X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=97b8669cd1d1c4f6e3aca9907081fe96f477ee03;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=882ed7ae2aa060d5451a8c9674d0d93965008f03;hpb=5150ffd5baa1f58bb6b4059616bc6b9050326553;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 882ed7a..97b8669 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,96 +1,179 @@
+/*
+ * 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.gui;
 
 import java.awt.*;
-import java.awt.Graphics2D.*;
 import java.awt.image.*;
 import javax.swing.*;
+
 import jalview.datamodel.*;
-import jalview.analysis.*;
-public class IdCanvas extends JPanel
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas
+    extends JPanel
 {
   protected AlignViewport av;
-
-  protected boolean showScores  = true;
-
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
+  protected boolean showScores = true;
+  protected int maxIdLength = -1;
+  protected String maxIdStr = null;
   BufferedImage image;
   Graphics2D gg;
-  int imgHeight=0;
+  int imgHeight = 0;
   boolean fastPaint = false;
-
   java.util.Vector searchResults;
-
+  FontMetrics fm;
+  AnnotationLabels labels = null;
+  AnnotationPanel ap;
+  Font idfont;
+
+  /**
+   * Creates a new IdCanvas object.
+   *
+   * @param av DOCUMENT ME!
+   */
   public IdCanvas(AlignViewport av)
   {
     setLayout(new BorderLayout());
-    this.av         = av;
-    PaintRefresher.Register(this);
+    this.av = av;
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
-  public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gg DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   * @param starty DOCUMENT ME!
+   * @param ypos DOCUMENT ME!
+   */
+  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+                           int ypos)
+  {
+    int xPos = 0;
+    int panelWidth = getWidth();
+    int charHeight = av.charHeight;
 
-      if(searchResults!=null && searchResults.contains(s))
-      {
-        gg.setColor(Color.black);
-        gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),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,getWidth(),charHeight);
-	  gg.setColor(Color.white);
-      } else {
-	  gg.setColor(s.getColor());
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
-	  gg.setColor(Color.black);
-      }
+    if ( (searchResults != null) && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
+                  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, getWidth(),
+                  charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
+                  charHeight);
+      gg.setColor(Color.black);
+    }
 
-      String string = s.getName();
-      if(av.getShowFullId())
-        string = s.getDisplayId();
+    if (av.rightAlignIds)
+    {
+      xPos = panelWidth - fm.stringWidth(
+          s.getDisplayId(av.getShowJVSuffix())
+          ) - 4;
+    }
+
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()),
+                  xPos,
+                  ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
+    if (av.hasHiddenRows && av.showHiddenMarkers)
+    {
+      drawMarker(i, starty, ypos);
+    }
 
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param vertical DOCUMENT ME!
+   */
   public void fastPaint(int vertical)
   {
-    if(gg==null)
-    {  repaint(); return;}
+    if (gg == null)
+    {
+      repaint();
 
-    gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight );
+      return;
+    }
 
-    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.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
 
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transY = 0;
 
+    if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
 
-        gg.translate(0, transY);
+      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;
 
-        drawIds(ss, es);
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
 
-        gg.translate( 0, -transY );
+    gg.translate(0, transY);
 
+    drawIds(ss, es);
 
-      fastPaint = true;
-      repaint();
+    gg.translate(0, -transY);
+
+    fastPaint = true;
+    repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
@@ -100,99 +183,292 @@ public class IdCanvas extends JPanel
     {
       fastPaint = false;
       g.drawImage(image, 0, 0, this);
+
       return;
     }
 
+    int oldHeight = imgHeight;
+
     imgHeight = getHeight();
-    imgHeight -= imgHeight % av.charHeight;
-    image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);
+    imgHeight -= (imgHeight % av.charHeight);
+
+    if (imgHeight < 1)
+    {
+      return;
+    }
+
+    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
+    {
+      image = new BufferedImage(getWidth(), imgHeight,
+                                BufferedImage.TYPE_INT_RGB);
+    }
+
     gg = (Graphics2D) image.getGraphics();
+
     //Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    gg.setFont(italic);
 
-    drawIds( av.getStartSeq(), av.endSeq);
+    drawIds(av.getStartSeq(), av.endSeq);
 
     g.drawImage(image, 0, 0, this);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param starty DOCUMENT ME!
+   * @param endy DOCUMENT ME!
+   */
   void drawIds(int starty, int endy)
   {
-    Color currentColor     = Color.white;
+    if (av.seqNameItalics)
+    {
+      idfont = new Font(av.getFont().getName(), Font.ITALIC,
+                        av.getFont().getSize());
+    }
+    else
+    {
+      idfont = av.getFont();
+    }
+
+    gg.setFont(idfont);
+    fm = gg.getFontMetrics();
+
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
+
+    Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
     if (av.getWrapAlignment())
     {
+      int maxwidth = av.alignment.getWidth();
+      int alheight = av.alignment.getHeight();
+
+      if (av.hasHiddenColumns)
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int annotationHeight = 0;
+
+      if (av.showAnnotation)
+      {
+        if (ap == null)
+        {
+          ap = new AnnotationPanel(av);
+        }
 
-          int rowSize =  av.getEndRes() - av.getStartRes();
-          // Draw the rest of the panels
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
+        {
+          labels = new AnnotationLabels(av);
+        }
+      }
 
-          for(int ypos=2*av.charHeight, row=av.startRes;
-              ypos <= getHeight() && row<av.alignment.getWidth();
-              ypos += av.chunkHeight, row+=rowSize )
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
+
+      int cHeight = alheight * av.charHeight
+          + hgap
+          + annotationHeight;
+
+      int rowSize = av.getEndRes() - av.getStartRes();
+
+      // Draw the rest of the panels
+      for (int ypos = hgap, row = av.startRes;
+           (ypos <= getHeight()) && (row < maxwidth);
+           ypos += cHeight, row += rowSize)
+      {
+        for (int i = starty; i < alheight; i++)
+        {
+          SequenceI s = av.alignment.getSequenceAt(i);
+          if (av.hasHiddenRows)
+          {
+            setHiddenFont(s);
+          }
+          else
           {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
-            {
-              SequenceI s = av.alignment.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
-            }
+            gg.setFont(idfont);
           }
 
+          drawIdString(gg, s, i, 0, ypos);
+        }
 
-    } else
+        if (labels != null && av.showAnnotation)
+        {
+          gg.translate(0, ypos + (alheight * av.charHeight));
+          labels.drawComponent(gg, getWidth());
+          gg.translate(0, -ypos - (alheight * av.charHeight));
+        }
+      }
+    }
+    else
     {
+      //No need to hang on to labels if we're not wrapped
+      labels = null;
 
       //Now draw the id strings
+      int panelWidth = getWidth();
+      int xPos = 0;
+
+      SequenceI sequence;
+      //Now draw the id strings
       for (int i = starty; i < endy; i++)
       {
-        // Selected sequence colours
+        sequence = av.alignment.getSequenceAt(i);
+
+        if (sequence == null)
+        {
+          continue;
+        }
 
-        if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))
+        if (av.hasHiddenRows)
+        {
+          setHiddenFont(sequence);
+        }
+
+        // Selected sequence colours
+        if ( (searchResults != null) &&
+            searchResults.contains(sequence))
         {
-          gg.setColor(Color.black);
           currentColor = Color.black;
           currentTextColor = Color.white;
-      }
-      else if (av.getSelectionGroup()!= null
-            && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))
+        }
+        else if ( (av.getSelectionGroup() != null) &&
+                 av.getSelectionGroup().getSequences(null).contains(
+                     sequence))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
         }
         else
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
+          currentColor = av.getSequenceColour(sequence);
           currentTextColor = Color.black;
         }
 
         gg.setColor(currentColor);
 
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getWidth(),
+        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
                     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));
+
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+        if (av.rightAlignIds)
+        {
+          xPos = panelWidth - fm.stringWidth(string) - 4;
+        }
+
+        gg.drawString(string, xPos,
+                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
+                      (av.charHeight / 5));
+
+        if (av.hasHiddenRows && av.showHiddenMarkers)
+        {
+          drawMarker(i, starty, 0);
+        }
+
       }
 
-      // add a border
-      gg.setColor(Color.white);
-      gg.fillRect(getWidth()-4,0,4,getHeight());
+    }
+  }
+
+  void drawMarker(int i, int starty, int yoffset)
+  {
+
+    SequenceI[] hseqs = av.alignment.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[]
+                     {getWidth() - av.charHeight,
+                     getWidth() - av.charHeight,
+                     getWidth()},
+                     new int[]
+                     {
+                     (i - starty) * av.charHeight + yoffset,
+                     (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
+                     (i - starty) * av.charHeight + yoffset
+      }, 3);
+    }
+    if (above)
+    {
+      gg.fillPolygon(new int[]
+                     {getWidth() - av.charHeight,
+                     getWidth() - av.charHeight,
+                     getWidth()},
+                     new int[]
+                     {
+                     (i - starty + 1) * av.charHeight + yoffset,
+                     (i - starty + 1) * av.charHeight + yoffset -
+                     av.charHeight / 4,
+                     (i - starty + 1) * av.charHeight + yoffset
+      }, 3);
+
+    }
+  }
+
+  void setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD,
+                         av.getFont().getSize());
+
+    if (av.hiddenRepSequences != null &&
+        av.hiddenRepSequences.containsKey(seq))
+    {
+      gg.setFont(bold);
+    }
+    else
+    {
+      gg.setFont(idfont);
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param found DOCUMENT ME!
+   */
   public void setHighlighted(java.util.Vector found)
   {
     searchResults = found;