);
+          }
+          bold = true;
+        }
+        else if (bold)
+        {
+          graphics.setFont(av.font);
+          bold = false;
+        }
+
+      }
+
+      charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+              charOffset + avCharWidth * (i - start), y1);
+    }
+
+  }
+
+  /**
+   * 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)
+  {
+    // 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))
+    {
+      sequenceChar = conservedChar;
+    }
+    return sequenceChar;
+  }
+
+  public void drawHighlightedText(SequenceI seq, int start, int end,
+          int x1, int y1)
+  {
+    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+    int pady = avCharHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, avCharWidth * (end - start + 1),
+            avCharHeight);
+    graphics.setColor(Color.white);
+
+    char s = '~';
+    // Need to find the sequence position here.
+    if (av.validCharWidth)
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
+
+        charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                charOffset + x1 + avCharWidth * (i - start),
+                y1 + avCharHeight - pady);
+      }
+    }
+  }
+
+  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  {
+    int pady = av.getCharHeight() / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+    graphics.setColor(Color.white);
+
+    graphics.setColor(Color.white);
+
+    char s = seq.getCharAt(res);
+    if (av.validCharWidth)
+    {
+
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.getCharHeight()) - pady);
+    }
+  }
+
+}