X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=b8255ca23457a3f3572adf95b1deee7188050c14;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=44ba2e066aee34a0a7eda05c57095682d98e86f8;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 44ba2e0..b8255ca 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,276 +1,345 @@
-/*
- * 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.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class IdCanvas
-    extends Panel
-{
-  protected AlignViewport av;
-
-  protected boolean showScores = true;
-
-  protected int maxIdLength = -1;
-  protected String maxIdStr = null;
-  Image image;
-  Graphics gg;
-  int imgHeight = 0;
-  boolean fastPaint = false;
-
-  java.util.Vector searchResults;
-
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(null);
-    this.av = av;
-    PaintRefresher.Register(this, av.alignment);
-  }
-
-  public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
-                           int ypos)
-  {
-    int charHeight = av.getCharHeight();
-
-    if (searchResults != null && searchResults.contains(s))
-    {
-      gg.setColor(Color.black);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
-                  getSize().width, 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,
-                  getSize().width, charHeight);
-      gg.setColor(Color.white);
-    }
-    else
-    {
-      gg.setColor(s.getColor());
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
-                  getSize().width, charHeight);
-      gg.setColor(Color.black);
-    }
-
-
-    gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,
-                  ((i - starty) * charHeight) + ypos +
-                  charHeight - (charHeight / 5));
-
-  }
-
-  public void fastPaint(int vertical)
-  {
-    if (gg == null)
-    {
-      repaint();
-      return;
-    }
-
-    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
-
-    int ss = av.startSeq, es = av.endSeq, 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();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    if (getSize().height < 0 || getSize().width < 0)
-    {
-      return;
-    }
-    if (fastPaint)
-    {
-      fastPaint = false;
-      g.drawImage(image, 0, 0, this);
-      return;
-    }
-
-    imgHeight = getSize().height;
-    imgHeight -= imgHeight % av.charHeight;
-
-    if (imgHeight < 1)
-    {
-      return;
-    }
-
-    if (image == null || imgHeight != image.getHeight(this))
-    {
-      image = createImage(getSize().width, imgHeight);
-      gg = image.getGraphics();
-      gg.setFont(av.getFont());
-    }
-
-    //Fill in the background
-    gg.setColor(Color.white);
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    gg.setFont(italic);
-
-    gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.getStartSeq(), av.endSeq);
-    g.drawImage(image, 0, 0, this);
-  }
-
-  void drawIds(int starty, int endy)
-  {
-    Color currentColor = Color.white;
-    Color currentTextColor = Color.black;
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                             av.getFont().getSize());
-
-    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 <= getSize().height) && (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, getSize().width);
-              gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));
-            }
-        }
-
-    }
-    else
-    {
-
-      //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),
-                    getSize().width,
-                    av.charHeight);
-
-        gg.setColor(currentTextColor);
-
-        gg.drawString(av.alignment.getSequenceAt(i)
-            .getDisplayId(av.getShowJVSuffix()), 0,
-                      ((i - starty) * av.charHeight) +
-                      av.charHeight - (av.charHeight / 5));
-      }
-
-      // add a border
-      gg.setColor(Color.white);
-      gg.fillRect(getSize().width - 4, 0, 4, getSize().height);
-    }
-
-  }
-
-  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.appletgui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class IdCanvas
+    extends Panel
+{
+  protected AlignViewport av;
+
+  protected boolean showScores = true;
+
+  protected int maxIdLength = -1;
+  protected String maxIdStr = null;
+  Image image;
+  Graphics gg;
+  int imgHeight = 0;
+  boolean fastPaint = false;
+
+  java.util.Vector searchResults;
+
+  public IdCanvas(AlignViewport av)
+  {
+    setLayout(null);
+    this.av = av;
+    PaintRefresher.Register(this, av.alignment);
+  }
+
+  public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
+                           int ypos)
+  {
+    int charHeight = av.getCharHeight();
+
+    if (searchResults != null && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+                  getSize().width, 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,
+                  getSize().width, charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(s.getColor());
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+                  getSize().width, charHeight);
+      gg.setColor(Color.black);
+    }
+
+
+    gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,
+                  ((i - starty) * charHeight) + ypos +
+                  charHeight - (charHeight / 5));
+
+    if (av.hasHiddenRows && av.showHiddenMarkers)
+          drawMarker(i, starty, ypos);
+
+  }
+
+  public void fastPaint(int vertical)
+  {
+    if (gg == null)
+    {
+      repaint();
+      return;
+    }
+
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
+
+    int ss = av.startSeq, es = av.endSeq, 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();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    if (getSize().height < 0 || getSize().width < 0)
+    {
+      return;
+    }
+    if (fastPaint)
+    {
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
+      return;
+    }
+
+    imgHeight = getSize().height;
+    imgHeight -= imgHeight % av.charHeight;
+
+    if (imgHeight < 1)
+    {
+      return;
+    }
+
+    if (image == null || imgHeight != image.getHeight(this))
+    {
+      image = createImage(getSize().width, imgHeight);
+      gg = image.getGraphics();
+      gg.setFont(av.getFont());
+    }
+
+    //Fill in the background
+    gg.setColor(Color.white);
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                           av.getFont().getSize());
+    gg.setFont(italic);
+
+    gg.fillRect(0, 0, getSize().width, getSize().height);
+    drawIds(av.startSeq, av.endSeq);
+    g.drawImage(image, 0, 0, this);
+  }
+
+  void drawIds(int starty, int endy)
+  {
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                           av.getFont().getSize());
+
+    gg.setFont(italic);
+
+    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 <= getSize().height) && (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, getSize().width);
+          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, getSize().width,
+                    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);
+      }
+    }
+  }
+
+  public void setHighlighted(java.util.Vector found)
+  {
+    searchResults = found;
+    repaint();
+  }
+
+  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[]
+                       {getSize().width- av.charHeight,
+                       getSize().width- av.charHeight,
+                       getSize().width},
+                       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[]
+                      {getSize().width- av.charHeight,
+                      getSize().width - av.charHeight,
+                      getSize().width },
+                      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)
+  {
+  /*  System.out.println(i+" "+av.alignment.getHeight());
+    if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+      gg.setFont(new Font(av.getFont().getName(), Font.BOLD,
+                          av.getFont().getSize()));
+    else
+      gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,
+                          av.getFont().getSize()));*/
+  }
+}