JAL-4048 fix disappearing sequence IDs, and non-positional feature descriptions

[jalview.git] / src / jalview / gui / IdCanvas.java

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 10c0787..68a7a1e 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -36,6 +36,9 @@ import javax.swing.JPanel;
 import jalview.datamodel.SequenceI;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.IdColumn;
+import jalview.viewmodel.seqfeatures.IdColumns;
+import jalview.viewmodel.seqfeatures.IdColumns.ColumnCell;
 
 /**
  * DOCUMENT ME!
@@ -55,7 +58,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
   BufferedImage image;
 
-//  Graphics2D gg;
+  // Graphics2D gg;
 
   int imgHeight = 0;
 
@@ -79,7 +82,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     this.av = av;
     PaintRefresher.Register(this, av.getSequenceSetId());
     av.getRanges().addPropertyChangeListener(this);
-    }
+  }
 
   /**
    * DOCUMENT ME!
@@ -203,7 +206,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     gg.translate(0, -transY);
 
     gg.dispose();
-    
+
     fastPaint = true;
 
     // Call repaint on alignment panel so that repaints from other alignment
@@ -223,41 +226,42 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   {
     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.getCharHeight());
-    
+
     if (imgHeight < 1)
     {
       return;
     }
-    
+
     if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
     {
-       image = new BufferedImage(getWidth(), imgHeight,
-                BufferedImage.TYPE_INT_RGB);
+      image = new BufferedImage(getWidth(), imgHeight,
+              BufferedImage.TYPE_INT_RGB);
     }
-    
+
     Graphics2D gg = image.createGraphics();
-    
+
     // Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
-    
-    drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
+
+    drawIds(gg, av, av.getRanges().getStartSeq(),
+            av.getRanges().getEndSeq(), searchResults);
 
     gg.dispose();
-    
+
     g.drawImage(image, 0, 0, this);
   }
 
@@ -273,14 +277,13 @@ public class IdCanvas extends JPanel implements ViewportListenerI
    * @param endSeq
    * @param selection
    */
-  void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq,
-          final int endSeq, List<SequenceI> selection)
+  void drawIds(Graphics2D g, AlignViewport alignViewport,
+          final int startSeq, final int endSeq, List<SequenceI> selection)
   {
     Font font = alignViewport.getFont();
     if (alignViewport.isSeqNameItalics())
     {
-      setIdfont(new Font(font.getName(), Font.ITALIC,
-              font.getSize()));
+      setIdfont(new Font(font.getName(), Font.ITALIC, font.getSize()));
     }
     else
     {
@@ -308,22 +311,31 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     }
 
     // Now draw the id strings
-    int panelWidth = getWidth();
-    int xPos = 0;
+    int fullPanelWidth = getWidth();
+
+    IdColumns id_cols = alignViewport.getIdColumns();
+    List<IdColumn> visible = id_cols.getVisible();
+    /**
+     * width of an idColumn
+     */
+    int colWid = 20;
+    int panelWidth = Math.max(fullPanelWidth / 2,
+            fullPanelWidth - (colWid * visible.size()));
 
     // Now draw the id strings
     for (int i = startSeq; i <= endSeq; i++)
     {
+      int xPos = 0;
       SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
 
       if (sequence == null)
       {
         continue;
       }
-
       if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
       {
         g.setFont(getHiddenFont(sequence, alignViewport));
+        fm = g.getFontMetrics();
       }
 
       // Selected sequence colours
@@ -347,8 +359,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       g.setColor(currentColor);
 
       int charHeight = alignViewport.getCharHeight();
-      g.fillRect(0, (i - startSeq) * charHeight,
-              getWidth(), charHeight);
+      g.fillRect(0, (i - startSeq) * charHeight, getWidth(), charHeight);
 
       g.setColor(currentTextColor);
 
@@ -360,9 +371,41 @@ public class IdCanvas extends JPanel implements ViewportListenerI
         xPos = panelWidth - fm.stringWidth(string) - 4;
       }
 
-      g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight)
-              - (charHeight / 5));
+      g.drawString(string, xPos,
+              (((i - startSeq) * charHeight) + charHeight)
+                      - (charHeight / 5));
 
+      if (visible != null && visible.size() > 0)
+      {
+        try
+        {
+          xPos = panelWidth + 2;
+          for (IdColumn col : visible)
+          {
+            ColumnCell col_cell = id_cols.getCellFor(sequence, col);
+            if (col_cell == null)
+            {
+              g.setColor(Color.gray);
+              g.fillRect(xPos + 1, (i - startSeq) * charHeight,
+                      xPos + colWid - 3, charHeight);
+            }
+            else
+            {
+              g.setColor(col_cell.bg);
+              g.fillRect(xPos + 1, (i - startSeq) * charHeight,
+                      xPos + colWid - 3, charHeight);
+              g.setColor(col_cell.fg);
+              g.drawString(col_cell.label, xPos,
+                      (((i - startSeq) * charHeight) + charHeight)
+                              - (charHeight / 5));
+            }
+            xPos += colWid;
+            g.setColor(currentTextColor);
+          }
+        } catch (Exception q)
+        {
+        }
+      }
       if (hasHiddenRows && av.getShowHiddenMarkers())
       {
         drawMarker(g, alignViewport, i, startSeq, 0);
@@ -447,7 +490,8 @@ public class IdCanvas extends JPanel implements ViewportListenerI
    * @param starty
    * @param yoffset
    */
-  void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
+  void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex,
+          int starty, int yoffset)
   {
     SequenceI[] hseqs = alignViewport.getAlignment()
             .getHiddenSequences().hiddenSequences;
@@ -490,8 +534,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     /*
      * vertices of the triangle, below or above hidden seqs
      */
-    int[] xPoints = new int[]
-    { getWidth() - charHeight,
+    int[] xPoints = new int[] { getWidth() - charHeight,
         getWidth() - charHeight, getWidth() };
     int yShift = seqIndex - starty;