X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=58a4f107519548f27d3e5398983a05484f67f677;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=5b7aa1e2bcf451a74d49bcfdc7fbaefa445017e5;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 5b7aa1e..58a4f10 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,226 +1,388 @@
-/*
-* 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.appletgui;
-
-import java.awt.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-public class IdCanvas extends Panel
-{
-  protected AlignViewport av;
-
-  protected boolean showScores  = true;
-
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
-  Image image;
-  Graphics gg;
-  int imgHeight=0;
-  boolean fastPaint = false;
-
-  java.util.Vector searchResults;
-
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(null);
-    this.av         = av;
-    PaintRefresher.Register(this);
-  }
-
-  public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
-
-      if(searchResults!=null && searchResults.contains(s))
-      {
-        gg.setColor(Color.black);
-        gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);
-        gg.setColor(Color.white);
-      }
-      else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {
-	  gg.setColor(Color.lightGray);
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);
-	  gg.setColor(Color.white);
-      } else {
-	  gg.setColor(s.getColor());
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);
-	  gg.setColor(Color.black);
-      }
-
-      String string = s.getName();
-      if(av.getShowFullId())
-        string = s.getDisplayId();
-
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
-
-  }
-
-  public void fastPaint(int vertical)
-  {
-    if(gg==null)
-    {  repaint(); return;}
-
-    gg.copyArea( 0,0, getSize().width, imgHeight, 0, -vertical*av.charHeight );
-
-    int ss=av.startSeq, es=av.endSeq, transY = 0;
-    if (vertical > 0) // scroll down
-     {
-       ss = es - vertical;
-       if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
-         ss = av.startSeq;
-       else
-         transY = imgHeight - vertical * av.charHeight;
-     }
-     else if (vertical < 0)
-     {
-       es = ss - vertical;
-       if(es > av.endSeq)
-         es = av.endSeq;
-     }
-
-
-
-        gg.translate(0, transY);
-
-        drawIds(ss, es);
-
-        gg.translate( 0, -transY );
-
-
-      fastPaint = true;
-      repaint();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-  public void paint(Graphics g)
-  {
-    if(getSize().height<0 || getSize().width<0)
-      return;
-    if (fastPaint)
-    {
-      fastPaint = false;
-      g.drawImage(image, 0, 0, this);
-      return;
-    }
-
-    imgHeight = getSize().height;
-    imgHeight -= imgHeight % av.charHeight;
-
-    if (imgHeight<1)
-      return;
-
-    if(image==null || imgHeight!=image.getHeight(this))
-    {
-      image = createImage(getSize().width, imgHeight);
-      gg = image.getGraphics();
-      gg.setFont(av.getFont());
-    }
-
-      //Fill in the background
-      gg.setColor(Color.white);
-      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-      gg.setFont(italic);
-
-    gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds( av.getStartSeq(), av.endSeq);
-    g.drawImage(image, 0, 0, this);
-  }
-
-  void drawIds(int starty, int endy)
-  {
-    Color currentColor     = Color.white;
-    Color currentTextColor = Color.black;
-
-    if (av.getWrapAlignment())
-    {
-
-          int rowSize =  av.getEndRes() - av.getStartRes();
-          // Draw the rest of the panels
-
-          for(int ypos=2*av.charHeight, row=av.startRes;
-              ypos <= getSize().height && row<av.alignment.getWidth();
-              ypos += av.chunkHeight, row+=rowSize )
-          {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
-            {
-              SequenceI s = av.alignment.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
-            }
-          }
-
-
-    } else
-    {
-
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        // Selected sequence colours
-
-        if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))
-        {
-          gg.setColor(Color.black);
-          currentColor = Color.black;
-          currentTextColor = Color.white;
-      }
-      else if (av.getSelectionGroup()!= null
-            && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))
-        {
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
-        }
-        else
-        {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
-          currentTextColor = Color.black;
-        }
-
-        gg.setColor(currentColor);
-
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getSize().width,
-                    av.charHeight);
-
-        gg.setColor(currentTextColor);
-        String string = av.alignment.getSequenceAt(i).getName();
-        if(av.getShowFullId())
-          string = av.alignment.getSequenceAt(i).getDisplayId();
-        gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
-                      av.charHeight - (av.charHeight / 5));
-      }
-
-      // add a border
-      gg.setColor(Color.white);
-      gg.fillRect(getSize().width-4,0,4,getSize().height);
-    }
-
-  }
-
-  public void setHighlighted(java.util.Vector found)
-  {
-    searchResults = found;
-    repaint();
-  }
-}
+/*
+ * 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.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.util.List;
+
+public class IdCanvas extends Panel
+{
+  protected AlignViewport av;
+
+  protected boolean showScores = true;
+
+  protected int maxIdLength = -1;
+
+  protected String maxIdStr = null;
+
+  Image image;
+
+  Graphics gg;
+
+  int imgHeight = 0;
+
+  boolean fastPaint = false;
+
+  List<SequenceI> searchResults;
+
+  public IdCanvas(AlignViewport av)
+  {
+    setLayout(null);
+    this.av = av;
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+          int i, int starty, int ypos)
+  {
+    int charHeight = av.getCharHeight();
+
+    if (searchResults != null && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+              charHeight);
+      gg.setColor(Color.white);
+    }
+    else if (av.getSelectionGroup() != null
+            && av.getSelectionGroup().getSequences(null).contains(s))
+    {
+      gg.setColor(Color.lightGray);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+              charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+              charHeight);
+      gg.setColor(Color.black);
+    }
+
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
+            ((i - starty) * charHeight) + ypos + charHeight
+                    - (charHeight / 5));
+
+    if (hiddenRows)
+    {
+      drawMarker(i, starty, ypos);
+    }
+
+  }
+
+  public void fastPaint(int vertical)
+  {
+    if (gg == null)
+    {
+      repaint();
+      return;
+    }
+
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+            -vertical * av.getCharHeight());
+
+    int ss = av.startSeq, es = av.endSeq, transY = 0;
+    if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      {
+        ss = av.startSeq;
+      }
+      else
+      {
+        transY = imgHeight - vertical * av.getCharHeight();
+      }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
+
+    gg.translate(0, transY);
+
+    drawIds(ss, es);
+
+    gg.translate(0, -transY);
+
+    fastPaint = true;
+    repaint();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    if (getSize().height < 0 || getSize().width < 0)
+    {
+      return;
+    }
+    if (fastPaint)
+    {
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
+      return;
+    }
+
+    imgHeight = getSize().height;
+    imgHeight -= imgHeight % av.getCharHeight();
+
+    if (imgHeight < 1)
+    {
+      return;
+    }
+
+    if (image == null || imgHeight != image.getHeight(this))
+    {
+      image = createImage(getSize().width, imgHeight);
+      gg = image.getGraphics();
+      gg.setFont(av.getFont());
+    }
+
+    // Fill in the background
+    gg.setColor(Color.white);
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+            .getFont().getSize());
+    gg.setFont(italic);
+
+    gg.fillRect(0, 0, getSize().width, getSize().height);
+    drawIds(av.startSeq, av.endSeq);
+    g.drawImage(image, 0, 0, this);
+  }
+
+  /**
+   * local copy of av.getCharHeight set at top of drawIds
+   */
+  private int avcharHeight;
+
+  void drawIds(int starty, int endy)
+  {
+    // hardwired italic IDs in applet currently
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+            .getFont().getSize());
+    // temp variable for speed
+    avcharHeight = av.getCharHeight();
+
+    gg.setFont(italic);
+
+    Color currentColor = Color.white;
+    Color currentTextColor = Color.black;
+
+    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+            && av.getShowHiddenMarkers();
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.getAlignment().getWidth();
+      int alheight = av.getAlignment().getHeight();
+
+      if (av.hasHiddenColumns())
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int annotationHeight = 0;
+      AnnotationLabels labels = null;
+
+      if (av.isShowAnnotation())
+      {
+        AnnotationPanel ap = new AnnotationPanel(av);
+        annotationHeight = ap.adjustPanelHeight();
+        labels = new AnnotationLabels(av);
+      }
+      int hgap = avcharHeight;
+      if (av.getScaleAboveWrapped())
+      {
+        hgap += avcharHeight;
+      }
+
+      int cHeight = alheight * avcharHeight + hgap + annotationHeight;
+
+      int rowSize = av.getEndRes() - av.getStartRes();
+      // Draw the rest of the panels
+      for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+              && (row < maxwidth); ypos += cHeight, row += rowSize)
+      {
+        for (int i = starty; i < alheight; i++)
+        {
+
+          SequenceI s = av.getAlignment().getSequenceAt(i);
+          gg.setFont(italic);
+          if (doHiddenCheck)
+          {
+            setHiddenFont(s);
+          }
+          drawIdString(gg, hiddenRows, s, i, 0, ypos);
+        }
+
+        if (labels != null)
+        {
+          gg.translate(0, ypos + (alheight * avcharHeight));
+          labels.drawComponent(gg, getSize().width);
+          gg.translate(0, -ypos - (alheight * avcharHeight));
+        }
+
+      }
+    }
+    else
+    {
+      // Now draw the id strings
+      SequenceI seq;
+      for (int i = starty; i < endy; i++)
+      {
+
+        seq = av.getAlignment().getSequenceAt(i);
+        if (seq == null)
+        {
+          continue;
+        }
+        gg.setFont(italic);
+        // boolean isrep=false;
+        if (doHiddenCheck)
+        {
+          // isrep =
+          setHiddenFont(seq);
+        }
+
+        // Selected sequence colours
+        if ((searchResults != null) && searchResults.contains(seq))
+        {
+          currentColor = Color.black;
+          currentTextColor = Color.white;
+        }
+        else if ((av.getSelectionGroup() != null)
+                && av.getSelectionGroup().getSequences(null).contains(seq))
+        {
+          currentColor = Color.lightGray;
+          currentTextColor = Color.black;
+        }
+        else
+        {
+          currentColor = av.getSequenceColour(seq);
+          currentTextColor = Color.black;
+        }
+
+        gg.setColor(currentColor);
+        // TODO: isrep could be used to highlight the representative in a
+        // different way
+        gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+                avcharHeight);
+        gg.setColor(currentTextColor);
+
+        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
+                (((i - starty) * avcharHeight) + avcharHeight)
+                        - (avcharHeight / 5));
+
+        if (hiddenRows)
+        {
+          drawMarker(i, starty, 0);
+        }
+      }
+    }
+  }
+
+  public void setHighlighted(List<SequenceI> list)
+  {
+    searchResults = list;
+    repaint();
+  }
+
+  void drawMarker(int i, int starty, int yoffset)
+  {
+    SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+    // Use this method here instead of calling hiddenSeq adjust
+    // 3 times.
+    int hSize = hseqs.length;
+
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
+
+    for (int j = 0; j < hSize; j++)
+    {
+      if (hseqs[j] != null)
+      {
+        if (j - 1 < hiddenIndex)
+        {
+          hiddenIndex++;
+        }
+        if (j - 1 < lastIndex)
+        {
+          lastIndex++;
+        }
+        if (j - 1 < nextIndex)
+        {
+          nextIndex++;
+        }
+      }
+    }
+
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 1);
+
+    gg.setColor(Color.blue);
+    if (below)
+    {
+      gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+          getSize().width - avcharHeight, getSize().width }, new int[] {
+          (i - starty) * avcharHeight + yoffset,
+          (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+          (i - starty) * avcharHeight + yoffset }, 3);
+    }
+    if (above)
+    {
+      gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+          getSize().width - avcharHeight, getSize().width }, new int[] {
+          (i - starty + 1) * avcharHeight + yoffset,
+          (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+          (i - starty + 1) * avcharHeight + yoffset }, 3);
+
+    }
+  }
+
+  boolean setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+            .getSize());
+
+    if (av.isHiddenRepSequence(seq))
+    {
+      gg.setFont(bold);
+      return true;
+    }
+    return false;
+  }
+}