X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=541c253be796dadb0943a6868953858eeb6e6c72;hb=2fa01dd888f9c0a8e22360fd50015f237184d209;hp=8f13ecadab066787fb37047fe50752344a8a5922;hpb=33f8761fdb05b594fd8a3341180256003d3a91df;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 8f13eca..541c253 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -20,10 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.SequenceI;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Font;
@@ -37,6 +33,10 @@ import java.util.List;
 
 import javax.swing.JPanel;
 
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * DOCUMENT ME!
  * 
@@ -63,10 +63,6 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
   List<SequenceI> searchResults;
 
-  FontMetrics fm;
-
-  AnnotationLabels labels = null;
-
   AnnotationPanel ap;
 
   private Font idfont;
@@ -88,7 +84,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   /**
    * DOCUMENT ME!
    * 
-   * @param gg
+   * @param g
    *          DOCUMENT ME!
    * @param hiddenRows
    *          true - check and display hidden row marker if need be
@@ -101,7 +97,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
    * @param ypos
    *          DOCUMENT ME!
    */
-  public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+  public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s,
           int i, int starty, int ypos)
   {
     int xPos = 0;
@@ -110,39 +106,40 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     if ((searchResults != null) && searchResults.contains(s))
     {
-      gg.setColor(Color.black);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+      g.setColor(Color.black);
+      g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
               charHeight);
-      gg.setColor(Color.white);
+      g.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(),
+      g.setColor(Color.lightGray);
+      g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
               charHeight);
-      gg.setColor(Color.white);
+      g.setColor(Color.white);
     }
     else
     {
-      gg.setColor(av.getSequenceColour(s));
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+      g.setColor(av.getSequenceColour(s));
+      g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
               charHeight);
-      gg.setColor(Color.black);
+      g.setColor(Color.black);
     }
 
     if (av.isRightAlignIds())
     {
+      FontMetrics fm = g.getFontMetrics();
       xPos = panelWidth
               - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
     }
 
-    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+    g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
             (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-    if (hiddenRows)
+    if (hiddenRows && av.getShowHiddenMarkers())
     {
-      drawMarker(i, starty, ypos);
+      drawMarker(g, av, i, starty, ypos);
     }
 
   }
@@ -199,7 +196,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     gg.translate(0, transY);
 
-    drawIds(ss, es);
+    drawIds(gg, av, ss, es, searchResults);
 
     gg.translate(0, -transY);
 
@@ -255,159 +252,150 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
     
-    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
+    drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
     
     g.drawImage(image, 0, 0, this);
   }
 
   /**
-   * DOCUMENT ME!
+   * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with
+   * the font and other display settings configured on the viewport. Ids of
+   * sequences included in the selection are coloured grey, otherwise the
+   * current id colour for the sequence id is used.
    * 
-   * @param starty
-   *          DOCUMENT ME!
-   * @param endy
-   *          DOCUMENT ME!
+   * @param g
+   * @param alignViewport
+   * @param startSeq
+   * @param endSeq
+   * @param selection
    */
-  void drawIds(int starty, int endy)
+  void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq,
+          final int endSeq, List<SequenceI> selection)
   {
-    if (av.isSeqNameItalics())
+    Font font = alignViewport.getFont();
+    if (alignViewport.isSeqNameItalics())
     {
-      setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
-              av.getFont().getSize()));
+      setIdfont(new Font(font.getName(), Font.ITALIC,
+              font.getSize()));
     }
     else
     {
-      setIdfont(av.getFont());
+      setIdfont(font);
     }
 
-    gg.setFont(getIdfont());
-    fm = gg.getFontMetrics();
+    g.setFont(getIdfont());
+    FontMetrics fm = g.getFontMetrics();
 
-    if (av.antiAlias)
+    if (alignViewport.antiAlias)
     {
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+      g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
               RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
-    boolean hasHiddenRows = av.hasHiddenRows();
+    boolean hasHiddenRows = alignViewport.hasHiddenRows();
 
-    if (av.getWrapAlignment())
+    if (alignViewport.getWrapAlignment())
     {
-      drawIdsWrapped(starty, hasHiddenRows);
+      drawIdsWrapped(g, alignViewport, startSeq, getHeight());
       return;
     }
 
-    // No need to hang on to labels if we're not wrapped
-    labels = null;
-
     // Now draw the id strings
     int panelWidth = getWidth();
     int xPos = 0;
 
-    SequenceI sequence;
     // Now draw the id strings
-    for (int i = starty; i <= endy; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
-      sequence = av.getAlignment().getSequenceAt(i);
+      SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
 
       if (sequence == null)
       {
         continue;
       }
 
-      if (hasHiddenRows || av.isDisplayReferenceSeq())
+      if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
       {
-        setHiddenFont(sequence);
+        g.setFont(getHiddenFont(sequence, alignViewport));
+        fm = g.getFontMetrics();
       }
 
       // Selected sequence colours
-      if ((searchResults != null) && searchResults.contains(sequence))
+      if (selection != null && selection.contains(sequence))
       {
         currentColor = Color.black;
         currentTextColor = Color.white;
       }
-      else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
-              .getSequences(null).contains(sequence))
+      else if ((alignViewport.getSelectionGroup() != null) && alignViewport
+              .getSelectionGroup().getSequences(null).contains(sequence))
       {
         currentColor = Color.lightGray;
         currentTextColor = Color.black;
       }
       else
       {
-        currentColor = av.getSequenceColour(sequence);
+        currentColor = alignViewport.getSequenceColour(sequence);
         currentTextColor = Color.black;
       }
 
-      gg.setColor(currentColor);
+      g.setColor(currentColor);
 
-      gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
-              av.getCharHeight());
+      int charHeight = alignViewport.getCharHeight();
+      g.fillRect(0, (i - startSeq) * charHeight,
+              getWidth(), charHeight);
 
-      gg.setColor(currentTextColor);
+      g.setColor(currentTextColor);
 
-      String string = sequence.getDisplayId(av.getShowJVSuffix());
+      String string = sequence
+              .getDisplayId(alignViewport.getShowJVSuffix());
 
-      if (av.isRightAlignIds())
+      if (alignViewport.isRightAlignIds())
       {
         xPos = panelWidth - fm.stringWidth(string) - 4;
       }
 
-      gg.drawString(string, xPos,
-              (((i - starty) * av.getCharHeight()) + av.getCharHeight())
-                      - (av.getCharHeight() / 5));
+      g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight)
+              - (charHeight / 5));
 
-      if (hasHiddenRows)
+      if (hasHiddenRows && av.getShowHiddenMarkers())
       {
-        drawMarker(i, starty, 0);
+        drawMarker(g, alignViewport, i, startSeq, 0);
       }
     }
   }
 
   /**
-   * Draws sequence ids in wrapped mode
+   * Draws sequence ids, and annotation labels if annotations are shown, in
+   * wrapped mode
    * 
-   * @param starty
-   * @param hasHiddenRows
+   * @param g
+   * @param alignViewport
+   * @param startSeq
    */
-  protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
+  void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+          int startSeq, int pageHeight)
   {
-    int maxwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight();
+    int alignmentWidth = alignViewport.getAlignment().getWidth();
+    final int alheight = alignViewport.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
-    }
+    /*
+     * assumption: SeqCanvas.calculateWrappedGeometry has been called
+     */
+    SeqCanvas seqCanvas = alignViewport.getAlignPanel()
+            .getSeqPanel().seqCanvas;
 
-    int annotationHeight = 0;
+    final int charHeight = alignViewport.getCharHeight();
 
-    if (av.isShowAnnotation())
+    AnnotationLabels labels = null;
+    if (alignViewport.isShowAnnotation())
     {
-      if (ap == null)
-      {
-        ap = new AnnotationPanel(av);
-      }
-
-      annotationHeight = ap.adjustPanelHeight();
-      if (labels == null)
-      {
-        labels = new AnnotationLabels(av);
-      }
+      labels = new AnnotationLabels(alignViewport);
     }
 
-    int hgap = av.getCharHeight();
-    if (av.getScaleAboveWrapped())
-    {
-      hgap += av.getCharHeight();
-    }
-
-    int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
-
-    ViewportRanges ranges = av.getRanges();
+    ViewportRanges ranges = alignViewport.getRanges();
 
     int rowSize = ranges.getViewportWidth();
 
@@ -415,49 +403,58 @@ public class IdCanvas extends JPanel implements ViewportListenerI
      * draw repeating sequence ids until out of sequence data or
      * out of visible space, whichever comes first
      */
-    int ypos = hgap;
-    int row = ranges.getStartRes();
-    while ((ypos <= getHeight()) && (row < maxwidth))
+    boolean hasHiddenRows = alignViewport.hasHiddenRows();
+    int ypos = seqCanvas.wrappedSpaceAboveAlignment;
+    int rowStartRes = ranges.getStartRes();
+    while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth))
     {
-      for (int i = starty; i < alheight; i++)
+      for (int i = startSeq; i < alheight; i++)
       {
-        SequenceI s = av.getAlignment().getSequenceAt(i);
-        if (hasHiddenRows || av.isDisplayReferenceSeq())
+        SequenceI s = alignViewport.getAlignment().getSequenceAt(i);
+        if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
         {
-          setHiddenFont(s);
+          g.setFont(getHiddenFont(s, alignViewport));
         }
         else
         {
-          gg.setFont(getIdfont());
+          g.setFont(getIdfont());
         }
-
-        drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
+        drawIdString(g, hasHiddenRows, s, i, 0, ypos);
       }
 
-      if (labels != null && av.isShowAnnotation())
+      if (labels != null && alignViewport.isShowAnnotation())
       {
-        gg.translate(0, ypos + (alheight * av.getCharHeight()));
-        labels.drawComponent(gg, getWidth());
-        gg.translate(0, -ypos - (alheight * av.getCharHeight()));
+        g.translate(0, ypos + (alheight * charHeight));
+        labels.drawComponent(g, getWidth());
+        g.translate(0, -ypos - (alheight * charHeight));
       }
 
-      ypos += cHeight;
-      row += rowSize;
+      ypos += seqCanvas.wrappedRepeatHeightPx;
+      rowStartRes += rowSize;
     }
   }
 
-  void drawMarker(int i, int starty, int yoffset)
+  /**
+   * Draws a marker (a blue right-pointing triangle) between sequences to
+   * indicate hidden sequences.
+   * 
+   * @param g
+   * @param alignViewport
+   * @param seqIndex
+   * @param starty
+   * @param yoffset
+   */
+  void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
   {
-
-    SequenceI[] hseqs = av.getAlignment()
+    SequenceI[] hseqs = alignViewport.getAlignment()
             .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;
+    int hiddenIndex = seqIndex;
+    int lastIndex = seqIndex - 1;
+    int nextIndex = seqIndex + 1;
 
     for (int j = 0; j < hSize; j++)
     {
@@ -478,52 +475,56 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       }
     }
 
+    /*
+     * are we below or above the hidden sequences?
+     */
     boolean below = (hiddenIndex > lastIndex + 1);
     boolean above = (nextIndex > hiddenIndex + 1);
 
-    gg.setColor(Color.blue);
+    g.setColor(Color.blue);
+    int charHeight = av.getCharHeight();
+
+    /*
+     * vertices of the triangle, below or above hidden seqs
+     */
+    int[] xPoints = new int[]
+    { getWidth() - charHeight,
+        getWidth() - charHeight, getWidth() };
+    int yShift = seqIndex - starty;
+
     if (below)
     {
-      gg.fillPolygon(
-              new int[]
-              { getWidth() - av.getCharHeight(),
-                  getWidth() - av.getCharHeight(), getWidth() },
-              new int[]
-              { (i - starty) * av.getCharHeight() + yoffset,
-                  (i - starty) * av.getCharHeight() + yoffset
-                          + av.getCharHeight() / 4,
-                  (i - starty) * av.getCharHeight() + yoffset },
-              3);
+      int[] yPoints = new int[] { yShift * charHeight + yoffset,
+          yShift * charHeight + yoffset + charHeight / 4,
+          yShift * charHeight + yoffset };
+      g.fillPolygon(xPoints, yPoints, 3);
     }
     if (above)
     {
-      gg.fillPolygon(
-              new int[]
-              { getWidth() - av.getCharHeight(),
-                  getWidth() - av.getCharHeight(), getWidth() },
-              new int[]
-              { (i - starty + 1) * av.getCharHeight() + yoffset,
-                  (i - starty + 1) * av.getCharHeight() + yoffset
-                          - av.getCharHeight() / 4,
-                  (i - starty + 1) * av.getCharHeight() + yoffset },
-              3);
-
+      yShift++;
+      int[] yPoints = new int[] { yShift * charHeight + yoffset,
+          yShift * charHeight + yoffset - charHeight / 4,
+          yShift * charHeight + yoffset };
+      g.fillPolygon(xPoints, yPoints, 3);
     }
   }
 
-  void setHiddenFont(SequenceI seq)
+  /**
+   * Answers the standard sequence id font, or a bold font if the sequence is
+   * set as reference or a hidden group representative
+   * 
+   * @param seq
+   * @param alignViewport
+   * @return
+   */
+  private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport)
   {
-    Font bold = new Font(av.getFont().getName(), Font.BOLD,
-            av.getFont().getSize());
-
     if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
     {
-      gg.setFont(bold);
-    }
-    else
-    {
-      gg.setFont(getIdfont());
+      return new Font(av.getFont().getName(), Font.BOLD,
+              av.getFont().getSize());
     }
+    return getIdfont();
   }
 
   /**