X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=30152ccc711ac7d4a3b96ba2e75d72b6063a74b8;hb=acc9fa6c42fcdde3d55b483f1dea91e0058be06e;hp=959c83c28264a1a1bc73219b2d3958a0e4483cf2;hpb=c3162a6dd5f226c743bce629cf125a17c9b67711;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 959c83c..30152cc 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,176 +1,394 @@
+/*
+ * 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 boolean showScores  = true;
-
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
-  BufferedImage image;
-  Graphics2D gg;
-  int imgHeight=0;
-  boolean fastPaint = false;
-
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av         = av;
-    PaintRefresher.Register(this);
-  }
-
-  public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
-
-
-      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
-     {
-       transY = imgHeight - vertical*av.charHeight;
-       ss = es - vertical;
-     }
-     else if(vertical<0)
-     {
-       es = ss-vertical;
-     }
+    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);
+    }
 
-        gg.translate(0, transY);
+    /**
+     * 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;
 
-        drawIds(ss, es);
+        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(false).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);
+        }
 
-        gg.translate( 0, -transY );
 
+        gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
+                      0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-      fastPaint = true;
-      repaint();
-  }
+        if (av.hasHiddenRows && av.showHiddenMarkers)
+          drawMarker(i, starty, ypos);
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
 
-    if (fastPaint)
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param vertical DOCUMENT ME!
+     */
+    public void fastPaint(int vertical)
     {
-      g.drawImage(image, 0, 0, this);
-      fastPaint = false;
-      return;
+        if (gg == null)
+        {
+            repaint();
+
+            return;
+        }
+
+        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;
+
+            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();
     }
 
-    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);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
 
-    drawIds( av.getStartSeq(), av.endSeq);
+        if (fastPaint)
+        {
+            fastPaint = false;
+            g.drawImage(image, 0, 0, this);
 
-    g.drawImage(image, 0, 0, this);
-  }
+            return;
+        }
+
+        int oldHeight = imgHeight;
+
+        imgHeight = getHeight();
+        imgHeight -= (imgHeight % av.charHeight);
+
+        if (imgHeight < 1)
+        {
+            return;
+        }
 
-  void drawIds(int starty, int endy)
-  {
+        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);
 
-    Color currentColor     = Color.white;
-    Color currentTextColor = Color.black;
+        drawIds(av.getStartSeq(), av.endSeq);
 
-    if (av.getWrapAlignment())
+        g.drawImage(image, 0, 0, this);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param starty DOCUMENT ME!
+     * @param endy DOCUMENT ME!
+     */
+    void drawIds(int starty, int endy)
     {
-          // Draw the rest of the panels
-          int chunkHeight =  (av.alignment.getHeight() + 2)*av.charHeight;
-          int row = av.getStartRes() / av.chunkWidth ;
-          for(int ypos=2*av.charHeight;
-              ypos <= getHeight() && row*av.chunkWidth<av.alignment.getWidth();
-              ypos += chunkHeight, row++ )
+      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 maxwidth = av.alignment.getWidth();
+          int alheight = av.alignment.getHeight();
+
+          if (av.hasHiddenColumns)
+            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+          int annotationHeight = 0;
+          AnnotationLabels labels = null;
+
+          if(av.showAnnotation)
           {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
+            AnnotationPanel ap = new AnnotationPanel(av);
+            annotationHeight = ap.adjustPanelHeight();
+            labels = new AnnotationLabels(av);
+          }
+
+          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)
             {
-              SequenceI s = av.alignment.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
+              for (int i = starty; i < alheight; i++)
+              {
+                if (av.hasHiddenRows)
+                {
+                  setHiddenFont(i);
+                }
+                else
+                  gg.setFont(italic);
+
+                SequenceI s = av.alignment.getSequenceAt(i);
+                drawIdString(gg, s, i, 0, ypos);
+              }
+
+                if(labels!=null)
+                {
+                  gg.translate(0, ypos+(alheight * av.charHeight));
+                  labels.drawComponent(gg, getWidth());
+                  gg.translate(0, -ypos-(alheight * av.charHeight));
+                }
+
+
+            }
+        }
+        else
+        {
+          //Now draw the id strings
+
+            //Now draw the id strings
+            for (int i = starty; i < endy; i++)
+            {
+              if (av.hasHiddenRows)
+              {
+                setHiddenFont(i);
+              }
+
+                // 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().getSequences(false).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(currentTextColor);
+
+                String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
+
+                gg.drawString(string, 0,
+                    (((i - starty) * av.charHeight) + av.charHeight) -
+                    (av.charHeight / 5));
+
+               if(av.hasHiddenRows && av.showHiddenMarkers)
+                 drawMarker(i, starty, 0);
+
             }
-          }
 
+        }
+    }
 
-    } else
+    void drawMarker(int i, int starty, int yoffset)
     {
+      int hiddenIndex = av.adjustForHiddenSeqs(i);
+      int lastIndex = av.adjustForHiddenSeqs(i - 1);
+      int nextIndex = av.adjustForHiddenSeqs(i + 1);
 
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        // Selected sequence colours
+      boolean below = (hiddenIndex > lastIndex + 1);
+      boolean above = (nextIndex>hiddenIndex+1);
 
-        if (av.getSelectionGroup()!= null
-            && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))
+        gg.setColor(Color.blue);
+        if(below)
         {
-       //   if(av.alignment.findGroup(al.getSequenceAt(i)).getEndRes()==
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
+          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);
         }
-        else
+        if(above)
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
-          currentTextColor = Color.black;
+          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);
+
         }
+    }
 
-        gg.setColor(currentColor);
-
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, 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));
-      }
-
-      // add a border
-      gg.setColor(Color.white);
-      gg.fillRect(getWidth()-4,0,4,getHeight());
+    void setHiddenFont(int i)
+    {
+      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                             av.getFont().getSize());
+      Font bold = new Font(av.getFont().getName(), Font.BOLD,
+                           av.getFont().getSize());
+
+      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+        gg.setFont(bold);
+      else
+        gg.setFont(italic);
     }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param found DOCUMENT ME!
+     */
+    public void setHighlighted(java.util.Vector found)
+    {
+        searchResults = found;
+        repaint();
+    }
 }