X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=97b8669cd1d1c4f6e3aca9907081fe96f477ee03;hb=27a5c083838bb51c6d7b60b499e9dade3a33599d;hp=9581cccfbcd61a7a82a144327c6d0f5999a2ffce;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 9581ccc..97b8669 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,15 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
 import java.awt.*;
 import java.awt.image.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -34,262 +30,448 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class IdCanvas extends JPanel
+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;
-    java.util.Vector searchResults;
-
-    /**
-     * Creates a new IdCanvas object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public IdCanvas(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;
+  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, av.getSequenceSetId());
+  }
+
+  /**
+   * 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);
+    }
+
+    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));
+
+    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;
+    }
+
+    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)
     {
-        setLayout(new BorderLayout());
-        this.av = av;
-        PaintRefresher.Register(this, av.alignment);
+      es = ss - vertical;
+
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
     }
 
-    /**
-     * 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)
+    gg.translate(0, transY);
+
+    drawIds(ss, es);
+
+    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());
+
+    if (fastPaint)
     {
-        int charHeight = av.charHeight;
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
+
+      return;
+    }
+
+    int oldHeight = imgHeight;
+
+    imgHeight = getHeight();
+    imgHeight -= (imgHeight % av.charHeight);
 
-        if ((searchResults != null) && searchResults.contains(s))
+    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);
+
+    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)
+  {
+    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)
         {
-            gg.setColor(Color.black);
-            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
-                charHeight);
-            gg.setColor(Color.white);
+          ap = new AnnotationPanel(av);
         }
-        else if ((av.getSelectionGroup() != null) &&
-                av.getSelectionGroup().sequences.contains(s))
+
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
         {
-            gg.setColor(Color.lightGray);
-            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
-                charHeight);
-            gg.setColor(Color.white);
+          labels = new AnnotationLabels(av);
         }
-        else
+      }
+
+      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++)
         {
-            gg.setColor(s.getColor());
-            gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
-                charHeight);
-            gg.setColor(Color.black);
+          SequenceI s = av.alignment.getSequenceAt(i);
+          if (av.hasHiddenRows)
+          {
+            setHiddenFont(s);
+          }
+          else
+          {
+            gg.setFont(idfont);
+          }
+
+          drawIdString(gg, s, i, 0, ypos);
         }
 
-        String string = s.getName();
-
-        if (av.getShowFullId())
+        if (labels != null && av.showAnnotation)
         {
-            string = s.getDisplayId();
+          gg.translate(0, ypos + (alheight * av.charHeight));
+          labels.drawComponent(gg, getWidth());
+          gg.translate(0, -ypos - (alheight * av.charHeight));
         }
-
-        gg.drawString(string, 0,
-            (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param vertical DOCUMENT ME!
-     */
-    public void fastPaint(int vertical)
+    else
     {
-        if (gg == null)
-        {
-            repaint();
-
-            return;
-        }
+      //No need to hang on to labels if we're not wrapped
+      labels = null;
 
-        gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+      //Now draw the id strings
+      int panelWidth = getWidth();
+      int xPos = 0;
 
-        int ss = av.startSeq;
-        int es = av.endSeq;
-        int transY = 0;
+      SequenceI sequence;
+      //Now draw the id strings
+      for (int i = starty; i < endy; i++)
+      {
+        sequence = av.alignment.getSequenceAt(i);
 
-        if (vertical > 0) // scroll down
+        if (sequence == null)
         {
-            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);
-            }
+          continue;
         }
-        else if (vertical < 0)
-        {
-            es = ss - vertical;
 
-            if (es > av.endSeq)
-            {
-                es = av.endSeq;
-            }
+        if (av.hasHiddenRows)
+        {
+          setHiddenFont(sequence);
         }
 
-        gg.translate(0, transY);
+        // 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 = av.getSequenceColour(sequence);
+          currentTextColor = Color.black;
+        }
 
-        drawIds(ss, es);
+        gg.setColor(currentColor);
 
-        gg.translate(0, -transY);
+        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+                    av.charHeight);
 
-        fastPaint = true;
-        repaint();
-    }
+        gg.setColor(currentTextColor);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
-    {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
 
-        if (fastPaint)
+        if (av.rightAlignIds)
         {
-            fastPaint = false;
-            g.drawImage(image, 0, 0, this);
-
-            return;
+          xPos = panelWidth - fm.stringWidth(string) - 4;
         }
 
-        imgHeight = getHeight();
-        imgHeight -= (imgHeight % av.charHeight);
+        gg.drawString(string, xPos,
+                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
+                      (av.charHeight / 5));
 
-        if (imgHeight < 1)
+        if (av.hasHiddenRows && av.showHiddenMarkers)
         {
-            return;
+          drawMarker(i, starty, 0);
         }
 
-        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);
+  void drawMarker(int i, int starty, int yoffset)
+  {
 
-        drawIds(av.getStartSeq(), av.endSeq);
+    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    //Use this method here instead of calling hiddenSeq adjust
+    //3 times.
+    int hSize = hseqs.length;
 
-        g.drawImage(image, 0, 0, this);
-    }
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param starty DOCUMENT ME!
-     * @param endy DOCUMENT ME!
-     */
-    void drawIds(int starty, int endy)
+    for (int j = 0; j < hSize; j++)
     {
-        Color currentColor = Color.white;
-        Color currentTextColor = Color.black;
-
-        if (av.getWrapAlignment())
+      if (hseqs[j] != null)
+      {
+        if (j - 1 < hiddenIndex)
         {
-            int rowSize = av.getEndRes() - av.getStartRes();
-
-            // Draw the rest of the panels
-            for (int ypos = 2 * av.charHeight, row = av.startRes;
-                    (ypos <= getHeight()) && (row < av.alignment.getWidth());
-                    ypos += av.chunkHeight, row += rowSize)
-            {
-                for (int i = starty; i < av.alignment.getHeight(); i++)
-                {
-                    SequenceI s = av.alignment.getSequenceAt(i);
-                    drawIdString(gg, s, i, 0, ypos);
-                }
-            }
+          hiddenIndex++;
         }
-        else
+        if (j - 1 < lastIndex)
         {
-            //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);
+          lastIndex++;
+        }
+        if (j - 1 < nextIndex)
+        {
+          nextIndex++;
+        }
+      }
+    }
 
-                gg.setColor(currentTextColor);
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 1);
 
-                String string = av.alignment.getSequenceAt(i).getName();
+    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);
 
-                if (av.getShowFullId())
-                {
-                    string = av.alignment.getSequenceAt(i).getDisplayId();
-                }
+    }
+  }
 
-                gg.drawString(string, 0,
-                    (((i - starty) * av.charHeight) + av.charHeight) -
-                    (av.charHeight / 5));
-            }
+  void setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD,
+                         av.getFont().getSize());
 
-            // add a border
-            gg.setColor(Color.white);
-            gg.fillRect(getWidth() - 4, 0, 4, getHeight());
-        }
+    if (av.hiddenRepSequences != null &&
+        av.hiddenRepSequences.containsKey(seq))
+    {
+      gg.setFont(bold);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param found DOCUMENT ME!
-     */
-    public void setHighlighted(java.util.Vector found)
+    else
     {
-        searchResults = found;
-        repaint();
+      gg.setFont(idfont);
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param found DOCUMENT ME!
+   */
+  public void setHighlighted(java.util.Vector found)
+  {
+    searchResults = found;
+    repaint();
+  }
 }