X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=f4c73800ae3194b98cc5b9ee57e0e4ec01ad389e;hb=c24071f7b9e6b70c94743214677871ae2dc88499;hp=d7a034c74f13e82d6bf79e8bf6631a6588e44124;hpb=23444dd246b45e21346f6cc85564cf3f876320fd;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index d7a034c..f4c7380 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,201 +1,310 @@
+/*
+ * 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 java.awt.*;
-import java.awt.Graphics2D.*;
 import java.awt.image.*;
+
 import javax.swing.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class IdCanvas extends JPanel
 {
-  protected AlignViewport av;
+    protected AlignViewport av;
+    protected boolean showScores = true;
+    protected int maxIdLength = -1;
+    protected String maxIdStr = null;
+    BufferedImage image;
+    Graphics2D gg;
+    int imgHeight = 0;
+    boolean fastPaint = false;
+    java.util.Vector searchResults;
+
+    /**
+     * Creates a new IdCanvas object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public IdCanvas(AlignViewport av)
+    {
+        setLayout(new BorderLayout());
+        this.av = av;
+        PaintRefresher.Register(this, av.alignment);
+    }
+
+    /**
+     * 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 charHeight = av.charHeight;
+
+        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().sequences.contains(s))
+        {
+            gg.setColor(Color.lightGray);
+            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+                charHeight);
+            gg.setColor(Color.white);
+        }
+        else
+        {
+            gg.setColor(s.getColor());
+            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+                charHeight);
+            gg.setColor(Color.black);
+        }
 
-  protected boolean showScores  = true;
 
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
-  BufferedImage image;
-  Graphics2D gg;
-  int imgHeight=0;
-  boolean fastPaint = false;
+        gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
+                      0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+    }
 
-  java.util.ArrayList searchResults;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int vertical)
+    {
+        if (gg == null)
+        {
+            repaint();
 
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av         = av;
-    PaintRefresher.Register(this);
-  }
+            return;
+        }
 
-  public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
+        gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * 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);
-      }
-
-      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, getWidth(), 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;
-     }
+        int ss = av.startSeq;
+        int es = av.endSeq;
+        int 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 );
+        gg.translate(0, -transY);
 
+        fastPaint = true;
+        repaint();
+    }
 
-      fastPaint = true;
-      repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+        if (fastPaint)
+        {
+            fastPaint = false;
+            g.drawImage(image, 0, 0, this);
 
-    if (fastPaint)
-    {
-      fastPaint = false;
-      g.drawImage(image, 0, 0, this);
-      return;
+            return;
+        }
+
+        imgHeight = getHeight();
+        imgHeight -= (imgHeight % av.charHeight);
+
+        if (imgHeight < 1)
+        {
+            return;
+        }
+
+        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);
+
+
+        drawIds(av.getStartSeq(), av.endSeq);
+
+        g.drawImage(image, 0, 0, this);
     }
 
-    imgHeight = getHeight();
-    imgHeight -= imgHeight % av.charHeight;
-    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);
-
-    g.drawImage(image, 0, 0, this);
-  }
-
-  void drawIds(int starty, int endy)
-  {
-    Color currentColor     = Color.white;
-    Color currentTextColor = Color.black;
-
-    if (av.getWrapAlignment())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param starty DOCUMENT ME!
+     * @param endy DOCUMENT ME!
+     */
+    void drawIds(int starty, int endy)
     {
+      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                             av.getFont().getSize());
+      gg.setFont(italic);
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+
+        Color currentColor = Color.white;
+        Color currentTextColor = Color.black;
 
-          int rowSize =  av.getEndRes() - av.getStartRes();
-          // Draw the rest of the panels
+        if (av.getWrapAlignment())
+        {
+          int annotationHeight = 0;
+          AnnotationLabels labels = null;
 
-          for(int ypos=2*av.charHeight, row=av.getEndRes()-rowSize;
-              ypos <= getHeight() && row<av.alignment.getWidth();
-              ypos += av.chunkHeight, row+=rowSize )
+          if(av.showAnnotation)
           {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
-            {
-              SequenceI s = av.alignment.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
-            }
+            AnnotationPanel ap = new AnnotationPanel(av);
+            annotationHeight = ap.adjustPanelHeight();
+            labels = new AnnotationLabels(av);
           }
 
+          int hgap = av.charHeight;
+          if (av.scaleAboveWrapped)
+            hgap += av.charHeight;
 
-    } else
-    {
+          int cHeight = av.getAlignment().getHeight() * av.charHeight
+              + hgap
+              + annotationHeight;
 
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        // Selected sequence colours
+            int rowSize = av.getEndRes() - av.getStartRes();
 
-        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;
+            // Draw the rest of the panels
+            for (int ypos = hgap, row = av.startRes;
+                    (ypos <= getHeight()) && (row < av.alignment.getWidth());
+                    ypos += cHeight, row += rowSize)
+            {
+                for (int i = starty; i < av.alignment.getHeight(); i++)
+                {
+                    SequenceI s = av.alignment.getSequenceAt(i);
+                    gg.setFont(italic);
+                    drawIdString(gg, s, i, 0, ypos);
+                }
+
+                if(labels!=null)
+                {
+                  gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));
+                  labels.drawComponent(gg, getWidth());
+                  gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));
+
+                }
+            }
         }
         else
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
-          currentTextColor = Color.black;
-        }
+            //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, (i - starty) * av.charHeight, getWidth(),
+                    av.charHeight);
 
-        gg.setColor(currentColor);
+                gg.setColor(currentTextColor);
 
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getWidth(),
-                    av.charHeight);
+                String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
 
-        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(getWidth()-4,0,4,getHeight());
-    }
+                gg.drawString(string, 0,
+                    (((i - starty) * av.charHeight) + av.charHeight) -
+                    (av.charHeight / 5));
+            }
 
-  }
+            // add a border
+            gg.setColor(Color.white);
+            gg.fillRect(getWidth() - 4, 0, 4, getHeight());
+        }
+    }
 
-  public void setHighlighted(java.util.ArrayList found)
-  {
-    searchResults = found;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param found DOCUMENT ME!
+     */
+    public void setHighlighted(java.util.Vector found)
+    {
+        searchResults = found;
+        repaint();
+    }
 }