X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;fp=src%2Fjalview%2Fgui%2FIdCanvas.java;h=e7f554c3b4166495289605146127471564d8e137;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=214f218c0294d16a65cecb7111c4c5669c5bf917;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 214f218..e7f554c 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,349 +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.image.*;
-
-import javax.swing.*;
-
-
-/**
- * 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;
-    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);
-        }
-
-
-        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();
-
-            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();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    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);
-
-            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);
-    }
-
-    /**
-     * 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);
-          }
-
-          int hgap = av.charHeight;
-          if (av.scaleAboveWrapped)
-            hgap += av.charHeight;
-
-          int cHeight = av.getAlignment().getHeight() * 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 < 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
-        {
-            //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();
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.image.*;
+
+import javax.swing.*;
+
+
+/**
+ * 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;
+    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().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.drawString( s.getDisplayId(av.getShowJVSuffix()),
+                      0, (((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)
+        {
+            es = ss - vertical;
+
+            if (es > av.endSeq)
+            {
+                es = av.endSeq;
+            }
+        }
+
+        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)
+        {
+            fastPaint = false;
+            g.drawImage(image, 0, 0, this);
+
+            return;
+        }
+
+        int oldHeight = imgHeight;
+
+        imgHeight = getHeight();
+        imgHeight -= (imgHeight % av.charHeight);
+
+        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)
+    {
+      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)
+          {
+            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)
+            {
+              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);
+
+            }
+
+        }
+    }
+
+    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);
+
+      boolean below = (hiddenIndex > lastIndex + 1);
+      boolean above = (nextIndex>hiddenIndex+1);
+
+        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);
+
+        }
+    }
+
+    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();
+    }
+}