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=7a52bcc7b82803a496931cb4e56b3ba70d7cb4dc;hpb=526094d494484bfa89f9659fccf83a37b8c19829;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 7a52bcc..3003c01 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,124 +1,567 @@
-package jalview.gui;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.util.*;
-
-public class SequenceRenderer implements RendererI
-{
-  FontMetrics fm;
-
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {
-
-    Color c  = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);
-    return c;
-
-  }
-
-
-  public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText, boolean colourText,Vector freq, int seqnum) {
-
-
-    if (displayBoxes)
-        drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq);
-
-    if (displayText)
-    {
-        fm = g.getFontMetrics();
-        drawText(g,cs,colourText,seq,start,end,x1,y1,(int)width,height);
-    }
-  }
-
-  public void drawBoxes(Graphics g,ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
-    int i      = start;
-    int length = seq.getLength();
-
-    Color currentColor = Color.WHITE;
-
-    int curStart = x1;
-    int curWidth = width;
-
-  //  int threshold = 80;
-
-    while (i <= end && i < length) {
-      Color c = getResidueBoxColour(cs,seq,i);
-
-    //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);
-    //  String    s     = (String)hash.get("maxResidue");
-    //  int       count = ((Integer)hash.get("maxCount")).intValue();
-  //    int       max   = ((Integer)hash.get("size")).intValue();
-   //   int       nongap = ((Integer)hash.get("nongap")).intValue();
-   //   float     frac  = (float)(count*1.0/(1.0*nongap));
-
-      //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);
-    /*  if (!seq.getSequence().substring(i,i+1).equals(s) ||
-	  s.equals("-") ||
-	  s.equals(".") ||
-	  s.equals(" "))
-      {
-	c = Color.white;
-      } else {
-	if (frac > 0.9) {
-	  c = Color.red;
-	} else if (frac > 0.8) {
-	  c = Color.orange;
-	} else if (frac > 0.7) {
-	  c = Color.pink;
-	} else if (frac > 0.5) {
-	  c = Color.yellow;
-	} else if (frac> 0.3) {
-	    c = Color.lightGray;
-	}
-      }*/
-
-      if (c != currentColor || c != null)
-      {
-        g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-
-        currentColor = c;
-        g.setColor(c);
-
-        curStart = i;
-        curWidth = width;
-      }
-      else
-        curWidth += width;
-
-      i++;
-    }
-    g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-  }
-
-  public void drawText(Graphics g, ColourSchemeI cs, boolean colText, SequenceI seq,int start, int end, int x1, int y1, int width, int height)
-  {
-    int pady = height/5;
-    int charOffset=0;
-    g.setColor(Color.black);
-
-    char s;
-    // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
-    {
-        if (i < end && i < seq.getLength())
-          s = seq.getSequence().charAt(i);
-        else if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
-        else
-          s = ' ';
-
-        if (colText)
-        {
-            Color c = getResidueBoxColour(cs, seq, i);
-            g.setColor(c.darker());
-        }
-
-      charOffset =  (width - fm.charWidth(s))/2;
-
-
-      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - 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.gui;
+
+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;
+
+public class SequenceRenderer implements jalview.api.SequenceRenderer
+{
+  final static int CHAR_TO_UPPER = 'A' - 'a';
+
+  AlignViewport av;
+
+  FontMetrics fm;
+
+  boolean renderGaps = true;
+
+  SequenceGroup currentSequenceGroup = null;
+
+  SequenceGroup[] allGroups = null;
+
+  Color resBoxColour;
+
+  Graphics graphics;
+
+  boolean monospacedFont;
+
+  boolean forOverview = false;
+
+  /**
+   * Creates a new SequenceRenderer object.
+   * 
+   * @param av
+   *          DOCUMENT ME!
+   */
+  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();
+
+    // If EPS graphics, stringWidth will be a double, not an int
+    double dwidth = fm.getStringBounds("M", g).getWidth();
+
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
+            .getCharWidth() == dwidth);
+
+    this.renderGaps = renderGaps;
+  }
+
+  @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))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      getBoxColour(av.getGlobalColourScheme(), seq, i);
+    }
+
+    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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param cs
+   *          DOCUMENT ME!
+   * @param seq
+   *          DOCUMENT ME!
+   * @param i
+   *          DOCUMENT ME!
+   */
+  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;
+    }
+  }
+
+  /**
+   * 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
+   *          DOCUMENT ME!
+   * @param width
+   *          DOCUMENT ME!
+   * @param height
+   *          DOCUMENT ME!
+   */
+  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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   * @param start
+   *          DOCUMENT ME!
+   * @param end
+   *          DOCUMENT ME!
+   * @param x1
+   *          DOCUMENT ME!
+   * @param y1
+   *          DOCUMENT ME!
+   * @param width
+   *          DOCUMENT ME!
+   * @param height
+   *          DOCUMENT ME!
+   */
+  public synchronized void drawBoxes(SequenceI seq, int start, int end,
+          int y1)
+  {
+    if (seq == null)
+    {
+      return; // fix for racecondition
+    }
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = 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(avWidth * (curStart - start), y1, curWidth,
+                  avHeight);
+        }
+
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = avWidth;
+        tempColour = resBoxColour;
+      }
+      else
+      {
+        curWidth += avWidth;
+      }
+
+      i++;
+    }
+
+    graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   * @param start
+   *          DOCUMENT ME!
+   * @param end
+   *          DOCUMENT ME!
+   * @param x1
+   *          DOCUMENT ME!
+   * @param y1
+   *          DOCUMENT ME!
+   * @param width
+   *          DOCUMENT ME!
+   * @param height
+   *          DOCUMENT ME!
+   */
+  public void drawText(SequenceI seq, int start, int end, int y1)
+  {
+    y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
+    int charOffset = 0;
+    char s;
+
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+    graphics.setColor(ColorUtils.getColor(av.getTextColour()));
+
+    if (monospacedFont && av.getShowText() && allGroups.length == 0
+            && !av.getColourText() && av.getThresholdTextColour() == 0)
+    {
+      if (av.isRenderGaps())
+      {
+        graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+      }
+      else
+      {
+        char gap = av.getGapCharacter();
+        graphics.drawString(seq.getSequenceAsString(start, end + 1)
+                .replace(gap, ' '), 0, y1);
+      }
+    }
+    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(ColorUtils.getColor(av.getTextColour()));
+        getboxColour = false;
+        s = seq.getCharAt(i);
+
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
+
+        if (inCurrentSequenceGroup(i))
+        {
+          if (!currentSequenceGroup.getDisplayText())
+          {
+            continue;
+          }
+
+          if (currentSequenceGroup.thresholdTextColour > 0
+                  || currentSequenceGroup.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+
+            if (currentSequenceGroup.getColourText())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+
+            if (currentSequenceGroup.thresholdTextColour > 0)
+            {
+              if (resBoxColour.getRed() + resBoxColour.getBlue()
+                      + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+              {
+                graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour2));
+              }
+            }
+          }
+          else
+          {
+            graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour));
+          }
+          if (!isarep && !isgrep
+                  && currentSequenceGroup.getShowNonconserved()) // todo
+                                                                 // optimize
+          {
+            // todo - use sequence group consensus
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+
+          }
+
+        }
+        else
+        {
+          if (!av.getShowText())
+          {
+            continue;
+          }
+
+          if (av.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
+
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+            else
+            {
+              graphics.setColor(resBoxColour);
+            }
+          }
+
+          if (av.getThresholdTextColour() > 0)
+          {
+            if (!getboxColour)
+            {
+              getBoxColour(av.getGlobalColourScheme(), seq, i);
+            }
+
+            if (resBoxColour.getRed() + resBoxColour.getBlue()
+                    + resBoxColour.getGreen() < av.getThresholdTextColour())
+            {
+              graphics.setColor(ColorUtils.getColor(av.getTextColour2()));
+            }
+          }
+          if (!isarep && av.getShowUnconserved())
+          {
+            s = getDisplayChar(srep, i, s, '.', null);
+
+          }
+
+        }
+
+        charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                charOffset + av.getCharWidth() * (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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param res
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   * @param start
+   *          DOCUMENT ME!
+   * @param end
+   *          DOCUMENT ME!
+   * @param x1
+   *          DOCUMENT ME!
+   * @param y1
+   *          DOCUMENT ME!
+   * @param width
+   *          DOCUMENT ME!
+   * @param height
+   *          DOCUMENT ME!
+   */
+  public void drawHighlightedText(SequenceI seq, int start, int end,
+          int x1, int y1)
+  {
+    int pady = av.getCharHeight() / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.BLACK);
+    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.isValidCharWidth())
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
+
+        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.getCharHeight() / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+
+    if (av.isValidCharWidth())
+    {
+      graphics.setColor(Color.white);
+
+      char s = seq.getCharAt(res);
+
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.getCharHeight()) - pady);
+    }
+
+  }
+}