X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=214f218c0294d16a65cecb7111c4c5669c5bf917;hb=e02486484d33e20dedb020a34f31f6024d5720a2;hp=9e64b1ed681b6ddccc903475cba70530bf829fe0;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 9e64b1e..214f218 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,145 +1,349 @@
+/*
+ * 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);
+    }
 
-  protected boolean showScores  = true;
+    /**
+     * 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;
 
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
+        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);
+        }
 
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av         = av;
-    PaintRefresher.Register(this);
-  }
 
-  public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
+        gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
+                      0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int vertical)
+    {
+        if (gg == null)
+        {
+            repaint();
 
-      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);
-      }
+            return;
+        }
 
-      String string = s.getName() + "/" + s.getStart() + "-" + s.getEnd();
+        gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
 
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
+        int ss = av.startSeq;
+        int es = av.endSeq;
+        int transY = 0;
 
-  }
+        if (vertical > 0) // scroll down
+        {
+            ss = es - vertical;
 
-  public void paintComponent(Graphics gg) {
-    AlignmentI al         = av.alignment;
-    int        charHeight = av.charHeight;
-    gg.setFont(av.getFont());
+            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;
 
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0,0,getWidth(),getHeight());
+            if (es > av.endSeq)
+            {
+                es = av.endSeq;
+            }
+        }
 
-    Color currentColor     = Color.white;
-    Color currentTextColor = Color.black;
+        gg.translate(0, transY);
 
-    //Which ids are we printing
-    int starty = av.getStartSeq();
-    int endy   = av.endSeq;
+        drawIds(ss, es);
 
-    if (av.getWrapAlignment())
-    {
-          // Draw the rest of the panels
-          int chunkHeight =  (al.getHeight() + 2)*av.charHeight;
-          int row = av.getStartRes() / av.chunkWidth ;
-          for(int ypos=2*av.charHeight;
-              ypos <= getHeight() && row*av.chunkWidth<al.getWidth();
-              ypos += chunkHeight, row++ )
-          {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
-            {
-              SequenceI s = al.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
-            }
-          }
+        gg.translate(0, -transY);
 
+        fastPaint = true;
+        repaint();
+    }
 
-    } else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
 
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        // Selected sequence colours
-
-        if (av.getSelectionGroup()!= null && av.getSelectionGroup().sequences.contains(al.getSequenceAt(i)))
+        if (fastPaint)
         {
-       //   if(av.alignment.findGroup(al.getSequenceAt(i)).getEndRes()==
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
+            fastPaint = false;
+            g.drawImage(image, 0, 0, this);
+
+            return;
         }
-        else
+
+        imgHeight = getHeight();
+        imgHeight -= (imgHeight % av.charHeight);
+
+        if (imgHeight < 1)
         {
-          currentColor = al.getSequenceAt(i).getColor();
-          currentTextColor = Color.black;
+            return;
         }
 
-        gg.setColor(currentColor);
+        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.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, charHeight),
-                    getWidth(),
-                    charHeight);
 
-        gg.setColor(currentTextColor);
-        String string = al.getSequenceAt(i).getDisplayId();
-        gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, charHeight) +
-                      charHeight - (charHeight / 5));
-      }
+        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)
+    {
+      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                             av.getFont().getSize());
+      gg.setFont(italic);
+
+      if (av.antiAlias)
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                            RenderingHints.VALUE_ANTIALIAS_ON);
+
+        Color currentColor = Color.white;
+        Color currentTextColor = Color.black;
+
+        if (av.getWrapAlignment())
+        {
+          int annotationHeight = 0;
+          AnnotationLabels labels = null;
 
+          if(av.showAnnotation)
+          {
+            AnnotationPanel ap = new AnnotationPanel(av);
+            annotationHeight = ap.adjustPanelHeight();
+            labels = new AnnotationLabels(av);
+          }
 
-  public Dimension getLabelWidth()
-  {
-    if(getGraphics()==null)
-      return null;
+          int hgap = av.charHeight;
+          if (av.scaleAboveWrapped)
+            hgap += av.charHeight;
 
-   FontMetrics fm = this.getGraphics().getFontMetrics(av.font);
-   AlignmentI al = av.getAlignment();
+          int cHeight = av.getAlignment().getHeight() * av.charHeight
+              + hgap
+              + annotationHeight;
 
-   int i   = 0;
-   int idWidth = 0;
+            int rowSize = av.getEndRes() - av.getStartRes();
 
-   while (i < al.getHeight() && al.getSequenceAt(i) != null)
-   {
-     SequenceI s   = al.getSequenceAt(i);
-     String str   = s.getDisplayId();
-     if (fm.stringWidth(str) > idWidth)
-       idWidth = fm.stringWidth(str);
-     i++;
-   }
+            // 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++)
+                {
 
-   return new Dimension(idWidth + 10,getHeight());
- }
+                    SequenceI s = av.alignment.getSequenceAt(i);
+                    gg.setFont(italic);
+                    drawIdString(gg, s, i, 0, ypos);
+                }
 
- public Dimension getPreferredSize()
- {
-   return getLabelWidth();
- }
+                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
+        {
+            //Now draw the id strings
+            int tmp, hiddenIndex = starty;
+            boolean markHidden = false;
+            for (int i = starty; i < endy; i++)
+            {
+              if (av.hasHiddenRows)
+              {
+                tmp = av.adjustForHiddenSeqs(i);
+                if(hiddenIndex != tmp)
+                {
+                    hiddenIndex = tmp;
+                    markHidden = true;
+                }
+                else
+                  markHidden = false;
+
+                hiddenIndex++;
+              }
+
+              if(av.hasHiddenRows && av.alignment.getSequenceAt(i).getHiddenSequences()!=null)
+              {
+                currentTextColor = Color.blue;
+              }
+              else
+                // Selected sequence colours
+                if ((searchResults != null) &&
+                        searchResults.contains(av.alignment.getSequenceAt(i)))
+                {
+                    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);
+
+                if (markHidden)
+                {
+                  gg.setColor(Color.blue);
+               //   gg.drawLine(0, (i-starty)*av.charHeight, getWidth(),(i-starty)*av.charHeight);
+                  gg.fillPolygon(new int[] { getWidth() - av.charHeight,
+                                         getWidth() - av.charHeight,
+                                         getWidth() },
+                                new int[]
+                                {
+                                    (i-starty)*av.charHeight -av.charHeight/4,
+                                    (i-starty)*av.charHeight +av.charHeight/4,
+                                    (i-starty)*av.charHeight
+                                }, 3);
+
+                }
+
+                gg.setColor(currentTextColor);
+
+                String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
+
+                gg.drawString(string, 0,
+                    (((i - starty) * av.charHeight) + av.charHeight) -
+                    (av.charHeight / 5));
+            }
 
+            // add a border
+         //   gg.setColor(Color.cyan);
+          //  gg.fillRect(getWidth() - 4, 0, 4, getHeight());
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param found DOCUMENT ME!
+     */
+    public void setHighlighted(java.util.Vector found)
+    {
+        searchResults = found;
+        repaint();
+    }
 }