X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=b8435260aed051b4a94b00080cf96c56da70ead1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=dea44169fd3c2b8856b6b2f1d1325b30163090fb;hpb=3f0f2fc8583156a04aab175b91ac27127374703e;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index dea4416..b843526 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,190 +1,399 @@
-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
-
-public class SequenceRenderer
-{
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-
-  public void renderGaps(boolean b)
-  {
-    renderGaps = b;
-  }
-
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    getBoxColour(cs, 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
-       resBoxColour = Color.white;
-  }
-
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
-  {
-    allGroups = sg;
-
-    graphics = g;
-
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
-
-    fm = g.getFontMetrics();
-    drawText(seq,start,end,x1,y1,(int)width,height);
-
-  }
-
-  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height) {
-    int i      = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = width;
-
-    Color tempColour = null;
-    while (i <= end && i < length)
-    {
-      if(inCurrentSequenceGroup(i))
-      {
-        if( currentSequenceGroup.getDisplayBoxes())
-             getBoxColour(currentSequenceGroup.cs, seq, i);
-        else
-             resBoxColour = Color.white;
-      }
-      else if(av.getShowBoxes())
-            getBoxColour(av.getGlobalColourScheme(), seq, i);
-      else
-        resBoxColour = Color.white;
-
-
-      if (resBoxColour != tempColour)
-      {
-        if(tempColour!=null)
-          graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = width;
-        tempColour = resBoxColour;
-
-      }
-      else
-        curWidth += width;
-
-      i++;
-    }
-
-
-     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-  }
-
-  public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
-  {
-    int pady = height/5;
-    int charOffset=0;
-    char s;
-    // Need to find the sequence position here.
-
-    String sequence  = seq.getSequence();
-    for (int i = start; i <= end; i++)
-    {
-        graphics.setColor(Color.black);
-        if(i<sequence.length())
-          s = sequence.charAt(i);
-        else
-          s = ' ';
-
-        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);
-           }
-        }
-
-          charOffset =  (width - fm.charWidth(s))/2;
-          graphics.drawString(String.valueOf(s),
-                              charOffset + x1 + width * (i - start),
-                              y1 + height - pady);
-        }
-
-
-  }
-
-  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 width, int height)
-  {
-    int pady = height/5;
-    int charOffset=0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1,y1,width*(end-start+1),height);
-    graphics.setColor(Color.white);
-
-    char s='~';
-    // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
-    {
-       if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
-
-     charOffset =  (width - fm.charWidth(s))/2;
-      graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
-    }
-  }
-
-
-}
+/*
+ * 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.
+ *  
+ * 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.api.FeatureRenderer;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+
+public class SequenceRenderer implements jalview.api.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.getAlignment().findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      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;
+  }
+
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+    }
+    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.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 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(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;
+      }
+
+      if (inCurrentSequenceGroup(i))
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
+
+        if (currentSequenceGroup.getColourText())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.setColor(resBoxColour.darker());
+        }
+        if (currentSequenceGroup.getShowNonconserved())
+        {
+          s = getDisplayChar(srep, i, s, '.');
+        }
+      }
+      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.getShowUnconserved())
+        {
+          s = getDisplayChar(srep, i, s, '.');
+
+        }
+      }
+
+      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);
+    }
+
+  }
+
+  private char getDisplayChar(final boolean usesrep, int position, char s,
+          char c)
+  {
+    // TODO - use currentSequenceGroup rather than alignment
+    // currentSequenceGroup.getConsensus()
+    char conschar = (usesrep) ? av.getAlignment().getSeqrep()
+            .getCharAt(position)
+            : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                    .charAt(0);
+    if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
+    {
+      s = c;
+    }
+    return s;
+  }
+
+  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 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);
+    }
+  }
+
+}