X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=691aa7e94ead35414afc54b23583a443da24c8b2;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=e36160a939d13b843aa20a86dbad19a2116a7115;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e36160a..691aa7e 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,338 +1,501 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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.gui;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceRenderer
-{
-    AlignViewport av;
-    FontMetrics fm;
-    boolean renderGaps = true;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
-    Color resBoxColour;
-    Graphics graphics;
-
-    /**
-     * Creates a new SequenceRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public SequenceRenderer(AlignViewport av)
-    {
-        this.av = av;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void renderGaps(boolean b)
-    {
-        renderGaps = b;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-    {
-        getBoxColour(cs, seq, i);
-
-        return resBoxColour;
-    }
-
-    /**
-     * 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.getSequence(i, i + 1), i);
-        }
-        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(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);
-    }
-
-    /**
-     * 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 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);
-    }
-
-    /**
-     * 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 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);
-        }
-    }
-
-    /**
-     * 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 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 2.8.2)
+ * Copyright (C) 2014 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
+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
+{
+  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() && (float) av.charWidth == dwidth);
+
+    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;
+  }
+
+  /**
+   * 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.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);
+
+  }
+
+  /**
+   * 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.charHeight - av.charHeight / 5; // height/5 replaces pady
+    int charOffset = 0;
+    char s;
+
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+    graphics.setColor(av.textColour);
+
+    if (monospacedFont && av.showText && allGroups.length == 0
+            && !av.getColourText() && av.thresholdTextColour == 0)
+    {
+      if (av.renderGaps)
+      {
+        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 getboxColour = false;
+      for (int i = start; i <= end; i++)
+      {
+        graphics.setColor(av.textColour);
+        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(currentSequenceGroup.textColour2);
+              }
+            }
+          }
+          else
+          {
+            graphics.setColor(currentSequenceGroup.textColour);
+          }
+          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+          {
+            // todo - use sequence group consensus
+            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                    '.');
+
+          }
+
+        }
+        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.thresholdTextColour > 0)
+          {
+            if (!getboxColour)
+            {
+              getBoxColour(av.getGlobalColourScheme(), seq, i);
+            }
+
+            if (resBoxColour.getRed() + resBoxColour.getBlue()
+                    + resBoxColour.getGreen() < av.thresholdTextColour)
+            {
+              graphics.setColor(av.textColour2);
+            }
+          }
+          if (av.getShowUnconserved())
+          {
+            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                    '.');
+
+          }
+
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+                * (i - start), y1);
+
+      }
+    }
+  }
+
+  private char getDisplayChar(AlignmentAnnotation consensus, int position,
+          char s, char c)
+  {
+    char conschar = consensus.annotations[position].displayCharacter
+            .charAt(0);
+    if (conschar != '-' && s == conschar)
+    {
+      s = c;
+    }
+    return s;
+  }
+
+  /**
+   * 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.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.getCharAt(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);
+
+    if (av.validCharWidth)
+    {
+      graphics.setColor(Color.white);
+
+      char s = seq.getCharAt(res);
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.charHeight) - pady);
+    }
+
+  }
+}