X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=97b8669cd1d1c4f6e3aca9907081fe96f477ee03;hb=27a5c083838bb51c6d7b60b499e9dade3a33599d;hp=c1df12d0e558e7dbc20ad5e116740d05418da495;hpb=b1081eceb6369009b51c960cb2c77c5b49546cc3;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c1df12d..97b8669 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,226 +1,477 @@
+/*
+ * 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
-{
-  protected Image    img;
-  protected Graphics2D gg;
 
-  protected int      imgWidth;
-  protected int      imgHeight;
+import jalview.datamodel.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas
+    extends JPanel
+{
   protected AlignViewport av;
-
-  public boolean paintFlag   = false;
-  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;
+  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(Graphics g,SequenceI ds,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
-
-      if (av.getSelection().contains(ds)) {
-	  gg.setColor(Color.gray);
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
-	  gg.setColor(Color.white);
-      } else {
-	  gg.setColor(ds.getColor());
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
-	  gg.setColor(Color.black);
-      }
+  /**
+   * 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, ( (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 = ds.getName() + "/" + ds.getStart() + "-" + ds.getEnd();
+    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);
+    }
 
   }
 
-  public void paintComponent(Graphics g) {
-    AlignmentI da         = av.getAlignment();
-    int        charHeight = av.getCharHeight();
-    Font       f          = av.getFont();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param vertical DOCUMENT ME!
+   */
+  public void fastPaint(int vertical)
+  {
+    if (gg == null)
+    {
+      repaint();
+
+      return;
+    }
+
+    gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
 
-    if (img == null ||
-        imgWidth != getWidth()   ||
-        imgHeight != getHeight() ||
-        paintFlag == true) {
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transY = 0;
 
-      imgWidth = getWidth();
-      imgHeight = getHeight();
+    if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
 
-      if (imgWidth <= 0 )  {
-        imgWidth  = 700;
+      if (ss < av.startSeq)
+      { // ie scrolling too fast, more than a page at a time
+        ss = av.startSeq;
       }
-      if (imgHeight <= 0 ) {
-        imgHeight = 500;
+      else
+      {
+        transY = imgHeight - (vertical * av.charHeight);
       }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
 
-      img = createImage(imgWidth,imgHeight);
-
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
 
-      gg = (Graphics2D)img.getGraphics();
-      gg.setColor(Color.white);
-      gg.fillRect(0,0,imgWidth,imgHeight);
+    gg.translate(0, transY);
 
-      gg.setFont(f);
+    drawIds(ss, es);
 
-      paintFlag = false;
+    gg.translate(0, -transY);
 
-    }
+    fastPaint = true;
+    repaint();
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
 
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0,0,imgWidth,imgHeight);
+    if (fastPaint)
+    {
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
 
-    Color currentColor     = Color.white;
-    Color currentTextColor = Color.black;
+      return;
+    }
 
-    //Which ids are we printing
-    int starty = av.getStartSeq();
-    int endy   = av.getEndSeq();
+    int oldHeight = imgHeight;
 
+    imgHeight = getHeight();
+    imgHeight -= (imgHeight % av.charHeight);
 
+    if (imgHeight < 1)
+    {
+      return;
+    }
 
-    if (av.getWrapAlignment())
+    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
     {
-	starty = starty%av.getChunkHeight();
+      image = new BufferedImage(getWidth(), imgHeight,
+                                BufferedImage.TYPE_INT_RGB);
+    }
 
-	int ypos     = 0;
-	int rowstart = starty;
+    gg = (Graphics2D) image.getGraphics();
 
-	if (starty == 0)
-	    ypos = 2*charHeight;
-       else if (starty == 1)
-       {
-	    starty = 0;
-	    ypos = charHeight;
-	}
+    //Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, getWidth(), imgHeight);
 
-	endy   = starty + da.getHeight();
+    drawIds(av.getStartSeq(), av.endSeq);
 
-	if (endy > da.getHeight()) {
-	    endy = da.getHeight();
-	}
+    g.drawImage(image, 0, 0, this);
+  }
 
-	for (int i = starty; i < endy; i++) {
-	  SequenceI s = da.getSequenceAt(i);
-	  drawIdString(gg,s,i,starty,ypos);
-	}
-	if (rowstart == 0) {
-	    ypos   = ypos +  av.getChunkHeight();
-	} else if (rowstart == 1) {
-	    ypos   = ypos +  av.getChunkHeight();
-	} else {
-	    ypos   = ypos +  av.getChunkHeight() - rowstart*charHeight;
-	}
+  /**
+   * DOCUMENT ME!
+   *
+   * @param starty DOCUMENT ME!
+   * @param endy DOCUMENT ME!
+   */
+  void drawIds(int starty, int endy)
+  {
+    if (av.seqNameItalics)
+    {
+      idfont = new Font(av.getFont().getName(), Font.ITALIC,
+                        av.getFont().getSize());
+    }
+    else
+    {
+      idfont = av.getFont();
+    }
 
-	starty = 0;
+    gg.setFont(idfont);
+    fm = gg.getFontMetrics();
 
-	int chunkwidth = av.getChunkWidth();
-	int startx = (int)(av.getEndSeq()/chunkwidth)*chunkwidth;
-	int endx   = startx + chunkwidth;
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
 
+    Color currentColor = Color.white;
+    Color currentTextColor = Color.black;
 
-	while (ypos <= getHeight() && endx < da.getWidth()) {
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.alignment.getWidth();
+      int alheight = av.alignment.getHeight();
 
-	    for (int i = starty; i < endy; i++) {
-	      SequenceI s = da.getSequenceAt(i);
-      	      drawIdString(gg,s,i,starty,ypos);
-	    }
+      if (av.hasHiddenColumns)
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
 
-	    ypos   += av.getChunkHeight();
-	    startx += chunkwidth;
-	    endx = startx + chunkwidth;
+      int annotationHeight = 0;
 
-	    if (endx > da.getWidth()) {
-		endx = da.getWidth();
-	    }
+      if (av.showAnnotation)
+      {
+        if (ap == null)
+        {
+          ap = new AnnotationPanel(av);
+        }
+
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
+        {
+          labels = new AnnotationLabels(av);
+        }
+      }
 
-	    starty = 0;
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
 
-	    if (endy > da.getHeight()) {
-		endy = da.getHeight();
-	    }
+      int cHeight = alheight * av.charHeight
+          + hgap
+          + annotationHeight;
 
-	}
-    } else {
+      int rowSize = av.getEndRes() - av.getStartRes();
 
-    //Now draw the id strings
-    for (int i = starty; i < endy; i++)
+      // 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
+          {
+            gg.setFont(idfont);
+          }
+
+          drawIdString(gg, s, i, 0, ypos);
+        }
+
+        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;
 
-      // Selected sequence colours
-      if (av.getSelection().contains(da.getSequenceAt(i)))
+      SequenceI sequence;
+      //Now draw the id strings
+      for (int i = starty; i < endy; i++)
       {
-          currentColor     = Color.gray;
+        sequence = av.alignment.getSequenceAt(i);
+
+        if (sequence == null)
+        {
+          continue;
+        }
+
+        if (av.hasHiddenRows)
+        {
+          setHiddenFont(sequence);
+        }
+
+        // Selected sequence colours
+        if ( (searchResults != null) &&
+            searchResults.contains(sequence))
+        {
+          currentColor = Color.black;
+          currentTextColor = Color.white;
+        }
+        else if ( (av.getSelectionGroup() != null) &&
+                 av.getSelectionGroup().getSequences(null).contains(
+                     sequence))
+        {
+          currentColor = Color.lightGray;
           currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = da.getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
-      }
+        }
+        else
+        {
+          currentColor = av.getSequenceColour(sequence);
+          currentTextColor = Color.black;
+        }
 
-      gg.setColor(currentColor);
+        gg.setColor(currentColor);
 
+        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+                    av.charHeight);
 
+        gg.setColor(currentTextColor);
 
-      gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty,i,charHeight),
-                    getWidth(),
-                    charHeight);
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
 
-      gg.setColor(currentTextColor);
+        if (av.rightAlignIds)
+        {
+          xPos = panelWidth - fm.stringWidth(string) - 4;
+        }
 
-      String string = da.getSequenceAt(i).getDisplayId();
+        gg.drawString(string, xPos,
+                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
+                      (av.charHeight / 5));
 
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) +  charHeight-   (charHeight/5));
-    }
-    }
+        if (av.hasHiddenRows && av.showHiddenMarkers)
+        {
+          drawMarker(i, starty, 0);
+        }
 
-    g.drawImage(img,0,0,this);
-  }
+      }
 
+    }
+  }
 
-  public Dimension getLabelWidth()
+  void drawMarker(int i, int starty, int yoffset)
   {
 
-   FontMetrics fm = this.getGraphics().getFontMetrics(av.font);
-   AlignmentI al = av.getAlignment();
+    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++;
+        }
+      }
+    }
 
-   int i   = 0;
-   int idWidth = 0;
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 1);
 
-   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++;
-   }
+    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);
 
-   return new Dimension(idWidth + 10,getHeight());
- }
+    }
+  }
 
- public Dimension getPreferredSize()
- {
-   return getLabelWidth();
- }
+  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;
+    repaint();
+  }
 }