X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=caf20ee7cfe6b8989555fb47533c11ca7c15f15d;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=daf971d406348f5682cc23ea8c67a66cffcd9768;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index daf971d..caf20ee 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,333 +1,362 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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.getCharAt(i), 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)
-  {
-    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.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.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);
-    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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+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.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.getCharAt(i), 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)
+  {
+    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.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());
+        }
+        if (currentSequenceGroup.getShowNonconserved())
+        {
+          // cheat - use this if we have a consensus for each group: s =
+          // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
+          s = getDisplayChar(av.consensus, 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(av.consensus, i, s, '.');
+
+        }
+      }
+
+      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);
+    }
+
+  }
+
+  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;
+  }
+
+  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.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);
+    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);
+    }
+  }
+
+}