X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=ac82e12a36e8925fd8478c825e4e2bfc3c05cf6d;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=3c3c52c896d2cfabc41ddeb24582c2a34e8d645b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 3c3c52c..ac82e12 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/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
@@ -21,7 +21,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 
 public class IdCanvas
@@ -44,7 +43,7 @@ public class IdCanvas
   {
     setLayout(null);
     this.av = av;
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
   public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
@@ -55,36 +54,35 @@ public class IdCanvas
     if (searchResults != null && searchResults.contains(s))
     {
       gg.setColor(Color.black);
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else if (av.getSelectionGroup() != null &&
-             av.getSelectionGroup().sequences.contains(s))
+             av.getSelectionGroup().getSequences(null).contains(s))
     {
       gg.setColor(Color.lightGray);
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else
     {
-      gg.setColor(s.getColor());
-      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.black);
     }
 
-    String string = s.getName();
-    if (av.getShowFullId())
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
+                  ( (i - starty) * charHeight) + ypos +
+                  charHeight - (charHeight / 5));
+
+    if (av.hasHiddenRows && av.showHiddenMarkers)
     {
-      string = s.getDisplayId();
+      drawMarker(i, starty, ypos);
     }
 
-    gg.drawString(string, 0,
-                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
-                  charHeight - (charHeight / 5));
-
   }
 
   public void fastPaint(int vertical)
@@ -169,85 +167,137 @@ public class IdCanvas
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.getStartSeq(), av.endSeq);
+    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 = 2 * av.charHeight, row = av.startRes;
-           ypos <= getSize().height && row < av.alignment.getWidth();
-           ypos += av.chunkHeight, row += rowSize)
+      // 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 < av.alignment.getHeight(); i++)
+        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
+      SequenceI seq;
       for (int i = starty; i < endy; i++)
       {
-        // Selected sequence colours
+        if (av.hasHiddenRows)
+        {
+          setHiddenFont(i);
+        }
 
-        if (searchResults != null &&
-            searchResults.contains(av.alignment.getSequenceAt(i)))
+        seq = av.alignment.getSequenceAt(i);
+        if (seq == null)
+        {
+          continue;
+        }
+
+        // Selected sequence colours
+        if ( (searchResults != null) &&
+            searchResults.contains(seq))
         {
-          gg.setColor(Color.black);
           currentColor = Color.black;
           currentTextColor = Color.white;
         }
-        else if (av.getSelectionGroup() != null
-                 &&
-                 av.getSelectionGroup().sequences.contains(av.alignment.
-            getSequenceAt(i)))
+        else if ( (av.getSelectionGroup() != null) &&
+                 av.getSelectionGroup().getSequences(null).contains(seq))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
         }
         else
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
+          currentColor = av.getSequenceColour(seq);
           currentTextColor = Color.black;
         }
 
         gg.setColor(currentColor);
 
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getSize().width,
+        gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
                     av.charHeight);
 
         gg.setColor(currentTextColor);
-        String string = av.alignment.getSequenceAt(i).getName();
-        if (av.getShowFullId())
+
+        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
+                      0,
+                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
+                      (av.charHeight / 5));
+
+        if (av.hasHiddenRows && av.showHiddenMarkers)
         {
-          string = av.alignment.getSequenceAt(i).getDisplayId();
+          drawMarker(i, starty, 0);
         }
-        gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, 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)
@@ -255,4 +305,79 @@ public class IdCanvas
     searchResults = found;
     repaint();
   }
+
+  void drawMarker(int i, int starty, int yoffset)
+  {
+    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;
+
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 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++;
+        }
+      }
+    }
+
+    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()));*/
+  }
 }