X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=ac82e12a36e8925fd8478c825e4e2bfc3c05cf6d;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=a8f84563ca3aedef8937bbb054c0086fb55030ac;hpb=c80292bb7e300539b0ea8665ed3bee3fa6735dad;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index a8f8456..ac82e12 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,19 +1,40 @@
+/*
+ * 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.appletgui;
 
 import java.awt.*;
+
 import jalview.datamodel.*;
-import jalview.analysis.*;
-public class IdCanvas extends Panel
+
+public class IdCanvas
+    extends Panel
 {
   protected AlignViewport av;
 
-  protected boolean showScores  = true;
+  protected boolean showScores = true;
 
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
+  protected int maxIdLength = -1;
+  protected String maxIdStr = null;
   Image image;
   Graphics gg;
-  int imgHeight=0;
+  int imgHeight = 0;
   boolean fastPaint = false;
 
   java.util.Vector searchResults;
@@ -21,81 +42,102 @@ public class IdCanvas extends Panel
   public IdCanvas(AlignViewport av)
   {
     setLayout(null);
-    this.av         = av;
-    PaintRefresher.Register(this);
+    this.av = av;
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
-  public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
+  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,AlignmentUtil.getPixelHeight(starty,i,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,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);
-	  gg.setColor(Color.white);
-      } else {
-	  gg.setColor(s.getColor());
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);
-	  gg.setColor(Color.black);
-      }
+    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(null).contains(s))
+    {
+      gg.setColor(Color.lightGray);
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
+                  getSize().width, charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      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())
-        string = s.getDisplayId();
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
+                  ( (i - starty) * charHeight) + ypos +
+                  charHeight - (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 fastPaint(int vertical)
   {
-    if(gg==null)
-    {  repaint(); return;}
+    if (gg == null)
+    {
+      repaint();
+      return;
+    }
 
-    gg.copyArea( 0,0, getSize().width, imgHeight, 0, -vertical*av.charHeight );
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
 
-    int ss=av.startSeq, es=av.endSeq, transY = 0;
+    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);
+    {
+      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;
+      }
+    }
 
-        drawIds(ss, es);
+    gg.translate(0, transY);
 
-        gg.translate( 0, -transY );
+    drawIds(ss, es);
 
+    gg.translate(0, -transY);
 
-      fastPaint = true;
-      repaint();
+    fastPaint = true;
+    repaint();
   }
 
   public void update(Graphics g)
   {
     paint(g);
   }
+
   public void paint(Graphics g)
   {
-    if(getSize().height<0 || getSize().width<0)
+    if (getSize().height < 0 || getSize().width < 0)
+    {
       return;
+    }
     if (fastPaint)
     {
       fastPaint = false;
@@ -106,97 +148,156 @@ public class IdCanvas extends Panel
     imgHeight = getSize().height;
     imgHeight -= imgHeight % av.charHeight;
 
-    if (imgHeight<1)
+    if (imgHeight < 1)
+    {
       return;
+    }
 
-    if(image==null || imgHeight!=image.getHeight(this))
+    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,
+    //Fill in the background
+    gg.setColor(Color.white);
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
                            av.getFont().getSize());
-      gg.setFont(italic);
+    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)
   {
-    Color currentColor     = Color.white;
+    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
+      int rowSize = av.getEndRes() - av.getStartRes();
 
-          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 < alheight; i++)
+        {
+          if (av.hasHiddenRows)
           {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
-            {
-              SequenceI s = av.alignment.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
-            }
+            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
+      }
+    }
+    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())
-          string = av.alignment.getSequenceAt(i).getDisplayId();
-        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);
-    }
+        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
+                      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)
@@ -204,4 +305,79 @@ public class IdCanvas extends Panel
     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()));*/
+  }
 }